Journal articles
Sweetapple C, Melville-Shreeve P, Chen AS, Grimsley JMS, Bunce JT, Gaze W, Fielding S, Wade MJ (In Press). Building knowledge of university campus population dynamics to enhance near-to-source sewage surveillance for SARS-CoV-2 detection.
Abstract:
Building knowledge of university campus population dynamics to enhance near-to-source sewage surveillance for SARS-CoV-2 detection
ABSTRACTWastewater surveillance has been widely implemented for monitoring of SARS-CoV-2 during the global COVID-19 pandemic, and near-to-source monitoring is of particular interest for outbreak management in discrete populations. However, variation in population size poses a challenge to the triggering of public health interventions using wastewater SARS-CoV-2 concentrations. This is especially important for near-to-source sites that are subject to significant daily variability in upstream populations. Focusing on a university campus in England, this study investigates methods to account for variation in upstream populations at a site with highly transient footfall and provides a better understanding of the impact of variable populations on the SARS-CoV-2 trends provided by wastewater-based epidemiology. The potential for complementary data to help direct response activities within the near-to-source population is also explored, and potential concerns arising due to the presence of heavily diluted samples during wet weather are addressed. Using wastewater biomarkers, it is demonstrated that population normalisation can reveal significant differences between days where SARS-CoV-2 concentrations are very similar. Confidence in the trends identified is strongest when samples are collected during dry weather periods; however, wet weather samples can still provide valuable information. It is also shown that building-level occupancy estimates based on complementary data aid identification of potential sources of SARS-CoV-2 and can enable targeted actions to be taken to identify and manage potential sources of pathogen transmission in localised communities.
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Murray AK, Zhang L, Snape J, Gaze W (In Press). Comparing the selective and co-selective effects of different antimicrobials in bacterial communities. International Journal of Antimicrobial Agents
Boase N, White M, Redshaw C, Gaze W (In Press). Evaluating the mental models approach to developing a risk communication: a scoping review of the evidence. Risk Analysis, In press
Longdon B, Samantha T (In Press). Metabarcoding of Hepatitis E virus genotype 3 and Norovirus GII from wastewater samples in England using nanopore sequencing.
Food and Environmental VirologyAbstract:
Metabarcoding of Hepatitis E virus genotype 3 and Norovirus GII from wastewater samples in England using nanopore sequencing
Norovirus is one of the largest causes of gastroenteritis worldwide, and Hepatitis E virus (HEV) is an emerging pathogen that has become the most dominant cause of acute viral hepatitis in recent years. The presence of norovirus and HEV has been reported within wastewater in many countries previously. Here we used amplicon deep sequencing (metabarcoding) to identify norovirus and HEV strains in wastewater samples from England collected in 2019 and 2020. For HEV, we sequenced a fragment of the RNA-dependent RNA polymerase (RdRp) gene targeting genotype 3 strains. For norovirus, we sequenced the 5’ portion of the major capsid protein gene (VP1) of genogroup II strains. Sequencing of the wastewater samples revealed eight different genotypes of norovirus GII (GII.2, GII.3, GII.4, GII.6, GII.7, GII.9, GII.13 and GII.17). Genotypes GII.3 and GII.4 were the most commonly found. The HEV metabarcoding assay was able to identify HEV genotype 3 strains in some samples with a very low viral concentration determined by RT-qPCR. Analysis showed that most HEV strains found in influent wastewater were typed as G3c and G3e and were likely to have originated from humans or swine. However, the small size of the HEV nested PCR amplicon could cause issues with typing, and so this method is more appropriate for samples with high CTs where methods targeting longer genomic regions are unlikely to be successful. This is the first report of HEV RNA in wastewater in England. This study demonstrates the utility of wastewater sequencing and the need for wider surveillance of norovirus and HEV within host species and environments.
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Zhang L, Murray AK, Gaze W (In Press). Novel clinically relevant antibiotic resistance genes associated with sewage sludge and industrial waste streams revealed by functional metagenomic screening. Environment International
Larsson DGJ, Gaze WH, Laxminarayan R, Topp E (2023). AMR, One Health and the environment.
Nat Microbiol,
8(5), 754-755.
Author URL.
Farrell ML, Chueiri A, O'Connor L, Duane S, Maguire M, Miliotis G, Cormican M, Hooban B, Leonard A, Gaze WH, et al (2023). Assessing the impact of recreational water use on carriage of antimicrobial resistant organisms. The Science of the Total Environment, 888
Munk P, Brinch C, Møller FD, Petersen TN, Hendriksen RS, Seyfarth AM, Kjeldgaard JS, Svendsen CA, van Bunnik B, Berglund F, et al (2023). Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance (Nature Communications, (2022), 13, 1, (7251), 10.1038/s41467-022-34312-7).
Nature Communications,
14(1).
Abstract:
Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance (Nature Communications, (2022), 13, 1, (7251), 10.1038/s41467-022-34312-7)
In this article, the author name Antoinette Ngandjio was incorrectly written as Antoinette Ngandijo. In this article, the affiliation details for Author Sara Cuadros-Orellana were incorrectly given as ‘Centro de Biotecnologνa de los Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Talca, Chile’ but should have been ‘Universidad Catolica del Maule, Centro de Biotecnología de los Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Talca, Chile’. The original article has been corrected.
Abstract.
Murray AK, Zhang L, Snape J, Gaze WH (2023). Functional metagenomic libraries generated from anthropogenically impacted environments reveal importance of metabolic genes in biocide and antibiotic resistance. Current Research in Microbial Sciences, 4, 100184-100184.
Sünderhauf D, Klümper U, Gaze WH, Westra ER, van Houte S (2023). Interspecific competition can drive plasmid loss from a focal species in a microbial community.
The ISME Journal,
17(10), 1765-1773.
Abstract:
Interspecific competition can drive plasmid loss from a focal species in a microbial community
AbstractPlasmids are key disseminators of antimicrobial resistance genes and virulence factors, and it is therefore critical to predict and reduce plasmid spread within microbial communities. The cost of plasmid carriage is a key metric that can be used to predict plasmids’ ecological fate, and it is unclear whether plasmid costs are affected by growth partners in a microbial community. We carried out competition experiments and tracked plasmid maintenance using a model system consisting of a synthetic and stable five-species community and a broad host-range plasmid, engineered to carry different payloads. We report that both the cost of plasmid carriage and its long-term maintenance in a focal strain depended on the presence of competitors, and that these interactions were species specific. Addition of growth partners increased the cost of a high-payload plasmid to a focal strain, and accordingly, plasmid loss from the focal species occurred over a shorter time frame. We propose that the destabilising effect of interspecific competition on plasmid maintenance may be leveraged in clinical and natural environments to cure plasmids from focal strains.
Abstract.
Walker-Sünderhauf D, Klümper U, Pursey E, Westra ER, Gaze WH, van Houte S (2023). Removal of AMR plasmids using a mobile, broad host-range CRISPR-Cas9 delivery tool.
Microbiology (Reading),
169(5).
Abstract:
Removal of AMR plasmids using a mobile, broad host-range CRISPR-Cas9 delivery tool.
Antimicrobial resistance (AMR) genes are widely disseminated on plasmids. Therefore, interventions aimed at blocking plasmid uptake and transfer may curb the spread of AMR. Previous studies have used CRISPR-Cas-based technology to remove plasmids encoding AMR genes from target bacteria, using either phage- or plasmid-based delivery vehicles that typically have narrow host ranges. To make this technology feasible for removal of AMR plasmids from multiple members of complex microbial communities, an efficient, broad host-range delivery vehicle is needed. We engineered the broad host-range IncP1-plasmid pKJK5 to encode cas9 programmed to target an AMR gene. We demonstrate that the resulting plasmid pKJK5::csg has the ability to block the uptake of AMR plasmids and to remove resident plasmids from Escherichia coli. Furthermore, due to its broad host range, pKJK5::csg successfully blocked AMR plasmid uptake in a range of environmental, pig- and human-associated coliform isolates, as well as in isolates of two species of Pseudomonas. This study firmly establishes pKJK5::csg as a promising broad host-range CRISPR-Cas9 delivery tool for AMR plasmid removal, which has the potential to be applied in complex microbial communities to remove AMR genes from a broad range of bacterial species.
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Author URL.
Lear L, Hesse E, Newsome L, Gaze W, Buckling A, Vos M (2023). The effect of metal remediation on the virulence and antimicrobial resistance of the opportunistic pathogen <i>Pseudomonas aeruginosa</i>.
Evolutionary Applications,
16(7), 1377-1389.
Abstract:
The effect of metal remediation on the virulence and antimicrobial resistance of the opportunistic pathogen Pseudomonas aeruginosa
AbstractAnthropogenic metal pollution can result in co‐selection for antibiotic resistance and potentially select for increased virulence in bacterial pathogens. Metal‐polluted environments can select for the increased production of siderophore molecules to detoxify non‐ferrous metals. However, these same molecules also aid the uptake of ferric iron, a limiting factor for within‐host pathogen growth, and are consequently a virulence factor. Anthropogenic methods to remediate environmental metal contamination commonly involve amendment with lime‐containing materials. However, whether this reduces in situ co‐selection for antibiotic resistance and siderophore‐mediated virulence remains unknown. Here, using microcosms containing non‐sterile metal‐contaminated river water and sediment, we test whether liming reduces co‐selection for these pathogenicity traits in the opportunistic pathogen Pseudomonas aeruginosa. To account for the effect of environmental structure, which is known to impact siderophore production, microcosms were incubated under either static or shaking conditions. Evolved P. aeruginosa populations had greater fitness in the presence of toxic concentrations of copper than the ancestral strain and showed increased resistance to the clinically relevant antibiotics apramycin, cefotaxime and trimethoprim, regardless of lime addition or environmental structure. Although we found virulence to be significantly associated with siderophore production, neither virulence nor siderophore production significantly differed between the four treatments. Furthermore, liming did not mitigate metal‐imposed selection for antibiotic resistance or virulence in P. aeruginosa. Consequently, metal‐contaminated environments may select for antibiotic resistance and virulence traits even when treated with lime.
Abstract.
Yin X, Chen X, Jiang X-T, Yang Y, Li B, Shum MH-H, Lam TTY, Leung GM, Rose J, Sanchez-Cid C, et al (2023). Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples.
Environ Sci Technol,
57(26), 9713-9721.
Abstract:
Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples.
Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health" framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts.
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Wu J, Guo S, Lin H, Li K, Li Z, Wang J, Gaze WH, Zou J (2023). Uncovering the prevalence and drivers of antibiotic resistance genes in soils across different land-use types.
J Environ Manage,
344Abstract:
Uncovering the prevalence and drivers of antibiotic resistance genes in soils across different land-use types.
The emergence and spread of antibiotic resistance genes (ARGs) in soil due to animal excreta and organic waste is a major threat to human health and ecosystems, and global efforts are required to tackle the issue. However, there is limited knowledge of the variation in ARG prevalence and diversity resulting from different land-use patterns and underlying driving factors in soils. This study aimed to comprehensively characterize the profile of ARGs and mobile genetic elements and their drivers in soil samples collected from 11 provinces across China, representing three different land-use types, using high-throughput quantitative polymerase chain reaction and 16S rRNA amplicon sequencing. Our results showed that agricultural soil had the highest abundance and diversity of ARGs, followed by tea plantation and forest land. A total of 124 unique ARGs were detected in all samples, with shared subtypes among different land-use patterns indicating a common origin or high transmission frequency. Moreover, significant differences in ARG distribution were observed among different geographical regions, with the greatest enrichment of ARGs found in southern China. Biotic and abiotic factors, including soil properties, climatic factors, and bacterial diversity, were identified as the primary drivers associated with ARG abundance, explaining 71.8% of total ARG variation. The findings of our study demonstrate that different land-use patterns are associated with variations in ARG abundance in soil, with agricultural practices posing the greatest risk to human health and ecosystems regarding ARGs. Our identification of biotic and abiotic drivers of ARG abundance provides valuable insights into strategies for mitigating the spread of these genes. This study emphasizes the need for coordinated and integrated approaches to address the global antimicrobial resistance crisis.
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Woods RD, Swaddle JP, Bearhop S, Colhoun K, Gaze WH, Kay SM, McDonald RA (2022). A Sonic Net deters European starlings <i>Sturnus vulgaris</i> from maize silage stores.
Wildlife Society Bulletin,
46(4).
Abstract:
A Sonic Net deters European starlings Sturnus vulgaris from maize silage stores
AbstractDeterrents against avian pest species might be more effective if they were based on some aspect of the target species' sensory salience. Sonic Nets broadcast a loud and spatially‐ focused pink noise that spans the frequency range of the target species' vocalizations, restricting interspecific communication so that it is costly for birds to remain in the treated area. In parts of their native and introduced ranges, European starlings (Sturnus vulgaris) impact livestock operations where they consume and contaminate animal feed, damage infrastructure, and may contribute to pathogen transmission. We evaluated Sonic Net technology to exclude starlings from outdoor maize silage stores on 10 dairy farms in Cornwall, U.K. in February–March and November–December 2019. We quantified frequency of starling presence and approximate flock size and combined these to estimate starling burden in starling‐minutes before, during, and after Sonic Net treatment. During an initial proof‐of‐concept trial, each phase lasted 2 days, whilst in a second, longer experiment, treatment lasted 14 days. During Sonic Net treatment, frequency of starling presence was reduced, flock sizes were smaller, and starling‐minutes were reduced by 94% and 89% in the 2‐day and 14‐day treatments, respectively. In the last 2 days of the 14‐day treatment, starling‐minutes remained 85% lower than before treatment, but 4 of 10 farms experienced some diminution of effects after 6 days. Sonic Nets had a significant and sustained effect, with potential for deterring avian pests from agricultural and other settings.
Abstract.
Stevenson EM, Gaze WH, Gow NAR, Hart A, Schmidt W, Usher J, Warris A, Wilkinson H, Murray AK (2022). Antifungal Exposure and Resistance Development: Defining Minimal Selective Antifungal Concentrations and Testing Methodologies. Frontiers in Fungal Biology, 3
Rajendran NB, Arieti F, Mena-Benítez CA, Galia L, Tebon M, Alvarez J, Gladstone BP, Collineau L, De Angelis G, Duro R, et al (2022). EPI-Net One Health reporting guideline for antimicrobial consumption and resistance surveillance data: a Delphi approach. The Lancet Regional Health - Europe, 26
Stanton IC, Bethel A, Leonard AFC, Gaze WH, Garside R (2022). Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map.
Environmental Evidence,
11(1).
Abstract:
Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map
Abstract
. Background
. Antimicrobial resistance (AMR) is predicted to become the leading cause of death by 2050 with antibiotic resistance being an important component. Anthropogenic pollution introduces antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) to the natural environment. Currently, there is limited empirical evidence demonstrating whether humans are exposed to environmental AMR and whether this exposure can result in measurable human health outcomes. In recent years there has been increasing interest in the role of the environment and disparate evidence on transmission of AMR to humans has been generated but there has been no systematic attempt to summarise this. We aim to create two systematic maps that will collate the evidence for (1) the transmission of antibiotic resistance from the natural environment to humans on a global scale and (2) the state of antibiotic resistance in the environment in the United Kingdom.
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. Methods
. Search strategies were developed for each map. Searches were undertaken in 13 bibliographic databases. Key websites were searched and experts consulted for grey literature. Search results were managed using EndNote X8. Titles and abstracts were screened, followed by the full texts. Articles were double screened at a minimum of 10% at both stages with consistency checking and discussion when disagreements arose. Data extraction occurred in Excel with bespoke forms designed. Data extracted from each selected study included: bibliographic information; study site location; exposure source; exposure route; human health outcome (Map 1); prevalence/percentage/abundance of ARB/antibiotic resistance elements (Map 2) and study design. EviAtlas was used to visualise outputs.
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. Results
. For Map 1, 40 articles were included, from 11,016 unique articles identified in searches, which investigated transmission of AMR from the environment to humans. Results from Map 1 showed that consumption/ingestion was the most studied transmission route. Exposure (n = 17), infection (n = 16) and colonisation (n = 11) being studied as an outcome a similar number of times, with mortality studied infrequently (n = 2). In addition, E. coli was the most highly studied bacterium (n = 16). For Map 2, we included 62 studies quantifying ARB or resistance elements in the environment in the UK, from 6874 unique articles were identified in the searches. The most highly researched species was mixed communities (n = 32). The most common methodology employed in this research question was phenotypic testing (n = 37). The most commonly reported outcome was the characterisation of ARBs (n = 40), followed by characterisation of ARGs (n = 35). Other genetic elements, such as screening for intI1 (n = 15) (which encodes a Class 1 integron which is used as a proxy for environmental ARGs) and point mutations (n = 1) were less frequently reported. Both maps showed that research was focused towards aquatic environments.
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. Conclusions
. Both maps can be used by policy makers to show the global (Map 1) and UK (Map 2) research landscapes and provide an overview of the state of AMR in the environment and human health impacts of interacting with the environment. We have also identified (1) clusters of research which may be used to perform meta-analyses and (2) gaps in the evidence base where future primary research should focus.
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Abstract.
Thornber K, Adshead F, Balayannis A, Brazier R, Brown R, Comber S, Court C, Davidson I, Depledge M, Farmer C, et al (2022). First, do no harm: time for a systems approach to address the problem of health-care-derived pharmaceutical pollution. The Lancet Planetary Health, 6(12), e935-e937.
Munk P, Brinch C, Møller FD, Petersen TN, Hendriksen RS, Seyfarth AM, Kjeldgaard JS, Svendsen CA, van Bunnik B, Berglund F, et al (2022). Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance.
Nature Communications,
13(1).
Abstract:
Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.
Abstract.
Leonard AF, Morris D, Schmitt H, Gaze WH (2022). Natural recreational waters and the risk that exposure to antibiotic resistant bacteria poses to human health.
Curr Opin Microbiol,
65, 40-46.
Abstract:
Natural recreational waters and the risk that exposure to antibiotic resistant bacteria poses to human health.
Antimicrobial resistance (AMR) is widely recognised as a considerable threat to human health, wellbeing and prosperity. Many clinically important antibiotic resistance genes are understood to have originated in the natural environment. However, the complex interactions between humans, animals and the environment makes the health implications of environmental AMR difficult to quantify. This narrative review focuses on the current state of knowledge regarding antibiotic resistant bacteria (ARB) in natural bathing waters and implications for human health. It considers the latest research focusing on the transmission of ARB from bathing waters to humans. The limitations of existing evidence are discussed, as well as research priorities. The authors are of the opinion that future studies should include faecally contaminated bathing waters and people exposed to these environments to accurately parameterise environment-to-human transmission.
Abstract.
Author URL.
Wang Y, Yu Z, Ding P, Lu J, Klümper U, Murray AK, Gaze WH, Guo J (2022). Non-antibiotic pharmaceuticals promote conjugative plasmid transfer at a community-wide level.
Microbiome,
10(1).
Abstract:
Non-antibiotic pharmaceuticals promote conjugative plasmid transfer at a community-wide level.
BACKGROUND: Horizontal gene transfer (HGT) plays a critical role in the spread of antibiotic resistance and the evolutionary shaping of bacterial communities. Conjugation is the most well characterized pathway for the spread of antibiotic resistance, compared to transformation and transduction. While antibiotics have been found to induce HGT, it remains unknown whether non-antibiotic pharmaceuticals can facilitate conjugation at a microbial community-wide level. RESULTS: in this study, we demonstrate that several commonly consumed non-antibiotic pharmaceuticals (including carbamazepine, ibuprofen, naproxen and propranolol), at environmentally relevant concentrations (0.5 mg/L), can promote the conjugative transfer of IncP1-α plasmid-borne antibiotic resistance across entire microbial communities. The over-generation of reactive oxygen species in response to these non-antibiotic pharmaceuticals may contribute to the enhanced conjugation ratios. Cell sorting and 16S rRNA gene amplicon sequencing analyses indicated that non-antibiotic pharmaceuticals modulate transconjugant microbial communities at both phylum and genus levels. Moreover, microbial uptake ability of the IncP1-α plasmid was also upregulated under non-antibiotic pharmaceutical exposure. Several opportunistic pathogens, such as Acinetobacter and Legionella, were more likely to acquire the plasmid conferring multidrug resistance. CONCLUSIONS: Considering the high possibility of co-occurrence of pathogenic bacteria, conjugative IncP1-α plasmids and non-antibiotic pharmaceuticals in various environments (e.g. activated sludge systems), our findings illustrate the potential risk associated with increased dissemination of antibiotic resistance promoted by non-antibiotic pharmaceuticals in complex environmental settings. Video abstract.
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Hayes A, May Murray L, Catherine Stanton I, Zhang L, Snape J, Hugo Gaze W, Kaye Murray A (2022). Predicting selection for antimicrobial resistance in UK wastewater and aquatic environments: Ciprofloxacin poses a significant risk.
Environ Int,
169Abstract:
Predicting selection for antimicrobial resistance in UK wastewater and aquatic environments: Ciprofloxacin poses a significant risk.
Antimicrobial resistance (AMR) is a threat to human and animal health, with the environment increasingly recognised as playing an important role in AMR evolution, dissemination, and transmission. Antibiotics can select for AMR at very low concentrations, similar to those in the environment, yet their release into the environment, e.g. from wastewater treatment plants, is not currently regulated. Understanding the selection risk antibiotics pose in wastewater and receiving waters is key to understanding if environmental regulation of antibiotics is required. We investigated the risk of selection occurring in UK wastewater and receiving waters by determining where measured environmental concentration data (n = 8187) for four antibiotics (ciprofloxacin, azithromycin, clarithromycin, and erythromycin) collected in England and Wales 2015-2018 (sites n = 67) exceeded selective concentration thresholds derived from complex microbial community evolution experiments undertaken previously. We show that selection for AMR by ciprofloxacin is likely to have occurred routinely in England and Wales wastewater during the 2015-2018 period, with some seasonal and regional trends. Wastewater treatment reduces the selection risk posed by ciprofloxacin significantly, but not completely, and predicted risk in surface waters remains high in several cases. Conversely, the potential risks posed by the macrolides (azithromycin, clarithromycin, and erythromycin) were lower than those posed by ciprofloxacin. Our data demonstrate further action is needed to prevent selection for AMR in wastewater, with environmental quality standards for some antibiotics required in the future, and that selection risk is not solely a concern in low/middle income countries.
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Elder FCT, Pascoe B, Wells S, Sheppard SK, Snape J, Gaze WH, Feil EJ, Kasprzyk-Hordern B (2022). Stereoselective metabolism of chloramphenicol by bacteria isolated from wastewater, and the importance of stereochemistry in environmental risk assessments for antibiotics.
Water Res,
217Abstract:
Stereoselective metabolism of chloramphenicol by bacteria isolated from wastewater, and the importance of stereochemistry in environmental risk assessments for antibiotics.
Wastewater treatment plants have been highlighted as a potential hotspot for the development and spread of antibiotic resistance. Although antibiotic resistant bacteria in wastewater present a public health threat, it is also possible that these bacteria play an important role in the bioremediation through the metabolism of antibiotics before they reach the wider environment. Here we address this possibility with a particular emphasis on stereochemistry using a combination of microbiology and analytical chemistry tools including the use of supercritical-fluid chromatography coupled with mass spectrometry for chiral analysis and high-resolution mass spectrometry to investigate metabolites. Due to the complexities around chiral analysis the antibiotic chloramphenicol was used as a proof of concept to demonstrate stereoselective metabolism due to its relatively simple chemical structure and availability over the counter in the U.K. The results presented here demonstrate the chloramphenicol can be stereoselectively transformed by the chloramphenicol acetyltransferase enzyme with the orientation around the first stereocentre being key for this process, meaning that accumulation of two isomers may occur within the environment with potential impacts on ecotoxicity and emergence of bacterial antibiotic resistance within the environment.
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Manaia CM, Aga DS, Cytryn E, Gaze WH, Graham DW, Guo J, Leonard AFC, Li L, Murray AK, Nunes OC, et al (2022). The Complex Interplay Between Antibiotic Resistance and Pharmaceutical and Personal Care Products in the Environment.
Environ Toxicol ChemAbstract:
The Complex Interplay Between Antibiotic Resistance and Pharmaceutical and Personal Care Products in the Environment.
Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are important environmental contaminants. Nonetheless, what drives the evolution, spread, and transmission of antibiotic resistance dissemination is still poorly understood. The abundance of ARB and ARGs is often elevated in human-impacted areas, especially in environments receiving fecal wastes, or in the presence of complex mixtures of chemical contaminants, such as pharmaceuticals and personal care products. Self-replication, mutation, horizontal gene transfer, and adaptation to different environmental conditions contribute to the persistence and proliferation of ARB in habitats under strong anthropogenic influence. Our review discusses the interplay between chemical contaminants and ARB and their respective genes, specifically in reference to co-occurrence, potential biostimulation, and selective pressure effects, and gives an overview of mitigation by existing man-made and natural barriers. Evidence and strategies to improve the assessment of human health risks due to environmental antibiotic resistance are also discussed. Environ Toxicol Chem 2023;00:1-16. © 2022 SETAC.
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Murray AK, Stanton I, Gaze WH, Snape J (2021). Dawning of a new ERA: Environmental Risk Assessment of antibiotics and their potential to select for antimicrobial resistance.
Water Res,
200Abstract:
Dawning of a new ERA: Environmental Risk Assessment of antibiotics and their potential to select for antimicrobial resistance.
Antibiotics and antimicrobials are used, misused and overused in human and veterinary medicine, animal husbandry and aquaculture. These compounds can persist in both human and animal waste and then enter the environment through a variety of mechanisms. Though generally measured environmental concentrations (MECs) of antibiotics in aquatic systems are significantly lower than point of therapeutic use concentrations, there is increasing evidence that suggests these concentrations may still enrich antimicrobial resistant bacteria. In light of this evidence, a rigorous and standardised novel methodology needs to be developed which can perform environmental risk assessment (ERA) of antimicrobials in terms of their selective potential as well as their environmental impact, to ensure that diffuse and point source discharges are safe. This review summarises and critically appraises the current methodological approaches that study selection at below point of therapeutic use, or sub-inhibitory, concentrations of antibiotics. We collate and compare selective concentration data generated to date. We recommend how these data can be interpreted in line with current ERA guidelines; outlining and describing novel concepts unique to risk assessment of AMR (such as direct selection of AMR or increased persistence of AMR). We consolidate terminology used thus far into a single framework that could be adopted moving forward, by proposing predicted no effect concentrations for resistance (PNECRs) and predicted no effect concentrations for persistence (PNECPs) be determined in AMR risk assessment. Such a framework will contribute to antibiotic stewardship and by extension, protection of human health, food security and the global economy.
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Hillary LS, Farkas K, Maher KH, Lucaci A, Thorpe J, Distaso MA, Gaze WH, Paterson S, Burke T, Connor TR, et al (2021). Monitoring SARS-CoV-2 in municipal wastewater to evaluate the success of lockdown measures for controlling COVID-19 in the UK.
Water Research,
200Abstract:
Monitoring SARS-CoV-2 in municipal wastewater to evaluate the success of lockdown measures for controlling COVID-19 in the UK
SARS-CoV-2 and the resulting COVID-19 pandemic represents one of the greatest recent threats to human health, wellbeing and economic growth. Wastewater-based epidemiology (WBE) of human viruses can be a useful tool for population-scale monitoring of SARS-CoV-2 prevalence and epidemiology to help prevent further spread of the disease, particularly within urban centres. Here, we present a longitudinal analysis (March–July 2020) of SARS-CoV-2 RNA prevalence in sewage across six major urban centres in the UK (total population equivalent 3 million) by q(RT-)PCR and viral genome sequencing. Our results demonstrate that levels of SARS-CoV-2 RNA generally correlated with the abundance of clinical cases recorded within the community in large urban centres, with a marked decline in SARS-CoV-2 RNA abundance following the implementation of lockdown measures. The strength of this association was weaker in areas with lower confirmed COVID-19 case numbers. Further, sequence analysis of SARS-CoV-2 from wastewater suggested that multiple genetically distinct clusters were co-circulating in the local populations covered by our sample sites, and that the genetic variants observed in wastewater reflected similar SNPs observed in contemporaneous samples from cases tested in clinical diagnostic laboratories. We demonstrate how WBE can be used for both community-level detection and tracking of SARS-CoV-2 and other virus’ prevalence, and can inform public health policy decisions. Although, greater understanding of the factors that affect SARS-CoV-2 RNA concentration in wastewater are needed for the full integration of WBE data into outbreak surveillance. In conclusion, our results lend support to the use of routine WBE for monitoring of SARS-CoV-2 and other human pathogenic viruses circulating in the population and assessment of the effectiveness of disease control measures.
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EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis K, Allende A, Álvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, Davies R, De Cesare A, Herman L, et al (2021). Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain.
EFSA J,
19(6).
Abstract:
Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain.
The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp. methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.
Abstract.
Author URL.
Elder FCT, Proctor K, Barden R, Gaze WH, Snape J, Feil EJ, Kasprzyk-Hordern B (2021). Spatiotemporal profiling of antibiotics and resistance genes in a river catchment: Human population as the main driver of antibiotic and antibiotic resistance gene presence in the environment.
Water Research,
203Abstract:
Spatiotemporal profiling of antibiotics and resistance genes in a river catchment: Human population as the main driver of antibiotic and antibiotic resistance gene presence in the environment
Studies to understand the role wastewater treatment plants (WWTPs) play in the dissemination of antibiotics (ABs), and in the emergence of antibiotic resistance (ABR), play an important role in tackling this global crisis. Here we describe the abundance and distribution of 16 ABs, and 4 corresponding antibiotic resistance genes (ARGs), sampled from the influent to five WWTPs within a single river catchment. We consider four classes of antibiotics: fluroquinolones, macrolides, sulfamethoxazole and chloramphenicol, as well the corresponding antibiotic resistance genes qnrS, ermB, sul1 and catA. All antibiotics, apart from four fluroquinolones (besifloxacin, lomefloxacin, ulifloxacin, prulifloxacin), were detected within all influent wastewater from the 5 cities (1 city = 1 WWTP), as were the corresponding antibiotic resistance genes (ARGs). Strong correlations were observed between the daily loads of ABs and ARGs versus the size of the population served by each WWTP, as well as between AB and ARG loads at a single site. The efficiency of ABs and ARGs removal by the WWTPs varied according to site (and treatment process utilized) and target, although strong correlations were maintained between the population size served by WWTPs and daily loads of discharged ABs and ARGs into the environment. We therefore conclude that population size is the main determinant of the magnitude of AB and ARG burden in the environment.
Abstract.
Elder FCT, Feil EJ, Pascoe B, Sheppard SK, Snape J, Gaze WH, Kasprzyk-Hordern B (2021). Stereoselective Bacterial Metabolism of Antibiotics in Environmental Bacteria - a Novel Biochemical Workflow.
FRONTIERS IN MICROBIOLOGY,
12 Author URL.
Leonard AFC, Garside R, Ukoumunne OC, Gaze WH (2020). A cross-sectional study on the prevalence of illness in coastal bathers compared to non-bathers in England and Wales: Findings from the Beach User Health Survey. Water Research, 176, 115700-115700.
Marano RBM, Fernandes T, Manaia CM, Nunes O, Morrison D, Berendonk TU, Kreuzinger N, Tenson T, Corno G, Fatta-Kassinos D, et al (2020). A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants. Environment International, 144, 106035-106035.
Ferraresso J, Lawton B, Bayliss S, Sheppard S, Cardazzo B, Gaze W, Buckling A, Vos M (2020). Determining the prevalence, identity and possible origin of bacterial pathogens in soil.
Environ Microbiol,
22(12), 5327-5340.
Abstract:
Determining the prevalence, identity and possible origin of bacterial pathogens in soil.
Soil biomes are vast, exceptionally diverse and crucial to the health of ecosystems and societies. Soils also contain an appreciable, but understudied, diversity of opportunistic human pathogens. With climate change and other forms of environmental degradation potentially increasing exposure risks to soilborne pathogens, it is necessary to gain a better understanding of their ecological drivers. Here we use the Galleria mellonella insect virulence model to selectively isolate pathogenic bacteria from soils in Cornwall (UK). We find a high prevalence of pathogenic soil bacteria with two genera, Providencia and Serratia, being especially common. Providencia alcalifaciens, P. rustigianii, Serratia liquefaciens and S. plymuthica strains were studied in more detail using phenotypic virulence and antibiotic resistance assays and whole-genome sequencing. Both genera displayed low levels of antibiotic resistance and antibiotic resistance gene carriage. However, Serratia isolates were found to carry the recently characterized metallo-β-lactamase blaSPR-1 that, although not conferring high levels of resistance in these strains, poses a potential risk of horizontal transfer to other pathogens where it could be fully functional. The Galleria assay can be a useful approach to uncover the distribution and identity of pathogenic bacteria in the environment, as well as uncover resistance genes with an environmental origin.
Abstract.
Author URL.
Stanton IC, Murray AK, Zhang L, Snape J, Gaze WH (2020). Evolution of antibiotic resistance at low antibiotic concentrations including selection below the minimal selective concentration.
Commun Biol,
3(1).
Abstract:
Evolution of antibiotic resistance at low antibiotic concentrations including selection below the minimal selective concentration.
Determining the selective potential of antibiotics at environmental concentrations is critical for designing effective strategies to limit selection for antibiotic resistance. This study determined the minimal selective concentrations (MSCs) for macrolide and fluoroquinolone antibiotics included on the European Commission's Water Framework Directive's priority hazardous substances Watch List. The macrolides demonstrated positive selection for ermF at concentrations 1-2 orders of magnitude greater (>500 and 7.8 and
Abstract.
Author URL.
Sheridan PO, Raguideau S, Quince C, Holden J, Zhang L, Gaze WH, Mead A, Singer AC, Wellington EMH, Zhang L, et al (2020). Gene duplication drives genome expansion in a major lineage of Thaumarchaeota.
Nature Communications,
11(1).
Abstract:
Gene duplication drives genome expansion in a major lineage of Thaumarchaeota
Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sampled Nitrososphaerales to investigate the impact of lateral gene transfer (LGT), gene duplication and loss across thaumarchaeotal evolution. We reveal a major role for gene duplication in driving genome expansion subsequent to early LGT. In particular, two large LGT events are identified into Nitrososphaerales and the fate of these gene families is highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles. Notably, some genes involved in carbohydrate transport or coenzyme metabolism were duplicated, likely facilitating niche specialisation in soils and sediments. Overall, our results suggest that LGT followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.
Abstract.
Landrigan PJ, Stegeman JJ, Fleming LE, Allemand D, Anderson DM, Backer LC, Brucker-Davis F, Chevalier N, Corra L, Czerucka D, et al (2020). Human Health and Ocean Pollution.
ANNALS OF GLOBAL HEALTH,
86(1).
Author URL.
Hayes A, Feil E, Kasprzyk-Horden B, Snape J, Zhang L, Gaze W, Murray A (2020). Investigating selection for antimicrobial resistance by non-antibiotic drugs (NADs). Access Microbiology, 2(7A).
Jones DL, Baluja MQ, Graham DW, Corbishley A, McDonald JE, Malham SK, Hillary LS, Connor TR, Gaze WH, Moura IB, et al (2020). Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19.
Sci Total Environ,
749Abstract:
Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19.
The recent detection of SARS-CoV-2 RNA in feces has led to speculation that it can be transmitted via the fecal-oral/ocular route. This review aims to critically evaluate the incidence of gastrointestinal (GI) symptoms, the quantity and infectivity of SARS-CoV-2 in feces and urine, and whether these pose an infection risk in sanitary settings, sewage networks, wastewater treatment plants, and the wider environment (e.g. rivers, lakes and marine waters). A review of 48 independent studies revealed that severe GI dysfunction is only evident in a small number of COVID-19 cases, with 11 ± 2% exhibiting diarrhea and 12 ± 3% exhibiting vomiting and nausea. In addition to these cases, SARS-CoV-2 RNA can be detected in feces from some asymptomatic, mildly- and pre-symptomatic individuals. Fecal shedding of the virus peaks in the symptomatic period and can persist for several weeks, but with declining abundances in the post-symptomatic phase. SARS-CoV-2 RNA is occasionally detected in urine, but reports in fecal samples are more frequent. The abundance of the virus genetic material in both urine (ca. 102-105 gc/ml) and feces (ca. 102-107 gc/ml) is much lower than in nasopharyngeal fluids (ca. 105-1011 gc/ml). There is strong evidence of multiplication of SARS-CoV-2 in the gut and infectious virus has occasionally been recovered from both urine and stool samples. The level and infectious capability of SARS-CoV-2 in vomit remain unknown. In comparison to enteric viruses transmitted via the fecal-oral route (e.g. norovirus, adenovirus), the likelihood of SARS-CoV-2 being transmitted via feces or urine appears much lower due to the lower relative amounts of virus present in feces/urine. The biggest risk of transmission will occur in clinical and care home settings where secondary handling of people and urine/fecal matter occurs. In addition, while SARS-CoV-2 RNA genetic material can be detected by in wastewater, this signal is greatly reduced by conventional treatment. Our analysis also suggests the likelihood of infection due to contact with sewage-contaminated water (e.g. swimming, surfing, angling) or food (e.g. salads, shellfish) is extremely low or negligible based on very low predicted abundances and limited environmental survival of SARS-CoV-2. These conclusions are corroborated by the fact that tens of million cases of COVID-19 have occurred globally, but exposure to feces or wastewater has never been implicated as a transmission vector.
Abstract.
Author URL.
Elder FCT, Feil EJ, Snape JN, Gaze WH, Kasprzyk-Hordern BA (2020). The role of stereochemistry of antibiotic agents in the development of antibiotic resistance in the environment.
Environment International,
139Abstract:
The role of stereochemistry of antibiotic agents in the development of antibiotic resistance in the environment
Antibiotic resistance (ABR) is now recognised as a serious global health and economic threat that is most efficiently managed via a ‘one health’ approach incorporating environmental risk assessment. Although the environmental dimension of ABR has been largely overlooked, recent studies have underlined the importance of non-clinical settings in the emergence and spread of resistant strains. Despite this, several research gaps remain in regard to the development of a robust and fit-for-purpose environmental risk assessment for ABR drivers such as antibiotics (ABs). Here we explore the role the environment plays in the dissemination of ABR within the context of stereochemistry and its particular form, enantiomerism. Taking chloramphenicol as a proof of principle, we argue that stereoisomerism of ABs impacts on biological properties and the mechanisms of resistance and we discuss more broadly the importance of stereochemistry (enantiomerism in particular) with respect to antimicrobial potency and range of action.
Abstract.
Murray L, Boxall A, Snape J, Gaze W, Murray A (2020). The selection and co-selection of antimicrobial resistance by non-antibiotic drugs and plant protection products. Access Microbiology, 2(7A).
Murray AK, Stanton IC, Wright J, Zhang L, Snape J, Gaze WH (2020). The ‘SELection end points in Communities of bacTeria’ (SELECT) Method: a Novel Experimental Assay to Facilitate Risk Assessment of Selection for Antimicrobial Resistance in the Environment. Environmental Health Perspectives, 128(10).
Stanton IC, Bethel A, Leonard AFC, Gaze WH, Garside R (2020). What is the research evidence for antibiotic resistance exposure and transmission to humans from the environment? a systematic map protocol.
Environmental Evidence,
9(1).
Abstract:
What is the research evidence for antibiotic resistance exposure and transmission to humans from the environment? a systematic map protocol
Abstract
Background
Antimicrobial resistance (AMR) is a public health crisis that is predicted to cause 10 million deaths per year by 2050. The environment has been implicated as a reservoir of AMR and is suggested to play a role in the dissemination of antibiotic resistance genes (ARGs). Currently, most research has focused on measuring concentrations of antibiotics and characterising the abundance and diversity of ARGs and antibiotic resistant bacteria (ARB) in the environment. To date, there has been limited empirical research on whether humans are exposed to this, and whether exposure can lead to measureable impacts on human health. Therefore, the objective of this work is to produce two linked systematic maps to investigate previous research on exposure and transmission of AMR to humans from the environment. The first map will investigate the available research relating to exposure and transmission of ARB/ARGs from the environment to humans on a global scale and the second will investigate the prevalence of ARB/ARGs in various environments in the UK. These two maps will be useful for policy makers and research funders to identify where there are significant gluts and gaps in the current research, and where more primary and synthesis research needs to be undertaken.
Methods
Separate search strategies will be developed for the two maps. Searches will be run in 13 databases, and grey literature will be sought from key websites and engagement with experts. Hits will be managed in EndNote and screened in two stages (title/abstract then full text) against predefined inclusion criteria. A minimum of 10% will be double screened with ongoing consistency checking. All included studies will have data extracted into a bespoke form designed and piloted for each map. Data to be extracted will include bibliographic details, study design, location, exposure source, exposure route, health outcome (Map 1); and prevalence/percentage of ARB/ARG (Map 2). No validity appraisal will be undertaken. Results will be tabulated and presented narratively, together with graphics showing the types and areas of research that has been undertaken and heatmaps for key exposure-health outcomes (Map 1) and exposure-prevalence (Map 2).
Abstract.
Vos M, Sibleyras L, Lo LK, Hesse E, Gaze W, Klümper U (2020). Zinc can counteract selection for ciprofloxacin resistance.
FEMS Microbiol Lett,
367(3).
Abstract:
Zinc can counteract selection for ciprofloxacin resistance.
Antimicrobial resistance (AMR) has emerged as one of the most pressing threats to public health. AMR evolution occurs in the clinic but also in the environment, where antibiotics and heavy metals can select and co-select for AMR. While the selective potential of both antibiotics and metals is increasingly well-characterized, experimental studies exploring their combined effects on AMR evolution are rare. It has previously been demonstrated that fluoroquinolone antibiotics such as ciprofloxacin can chelate metal ions. To investigate how ciprofloxacin resistance is affected by the presence of metals, we quantified selection dynamics between a ciprofloxacin-susceptible and a ciprofloxacin-resistant Escherichia coli strain across a gradient of ciprofloxacin concentrations in presence and absence of zinc. The presence of zinc reduced growth of both strains, while ciprofloxacin inhibited exclusively the susceptible one. When present in combination zinc retained its inhibitory effect, while ciprofloxacin inhibition of the susceptible strain was reduced. Consequently, the minimal selective concentration for ciprofloxacin resistance increased up to five-fold in the presence of zinc. Environmental pollution usually comprises complex mixtures of antimicrobial agents. In addition to the usual focus on additive or synergistic interactions in complex selective mixtures, our findings highlight the importance of antagonistic selective interactions when considering resistance evolution.
Abstract.
Author URL.
Sünderhauf D, Pursey E, Klümper U, Westra E, Gaze W, van Houte S (2019). AMR gene removal by conjugative delivery of CRISPR-Cas9. Access Microbiology, 1(1A).
Rauseo J, Barra Caracciolo A, Ademollo N, Cardoni M, Di Lenola M, Gaze W, Stanton I, Grenni P, Pescatore T, Spataro F, et al (2019). Dissipation of the antibiotic sulfamethoxazole in a soil amended with anaerobically digested cattle manure.
J Hazard Mater,
378Abstract:
Dissipation of the antibiotic sulfamethoxazole in a soil amended with anaerobically digested cattle manure.
The application of anaerobically digested cattle manure on agricultural land for both improving its quality and recycling a farm waste is an increasingly frequent practice in line with the circular economy. However, knowledge on the potential risk of spreading antibiotic resistance through this specific practice is quite scarce. The antibiotic sulfamethoxazole (SMX) is one of the most heavily prescribed in veterinary medicine. In this study, SMX dissipation and the possible effects on natural microorganisms were investigated in a soil amended with an anaerobically digested cattle manure produced from a biogas plant inside a livestock farm. Microcosm experiments were performed using amended soil treated with SMX (20 mg/kg soil). During the experimental time (61 days), soil samples were analysed for SMX and N4-acetylsulfamethoxazole, microbial abundance, activity and structure. Furthermore, the prevalence of the intI1 gene was also determined. The overall results showed that, although there was an initial negative effect on microbial abundance, SMX halved in about 7 days in the digestate-amended soil. The intI1 gene found in both the digestate and amended soil suggested that the use of anaerobically digested cattle manure as fertilizer can be a source of antibiotic resistant bacteria (ARBs) and genes (ARGs) in agroecosystems.
Abstract.
Author URL.
Klümper U, Recker M, Zhang L, Yin X, Zhang T, Buckling A, Gaze W (2019). Selection for antibiotic resistance is reduced when embedded in a natural microbial community.
Abstract:
Selection for antibiotic resistance is reduced when embedded in a natural microbial community
AbstractAntibiotic resistance has emerged as one of the most pressing, global threats to public health. In single-species experiments selection for antibiotic resistance occurs at very low antibiotic concentrations. However, it is unclear how far these findings can be extrapolated to natural environments, where species are embedded within complex communities. We competed isogenic strains of Escherichia coli, differing exclusively in a single chromosomal resistance determinant, in the presence and absence of a pig fecal microbial community across a gradient of antibiotic concentration for two relevant antibiotics: gentamicin and kanamycin. We show that the minimal selective concentration was increased by more than one order of magnitude for both antibiotics when embedded in the community. We identified two general mechanisms were responsible for the increase in minimal selective concentration: an increase in the cost of resistance and a protective effect of the community for the susceptible phenotype. These findings have implications for our understanding of the evolution and selection of antibiotic resistance, and can inform future risk assessment efforts on antibiotic concentrations.
Abstract.
Klumper U, Recker M, Zhang L, Yin X, Zhang T, Buckling A, Gaze W (2019). Selection for antimicrobial resistance is reduced when embedded in a natural microbial community. The ISME Journal
Klümper U, Maillard A, Hesse E, Bayer F, Houte SV, Longdon B, Gaze W, Buckling A (2019). Short-term evolution under copper stress increases probability of plasmid uptake.
Abstract:
Short-term evolution under copper stress increases probability of plasmid uptake
AbstractUnderstanding plasmid transfer dynamics remains a key knowledge gap in the mitigation of antibiotic resistance gene spread. Direct effects of exposure to stressors on plasmid uptake are well monitored. However, it remains untested whether evolution of strains under stress conditions modulates subsequent plasmid uptake. Here, we evolved a compost derived microbial community for six weeks under copper stress and non-exposed control conditions. We then tested the ability of isolated clones from both treatments to take up the broad host range plasmid pKJK5 from anE.colidonor strain. Clones pre-adapted to copper displayed a significantly increased probability to be permissive towards the plasmid compared to those isolated from the control treatment. Further, increased phylogenetic distance to the donor strain was significantly and negatively correlated with plasmid uptake probabilities across both treatments.
Abstract.
Grenni P, Patrolecco L, Rauseo J, Spataro F, Di Lenola M, Aimola G, Zacchini M, Pietrini F, Di Baccio D, Stanton IC, et al (2019). Sulfamethoxazole persistence in a river water ecosystem and its effects on the natural microbial community and Lemna minor plant.
Microchemical Journal,
149Abstract:
Sulfamethoxazole persistence in a river water ecosystem and its effects on the natural microbial community and Lemna minor plant
Sulfamethoxazole (SMX) is a sulfonamide antibiotic commonly used in human and veterinary medicine and frequently detected in surface water as a micro-contaminant. The presence of this antibiotic and its main transformation product N4-acetyl-sulfamethoxazole (Ac-SMX) was evaluated in an Italian river water by Solid Phase Extraction (SPE) and subsequent LC MS/MS determination. River water microcosm experiments were set up in the presence and absence of duckweed (Lemna minor L.) adding SMX (500 μg L−1) with the aim of evaluating the persistence of antibiotic and its effects on both the microbial community naturally occurred in a river and the plant. The concentrations of SMX and Ac-SMX were measured at fixed times over a period of 28 days. The microbial abundance, intI1 gene and plant morpho-physiological analyses were also conducted. In the river water samples, SMX was not detected as a parent compound, but its acetylate metabolite Ac-SMX was found as a micro-contaminant. The results of the microcosm experiment showed that SMX did not substantially degrade, except in the presence of L. minor where a slight decrease (17%) was observed. The river residual concentration of Ac-SMX remained quite constant during the experimental period. The river microbial community was initially affected by adding the antibiotic with a decrease in its abundance; however, although it was not able to degrade SMX, it displayed an overall antibiotic resistance. In fact, the intI1 gene was found throughout the entire experimental period. Finally, SMX did not cause evident inhibition or suffering symptoms for the plant.
Abstract.
Pursey E, Sünderhauf D, Paganelli F, Gaze W, Westra E, van Houte S (2019). Targeting antimicrobial resistance genes in clinical isolates from healthcare-associated infections using CRISPR-Cas9. Access Microbiology, 1(1A).
Hernandez RJ, Hesse E, Dowling AJ, Coyle NM, Feil EJ, Gaze WH, Vos M (2019). Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens. PeerJ, 6
Boase NJ, White MP, Gaze WH, Redshaw CH (2019). Why don't the British eat locally harvested shellfish? the role of misconceptions and knowledge gaps.
Appetite,
143Abstract:
Why don't the British eat locally harvested shellfish? the role of misconceptions and knowledge gaps.
Although the UK consumes a substantial amount of shellfish, most is imported (e.g. prawns), while locally harvested molluscs and crustaceans (e.g. mussels, crab) tend to be exported. This study aimed to investigate whether a low rate of local shellfish consumption in the UK is due to misunderstandings or knowledge gaps about the potential health and environmental risks and benefits of consumption. Following the Mental Models Approach, the present paper reveals: 1) qualitative results from 26 stakeholder/public interviews which identified 10 key misunderstandings and knowledge gaps, including incorrect beliefs about health risks and a lack of knowledge about the relative environmental benefits compared to other foods (key misunderstandings included some parts of a crab are poisonous if eaten, and the majority of UK shellfish is farmed), and 2) quantitative results from a survey (n = 1,433) that explored the degree to which these misunderstandings and knowledge gaps may influence consumption intentions in the wider UK population. Survey results suggested the number of misunderstandings and knowledge gaps significantly predicted shellfish consumption intentions even after controlling for demographics, food related values, and past consumption behaviour. Path analyses revealed their impact on intentions was partially mediated via Theory of Planned Behaviour variables. Results could inform information campaigns supporting consumers to make more informed decisions regarding a group of foods that are potentially both healthy and relatively environmentally friendly.
Abstract.
Author URL.
Vos M, Sibleyras L, Lo LK, Hesse E, Gaze W, Klümper U (2019). Zinc can counteract selection for ciprofloxacin resistance.
Abstract:
Zinc can counteract selection for ciprofloxacin resistance
AbstractAntimicrobial resistance (AMR) has emerged as one of the most pressing global threats to public health. AMR evolution occurs in the clinic but also in the environment, where low concentrations of antibiotics and heavy metals can respectively select and co-select for resistance. While the selective potential for AMR of both antibiotics and metals is increasingly well-characterized, studies exploring the combined effect of both types of selective agents are rare. It has previously been demonstrated that fluoroquinolone antibiotics such as ciprofloxacin can chelate metal ions. To investigate how ciprofloxacin resistance is affected by the presence of metals, we quantified selection dynamics between a ciprofloxacin-susceptible and an isogenic ciprofloxacin-resistantEscherichia coliMG1655 strain across a gradient of ciprofloxacin concentrations in the presence and absence of Zinc cations (Zn2+). The minimal selective concentration (MSC) for ciprofloxacin resistance significantly increased up to 5-fold in the presence of Zn2+. No such effect on the MSC was found for gentamicin, an antibiotic not known to chelate zinc cations. Environmental pollution usually consists of complex mixtures of antimicrobial agents. Our findings highlight the importance of taking antagonistic as well as additive or synergistic interactions between different chemical compounds into account when considering their effect on bacterial resistance evolution.Graphical abstractOne sentence summaryThe minimal selective concentration for a ciprofloxacin resistantE. colistrain increases up to 5-fold in the presence of Zinc cations.
Abstract.
Leonard AFC, Yin XL, Zhang T, Hui M, Gaze WH (2018). A coliform-targeted metagenomic method facilitating human exposure estimates to Escherichia coli-borne antibiotic resistance genes.
FEMS Microbiol Ecol,
94(3).
Abstract:
A coliform-targeted metagenomic method facilitating human exposure estimates to Escherichia coli-borne antibiotic resistance genes.
Antimicrobial resistance and the spread of antibiotic resistance genes (ARGs) pose a threat to human health. Community-acquired infections resistant to treatment with first-line antibiotics are increasing, and there are few studies investigating environmental exposures and transmission. Our objective is to develop a novel targeted metagenomic method to quantify the abundance and diversity of ARGs in a faecal indicator bacterium, and to estimate human exposure to resistant bacteria in a natural environment. Sequence data from Escherichia coli metagenomes from 13 bathing waters in England were analysed using the ARGs Online Analysis Pipeline to estimate the abundance and diversity of resistance determinants borne by this indicator bacterium. These data were averaged over the 13 sites and used along with data on the levels of E. coli in English bathing waters in 2016 and estimates of the volume of water that water users typically ingest in an average session of their chosen activityto quantify the numbers of ARGs that water users ingest. Escherichia coli in coastal bathing waters were found to harbour on average 1.24 ARGs per cell. Approximately 2.5 million water sports sessions occurred in England in 2016 that resulted in water users ingesting at least 100 E. coli-borne ARGs.
Abstract.
Author URL.
Pursey E, Sünderhauf D, Gaze WH, Westra ER, van Houte S (2018). CRISPR-Cas antimicrobials: Challenges and future prospects.
PLoS Pathog,
14(6).
Author URL.
Djenadi K, Zhang L, Murray AK, Gaze WH (2018). Carbapenem resistance in bacteria isolated from soil and water environments in Algeria.
J Glob Antimicrob Resist,
15, 262-267.
Abstract:
Carbapenem resistance in bacteria isolated from soil and water environments in Algeria.
OBJECTIVES: Recent research has demonstrated that natural populations of bacteria carry large numbers of mobile genetic elements that may harbour antibiotic resistance determinants. This study aimed to investigate carbapenem resistance in Gram-negative bacteria isolated from natural environments in Béjaïa (Algeria) and to determine the horizontal gene transfer potential of a subset of these antibiotic resistance genes (ARGs). METHODS: Antibiotic-resistant bacteria were isolated and the host was identified using MALDI-TOF/MS and 16S rRNA sequencing. ARG carriage was investigated by the double-disk synergy test, metallo-β-lactamase (MBL) production test and PCR screening for carbapenemase genes. Conjugation experiments were performed to determine potential ARG mobility. To identify ARGs, genomic libraries were constructed and functionally screened and inserts were sequenced. RESULTS: a total of 62 antibiotic-resistant strains isolated from soil and water samples were classified as belonging to the Enterobacteriaceae, Pseudomonadaceae, Xanthomonadaceae and Aeromonadaceae families. Four highly imipenem-resistant (MIC>64μg/mL) and cefotaxime-resistant (MIC>8μg/mL) clinically-relevant strains were selected for further characterisation. All four strains produced extended-spectrum β-lactamases, but MBL production was not confirmed. Imipenem and cefotaxime resistance was transferable to Escherichia coli but was not conferred by blaAmpC, blaIMP, blaNDM, blaKPC, blaOXA-48 or blaGES genes. Novel putative resistance mechanisms were identified, including a novel DHA β-lactamase conferring clinical resistance to cefotaxime. CONCLUSIONS: the environment is a reservoir of carbapenem-resistant bacteria. Further investigation of the evolution and dissemination of antibiotic resistance in environmental bacteria is required in order to understand and prevent the emergence of resistance in the clinical environment.
Abstract.
Author URL.
Larsson DGJ, Andremont A, Bengtsson-Palme J, Brandt KK, de Roda Husman AM, Fagerstedt P, Fick J, Flach C-F, Gaze WH, Kuroda M, et al (2018). Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance.
Environ Int,
117, 132-138.
Abstract:
Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance.
There is growing understanding that the environment plays an important role both in the transmission of antibiotic resistant pathogens and in their evolution. Accordingly, researchers and stakeholders world-wide seek to further explore the mechanisms and drivers involved, quantify risks and identify suitable interventions. There is a clear value in establishing research needs and coordinating efforts within and across nations in order to best tackle this global challenge. At an international workshop in late September 2017, scientists from 14 countries with expertise on the environmental dimensions of antibiotic resistance gathered to define critical knowledge gaps. Four key areas were identified where research is urgently needed: 1) the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment; 2) the role of the environment, and particularly anthropogenic inputs, in the evolution of resistance; 3) the overall human and animal health impacts caused by exposure to environmental resistant bacteria; and 4) the efficacy and feasibility of different technological, social, economic and behavioral interventions to mitigate environmental antibiotic resistance.1.
Abstract.
Author URL.
Leonard AFC, Zhang L, Balfour AJ, Garside R, Hawkey PM, Murray AK, Ukoumunne OC, Gaze WH (2018). Exposure to and colonisation by antibiotic-resistant E. coli in UK coastal water users: Environmental surveillance, exposure assessment, and epidemiological study (Beach Bum Survey).
Environ Int,
114, 326-333.
Abstract:
Exposure to and colonisation by antibiotic-resistant E. coli in UK coastal water users: Environmental surveillance, exposure assessment, and epidemiological study (Beach Bum Survey).
BACKGROUND: Antibiotic-resistant bacteria (ARB) present a global public health problem. With numbers of community-acquired resistant infections increasing, understanding the mechanisms by which people are exposed to and colonised by ARB can help inform effective strategies to prevent their spread. The role natural environments play in this is poorly understood. This is the first study to combine surveillance of ARB in bathing waters, human exposure estimates and association between exposure and colonisation by ARB in water users. METHODS: 97 bathing water samples from England and Wales were analysed for the proportion of E. coli harbouring blaCTX-M. These data were used to estimate the likelihood of water users ingesting blaCTX-M-bearing E. coli. Having identified surfers as being at risk of exposure to ARB, a cross-sectional study was conducted. Regular surfers and non-surfers were recruited to assess whether there is an association between surfing and gut colonisation by blaCTX-M-bearing E. coli. RESULTS: 11 of 97 bathing waters sampled were found to contain blaCTX-M-bearing E. coli. While the percentage of blaCTX-M-bearing E. coli in bathing waters was low (0.07%), water users are at risk of ingesting these ARB. It is estimated that over 2.5 million water sports sessions occurred in 2015 resulting in the ingestion of at least one blaCTX-M-bearing E. coli. In the epidemiological survey, 9/143 (6.3%) surfers were colonised by blaCTX-M-bearing E. coli, as compared to 2/130 (1.5%) of non-surfers (risk ratio=4.09, 95% CI 1.02 to 16.4, p=0.046). CONCLUSIONS: Surfers are at risk of exposure to and colonisation by clinically important antibiotic-resistant E. coli in coastal waters. Further research must be done on the role natural environments play in the transmission of ARB.
Abstract.
Author URL.
Leonard AFC, Singer A, Ukoumunne OC, Gaze WH, Garside R (2018). Is it safe to go back into the water? a systematic review and meta-analysis of the risk of acquiring infections from recreational exposure to seawater.
Int J Epidemiol,
47(2), 572-586.
Abstract:
Is it safe to go back into the water? a systematic review and meta-analysis of the risk of acquiring infections from recreational exposure to seawater.
BACKGROUND: Numerous illnesses are associated with bathing in natural waters, although it is assumed that the risk of illness among bathers exposed to relatively clean waters found in high-income countries is negligible. A systematic review was carried out to quantify the increased risk of experiencing a range of adverse health outcomes among bathers exposed to coastal water compared with non-bathers. METHODS: in all 6919 potentially relevant titles and abstracts were screened, and from these 40 studies were eligible for inclusion in the review. Odds ratios (OR) were extracted from 19 of these reports and combined in random-effect meta-analyses for the following adverse health outcomes: incident cases of any illness, ear infections, gastrointestinal illness and infections caused by specific microorganisms. RESULTS: There is an increased risk of experiencing symptoms of any illness [OR = 1.86, 95% confidence interval (CI): 1.31 to 2.64, P = 0.001] and ear ailments (OR = 2.05, 95% CI: 1.49 to 2.82, P < 0.001) in bathers compared with non-bathers. There is also an increased risk of experiencing gastrointestinal ailments (OR = 1.29, 95% CI: 1.12 to 1.49, P < 0.001). CONCLUSIONS: This is the first systematic review to evaluate evidence on the increased risk of acquiring illnesses from bathing in seawater compared with non-bathers. Our results support the notion that infections are acquired from bathing in coastal waters, and that bathers have a greater risk of experiencing a variety of illnesses compared with non-bathers.
Abstract.
Author URL.
Murray AK, Zhang L, Yin X, Zhang T, Buckling A, Snape J, Gaze WH (2018). Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities.
Abstract:
Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities
ABSTRACTRecent research has demonstrated selection for antibiotic resistance occurs at very low antibiotic concentrations in single species experiments, but the relevance of these findings when species are embedded in complex microbial communities is unclear. We show the strength of selection for naturally occurring resistance alleles in a complex community remains constant from low sub-inhibitory to above clinically relevant concentrations. Selection increases with antibiotic concentration before reaching a plateau where selection remains constant over a two order magnitude concentration range. This is likely to be due to cross-protection of the susceptible bacteria in the community following rapid extracellular antibiotic degradation by the resistant population, shown experimentally through a combination of chemical quantification and bacterial growth experiments. Metagenome and 16S rRNA analyses on sewage-derived bacterial communities evolved under cefotaxime exposure show preferential enrichment forblaCTX-Mgenes over all other beta-lactamase genes, as well as positive selection and co-selection for antibiotic resistant, opportunistic pathogens. These findings have far reaching implications for our understanding of the evolution of antibiotic resistance, by challenging the long-standing assumption that selection occurs in a dose-dependent manner.
Abstract.
Murray AK, Zhang L, Yin X, Zhang T, Buckling A, Snape J, Gaze W (2018). Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities. mBio
Zhang L (2018). Staphylococcus cornubiensis sp. nov. a member of the Staphylococcus intermedius Group (SIG). International Journal of Systematic and Evolutionary Microbiology
Amos GCA, Ploumakis S, Zhang L, Hawkey PM, Gaze WH, Wellington EMH (2018). The widespread dissemination of integrons throughout bacterial communities in a riverine system.
ISME Journal,
12(3), 681-691.
Abstract:
The widespread dissemination of integrons throughout bacterial communities in a riverine system
Anthropogenic inputs increase levels of antimicrobial resistance (AMR) in the environment, however, it is unknown how these inputs create this observed increase, and if anthropogenic sources impact AMR in environmental bacteria. The aim of this study was to characterise the role of waste water treatment plants (WWTPs) in the dissemination of class 1 integrons (CL1s) in the riverine environment. Using sample sites from upstream and downstream of a WWTP, we demonstrate through isolation and culture-independent analysis that WWTP effluent significantly increases both CL1 abundance and antibiotic resistance in the riverine environment. Characterisation of CL1-bearing isolates revealed that CL1s were distributed across a diverse range of bacteria, with identical complex genetic resistance determinants isolated from both human-associated and common environmental bacteria across connected sites. Over half of sequenced CL1s lacked the 3′-conserved sequence ('atypical' CL1s); surprisingly, bacteria carrying atypical CL1s were on average resistant to more antibiotics than bacteria carrying 3′-CS CL1s. Quaternary ammonium compound (QAC) resistance genes were observed across 75% of sequenced CL1 gene cassette arrays. Chemical data analysis indicated high levels of boron (a detergent marker) downstream of the WWTP. Subsequent phenotypic screening of CL1-bearing isolates demonstrated that ~90% were resistant to QAC detergents, with in vitro experiments demonstrating that QACs could solely select for the transfer of clinical antibiotic resistance genes to a naive Escherichia coli recipient. In conclusion, this study highlights the significant impact of WWTPs on environmental AMR, and demonstrates the widespread carriage of clinically important resistance determinants by environmentally associated bacteria.
Abstract.
Bürgmann H, Frigon D, H Gaze W, M Manaia C, Pruden A, Singer AC, F Smets B, Zhang T (2018). Water and sanitation: an essential battlefront in the war on antimicrobial resistance.
FEMS Microbiol Ecol,
94(9).
Abstract:
Water and sanitation: an essential battlefront in the war on antimicrobial resistance.
Water and sanitation represent a key battlefront in combatting the spread of antimicrobial resistance (AMR). Basic water sanitation infrastructure is an essential first step towards protecting public health, thereby limiting the spread of pathogens and the need for antibiotics. AMR presents unique human health risks, meriting new risk assessment frameworks specifically adapted to water and sanitation-borne AMR. There are numerous exposure routes to AMR originating from human waste, each of which must be quantified for its relative risk to human health. Wastewater treatment plants play a vital role in centralized collection and treatment of human sewage, but there are numerous unresolved issues in terms of the microbial ecological processes occurring within them and the extent to which they attenuate or amplify AMR. Research is needed to advance understanding of the fate of resistant bacteria and antibiotic resistance genes in various waste management systems, depending on the local constraints and intended reuse applications. World Health Organization and national AMR action plans would benefit from a more holistic 'One Water' understanding. In this article we provide a framework for research, policy, practice and public engagement aimed at limiting the spread of AMR from water and sanitation in low-, medium- and high-income countries.
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Author URL.
Powell N, Davidson I, Yelling P, Collinson A, Pollard A, Johnson L, Gibson N, Taylor J, Wisner K, Gaze W, et al (2017). Developing a local antimicrobial resistance action plan: the Cornwall One Health Antimicrobial Resistance Group.
J Antimicrob Chemother,
72(9), 2661-2665.
Abstract:
Developing a local antimicrobial resistance action plan: the Cornwall One Health Antimicrobial Resistance Group.
OBJECTIVES: the UK Five Year Antimicrobial Resistance (AMR) Strategy was published in September 2013 and recommended a One Health approach emphasizing the importance of collaboration to tackle AMR. We describe the inauguration of what we believe to be the first regional One Health group established in the UK. The purpose of the group was to ensure the implementation of a coordinated Cornwall-wide response to the UK AMR Strategy and we describe the outputs of the group to date. METHODS: the Cornwall Antimicrobial Resistance Group was set up as a sub-group of the Health & Wellbeing Board's Health Protection Committee. Stakeholders reviewed the key objectives set out within the Five Year AMR strategy, identified local priorities and existing work streams within Cornwall, and completed a gap analysis. The annual work plan was developed from the gap analysis and provided a foundation for improved coordination of One Health antimicrobial stewardship (AMS) activity in Cornwall. RESULTS: to date, outputs from the group can be arranged under the following themes: education and engagement with the public; education and engagement with healthcare workers and veterinarians; and a comprehensive AMS programme for all sectors. The group continues to grow in size with wider stakeholder engagement and increased variety of work streams. CONCLUSIONS: This unique group facilitates discussions across sectors, which has enabled the sharing of knowledge, ideas and resources, stimulated local AMS initiatives, and ensured a platform for the development of future AMR and AMS work.
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Author URL.
Furness LE, Campbell A, Zhang L, Gaze WH, McDonald RA (2017). Wild small mammals as sentinels for the environmental transmission of antimicrobial resistance.
Environ Res,
154, 28-34.
Abstract:
Wild small mammals as sentinels for the environmental transmission of antimicrobial resistance.
Antimicrobial resistance (AMR) represents a serious threat to human health worldwide. We have tested the use of free-living small mammals (mice, voles and shrews) as sentinels of variation in the distribution of AMR in the environment and the potential for transmission from the natural environment to animal hosts. Escherichia coli isolated from the faeces of small mammals trapped at paired coastal and inland sites were tested for resistance to four antibiotics: trimethoprim, ampicillin, ciprofloxacin and cefotaxime. Coastal individuals were over twice as likely to carry AMR E. coli than inland individuals (79% and 35% respectively), and both between-site and between-species variation was observed. Animals from coastal populations also excreted increased numbers of AMR E. coli and a greater diversity of E. coli phylotypes, including human-associated pathogenic strains. Small mammals appear to be useful bioindicators of fine-scale spatial variation in the distribution of AMR and, potentially, of the risks of AMR transmission to mammalian hosts, including humans.
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Author URL.
Hunter JG, Madden RG, Stone AM, Osborne N, Wheeler B, Vine L, Dickson A, Barlow M, Lewis J, Bendall RP, et al (2016). Coastal clustering of HEV; Cornwall, UK.
Eur J Gastroenterol Hepatol,
28(3), 323-327.
Abstract:
Coastal clustering of HEV; Cornwall, UK.
BACKGROUND AND AIMS: Autochthonous hepatitis E virus (HEV) infection is a porcine zoonosis and increasingly recognized in developed countries. In most cases the route of infection is uncertain. A previous study showed that HEV was associated geographically with pig farms and coastal areas. AIM: the aim of the present research was to study the geographical, environmental and social factors in autochthonous HEV infection. METHODS: Cases of HEV genotype 3 infection and controls were identified from 2047 consecutive patients attending a rapid-access hepatology clinic. For each case/control the following were recorded: distance from home to nearest pig farm, distance from home to coast, rainfall levels during the 8 weeks before presentation, and socioeconomic status. RESULTS: a total of 36 acute hepatitis E cases, 170 age/sex-matched controls and 53 hepatitis controls were identified. The geographical spread of hepatitis E cases was not even when compared with both control groups. Cases were more likely to live within 2000 m of the coast (odds ratio=2.32, 95% confidence interval=1.08-5.19, P=0.03). There was no regional difference in the incidence of cases and controls between west and central Cornwall. There was no difference between cases and controls in terms of distance from the nearest pig farm, socioeconomic status or rainfall during the 8 weeks before disease presentation. CONCLUSION: Cases of HEV infection in Cornwall are associated with coastal residence. The reason for this observation is uncertain, but might be related to recreational exposure to beach areas exposed to HEV-contaminated 'run-off' from pig farms. This hypothesis merits further study.
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Author URL.
Cleary DW, Bishop AH, Zhang L, Topp E, Wellington EMH, Gaze WH (2016). Long-term antibiotic exposure in soil is associated with changes in microbial community structure and prevalence of class 1 integrons.
FEMS Microbiol Ecol,
92(10).
Abstract:
Long-term antibiotic exposure in soil is associated with changes in microbial community structure and prevalence of class 1 integrons.
Antimicrobial resistance is one of the most significant challenges facing the global medical community and can be attributed to the use and misuse of antibiotics. This includes use as growth promoters or for prophylaxis and treatment of bacterial infection in intensively farmed livestock from where antibiotics can enter the environment as residues in manure. We characterised the impact of the long-term application of a mixture of veterinary antibiotics alone (tylosin, sulfamethazine and chlortetracycline) on class 1 integron prevalence and soil microbiota composition. Class 1 integron prevalence increased significantly (P < 0.005) from 0.006% in control samples to 0.064% in the treated plots. Soil microbiota was analysed using 16S rRNA gene sequencing and revealed significant alterations in composition. of the 19 significantly different (P < 0.05) OTUs identified, 16 were of the Class Proteobacteria and these decreased in abundance relative to the control plots. Only one OTU, of the Class Cyanobacteria, was shown to increase in abundance significantly; a curiosity given the established sensitivity of this class to antibiotics. We hypothesise that the overrepresentation of Proteobacteria as OTUs that decreased significantly in relative abundance, coupled with the observations of an increase in integron prevalence, may represent a strong selective pressure on these taxa.
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Author URL.
Salimraj R, Zhang L, Hinchliffe P, Wellington EMH, Brem J, Schofield CJ, Gaze WH, Spencer J (2016). Structural and Biochemical Characterization of Rm3, a Subclass B3 Metallo-β-Lactamase Identified from a Functional Metagenomic Study.
Antimicrob Agents Chemother,
60(10), 5828-5840.
Abstract:
Structural and Biochemical Characterization of Rm3, a Subclass B3 Metallo-β-Lactamase Identified from a Functional Metagenomic Study.
β-Lactamase production increasingly threatens the effectiveness of β-lactams, which remain a mainstay of antimicrobial chemotherapy. New activities emerge through both mutation of previously known β-lactamases and mobilization from environmental reservoirs. The spread of metallo-β-lactamases (MBLs) represents a particular challenge because of their typically broad-spectrum activities encompassing carbapenems, in addition to other β-lactam classes. Increasingly, genomic and metagenomic studies have revealed the distribution of putative MBLs in the environment, but in most cases their activity against clinically relevant β-lactams and, hence, the extent to which they can be considered a resistance reservoir remain uncharacterized. Here we characterize the product of one such gene, blaRm3, identified through functional metagenomic sampling of an environment with high levels of biocide exposure. blaRm3 encodes a subclass B3 MBL that, when expressed in a recombinant Escherichia coli strain, is exported to the bacterial periplasm and hydrolyzes clinically used penicillins, cephalosporins, and carbapenems with an efficiency limited by high Km values. An Rm3 crystal structure reveals the MBL superfamily αβ/βα fold, which more closely resembles that in mobilized B3 MBLs (AIM-1 and SMB-1) than other chromosomal enzymes (L1 or FEZ-1). A binuclear zinc site sits in a deep channel that is in part defined by a relatively extended N terminus. Structural comparisons suggest that the steric constraints imposed by the N terminus may limit its affinity for β-lactams. Sequence comparisons identify Rm3-like MBLs in numerous other environmental samples and species. Our data suggest that Rm3-like enzymes represent a distinct group of B3 MBLs with a wide distribution and can be considered an environmental reservoir of determinants of β-lactam resistance.
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Author URL.
Lehmann K, Bell T, Bowes MJ, Amos GCA, Gaze WH, Wellington EMH, Singer AC (2016). Trace levels of sewage effluent are sufficient to increase class 1 integron prevalence in freshwater biofilms without changing the core community.
Water Res,
106, 163-170.
Abstract:
Trace levels of sewage effluent are sufficient to increase class 1 integron prevalence in freshwater biofilms without changing the core community.
Most river systems are impacted by sewage effluent. It remains unclear if there is a lower threshold to the concentration of sewage effluent that can significantly change the structure of the microbial community and its mobile genetic elements in a natural river biofilm. We used novel in situ mesocosms to conduct replicated experiments to study how the addition of low-level concentrations of sewage effluent (nominally 2.5 ppm) affects river biofilms in two contrasting Chalk river systems, the Rivers Kennet and Lambourn (high/low sewage impact, respectively). 16S sequencing and qPCR showed that community composition was not significantly changed by the sewage effluent addition, but class 1 integron prevalence (Lambourn control 0.07% (SE ± 0.01), Lambourn sewage effluent 0.11% (SE ± 0.006), Kennet control 0.56% (SE ± 0.01), Kennet sewage effluent 1.28% (SE ± 0.16)) was significantly greater in the communities exposed to sewage effluent than in the control flumes (ANOVA, F = 5.11, p = 0.045) in both rivers. Furthermore, the difference in integron prevalence between the Kennet control (no sewage effluent addition) and Kennet sewage-treated samples was proportionally greater than the difference in prevalence between the Lambourn control and sewage-treated samples (ANOVA (interaction between treatment and river), F = 6.42, p = 0.028). Mechanisms that lead to such differences could include macronutrient/biofilm or phage/bacteria interactions. Our findings highlight the role that low-level exposure to complex polluting mixtures such as sewage effluent can play in the spread of antibiotic resistance genes. The results also highlight that certain conditions, such as macronutrient load, might accelerate spread of antibiotic resistance genes.
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Author URL.
Leonard AFC, Zhang L, Balfour AJ, Garside R, Gaze WH (2015). Human recreational exposure to antibiotic resistant bacteria in coastal bathing waters.
Environment International,
82, 92-100.
Abstract:
Human recreational exposure to antibiotic resistant bacteria in coastal bathing waters
Infections caused by antibiotic resistant bacteria (ARB) are associated with poor health outcomes and are recognised globally as a serious health problem. Much research has been conducted on the transmission of ARB to humans. Yet the role the natural environment plays in the spread of ARB and antibiotic resistance genes is not well understood. Antibiotic resistant bacteria have been detected in natural aquatic environments, and ingestion of seawater during water sports is one route by which many people could be directly exposed. The aim was to estimate the prevalence of resistance to one clinically important class of antibiotics (third-generation cephalosporins (3GCs)) amongst Escherichia coli in coastal surface waters in England and Wales. Prevalence data was used to quantify ingestion of 3GC-resistant E. coli (3GCREC) by people participating in water sports in designated coastal bathing waters. A further aim was to use this value to derive a population-level estimate of exposure to these bacteria during recreational use of coastal waters in 2012. The prevalence of 3GC-resistance amongst E. coli isolated from coastal surface waters was estimated using culture-based methods. This was combined with the density of E. coli reported in designated coastal bathing waters along with estimations of the volumes of water ingested during various water sports reported in the literature to calculate the mean number of 3GCREC ingested during different water sports.0.12% of E. coli isolated from surface waters were resistant to 3GCs. This value was used to estimate that in England and Wales over 6.3 million water sport sessions occurred in 2012 that resulted in the ingestion of at least one 3GCREC.Despite the low prevalence of resistance to 3GCs amongst E. coli in surface waters, there is an identifiable human exposure risk for water users, which varies with the type of water sport undertaken. The relative importance of this exposure is likely to be greater in areas where a large proportion of the population enjoys water sports. Millions of water sport sessions occurred in 2012 that were likely to have resulted in people ingesting E. coli resistant to a single class of antibiotics (3GCs). However, this is expected to be a significant underestimate of recreational exposure to all ARB in seawater. This is the first study to use volumes of water ingested during different water sports to estimate human exposure to ARB. Further work needs to be done to elucidate the health implications and clinical relevance of exposure to ARB in both marine and fresh waters in order to fully understand the risk to public health.
Abstract.
Lee J, Murray A, Bendall R, Gaze W, Zhang L, Vos M (2015). Improved detection of Staphylococcus intermedius group in a routine diagnostic laboratory.
J Clin Microbiol,
53(3), 961-963.
Abstract:
Improved detection of Staphylococcus intermedius group in a routine diagnostic laboratory.
The Staphylococcus intermedius group (SIG) includes zoonotic pathogens traditionally associated with dog bites. We describe a simple scheme for improved detection of SIG using routine laboratory methods, report its effect on isolation rates, and use sequencing to confirm that, apart from one atypical SIG strain, most isolates are Staphylococcus pseudintermedius.
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Author URL.
King HC, Murphy A, James P, Travis E, Porter D, Sawyer J, Cork J, Delahay RJ, Gaze W, Courtenay O, et al (2015). Performance of a Noninvasive Test for Detecting Mycobacterium bovis Shedding in European Badger (Meles meles) Populations.
J Clin Microbiol,
53(7), 2316-2323.
Abstract:
Performance of a Noninvasive Test for Detecting Mycobacterium bovis Shedding in European Badger (Meles meles) Populations.
The incidence of Mycobacterium bovis, the causative agent of bovine tuberculosis, in cattle herds in the United Kingdom is increasing, resulting in substantial economic losses. The European badger (Meles meles) is implicated as a wildlife reservoir and is the subject of control measures aimed at reducing the incidence of infection in cattle populations. Understanding the epidemiology of M. bovis in badger populations is essential for directing control interventions and understanding disease spread; however, accurate diagnosis in live animals is challenging and currently uses invasive methods. Here we present a noninvasive diagnostic procedure and sampling regimen using field sampling of latrines and detection of M. bovis with quantitative PCR tests, the results of which strongly correlate with the results of immunoassays in the field at the social group level. This method allows M. bovis infections in badger populations to be monitored without trapping and provides additional information on the quantities of bacterial DNA shed. Therefore, our approach may provide valuable insights into the epidemiology of bovine tuberculosis in badger populations and inform disease control interventions.
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Author URL.
Amos GCA, Carter A, Hawkey PM, Gaze WH, Wellington EM (2015). The hidden resistome of retail chicken meat. Journal of Global Antimicrobial Resistance, 3(1), 44-46.
King HC, Murphy A, James P, Travis E, Porter D, Hung Y-J, Sawyer J, Cork J, Delahay RJ, Gaze W, et al (2015). The variability and seasonality of the environmental reservoir of Mycobacterium bovis shed by wild European badgers.
Sci Rep,
5Abstract:
The variability and seasonality of the environmental reservoir of Mycobacterium bovis shed by wild European badgers.
The incidence of Mycobacterium bovis, the causative agent of bovine tuberculosis, has been increasing in UK cattle herds resulting in substantial economic losses. The European badger (Meles meles) is implicated as a wildlife reservoir of infection. One likely route of transmission to cattle is through exposure to infected badger urine and faeces. The relative importance of the environment in transmission remains unknown, in part due to the lack of information on the distribution and magnitude of environmental reservoirs. Here we identify potential infection hotspots in the badger population and quantify the heterogeneity in bacterial load; with infected badgers shedding between 1 × 10(3)- 4 × 10(5) M. bovis cells g(-1) of faeces, creating a substantial and seasonally variable environmental reservoir. Our findings highlight the potential importance of monitoring environmental reservoirs of M. bovis which may constitute a component of disease spread that is currently overlooked and yet may be responsible for a proportion of transmission amongst badgers and onwards to cattle.
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Author URL.
Gillings MR, Gaze WH, Pruden A, Smalla K, Tiedje JM, Zhu YG (2015). Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution.
ISME Journal,
9(6), 1269-1279.
Abstract:
Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution
Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.
Abstract.
Gillings MR, Gaze WH, Pruden A, Smalla K, Tiedje JM, Zhu Y-G (2015). Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution.
ISME J,
9(6), 1269-1279.
Abstract:
Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution.
Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.
Abstract.
Author URL.
Amos GC, Gozzard E, Carter CE, Mead A, Bowes MJ, Hawkey PM, Zhang L, Singer AC, Gaze WH, Wellington EMH, et al (2015). Validated predictive modelling of the environmental resistome.
ISME Journal,
9(6), 1467-1476.
Abstract:
Validated predictive modelling of the environmental resistome
Multi-drug-resistant bacteria pose a significant threat to public health. The role of the environment in the overall rise in antibiotic-resistant infections and risk to humans is largely unknown. This study aimed to evaluate drivers of antibiotic-resistance levels across the River Thames catchment, model key biotic, spatial and chemical variables and produce predictive models for future risk assessment. Sediment samples from 13 sites across the River Thames basin were taken at four time points across 2011 and 2012. Samples were analysed for class 1 integron prevalence and enumeration of third-generation cephalosporin-resistant bacteria. Class 1 integron prevalence was validated as a molecular marker of antibiotic resistance; levels of resistance showed significant geospatial and temporal variation. The main explanatory variables of resistance levels at each sample site were the number, proximity, size and type of surrounding wastewater-treatment plants. Model 1 revealed treatment plants accounted for 49.5% of the variance in resistance levels. Other contributing factors were extent of different surrounding land cover types (for example, Neutral Grassland), temporal patterns and prior rainfall; when modelling all variables the resulting model (Model 2) could explain 82.9% of variations in resistance levels in the whole catchment. Chemical analyses correlated with key indicators of treatment plant effluent and a model (Model 3) was generated based on water quality parameters (contaminant and macro- and micro-nutrient levels). Model 2 was beta tested on independent sites and explained over 78% of the variation in integron prevalence showing a significant predictive ability. We believe all models in this study are highly useful tools for informing and prioritising mitigation strategies to reduce the environmental resistome.
Abstract.
Amos GCA, Gozzard E, Carter CE, Mead A, Bowes MJ, Hawkey PM, Zhang L, Singer AC, Gaze WH, Wellington EMH, et al (2015). Validated predictive modelling of the environmental resistome.
ISME J,
9(6), 1467-1476.
Abstract:
Validated predictive modelling of the environmental resistome.
Multi-drug-resistant bacteria pose a significant threat to public health. The role of the environment in the overall rise in antibiotic-resistant infections and risk to humans is largely unknown. This study aimed to evaluate drivers of antibiotic-resistance levels across the River Thames catchment, model key biotic, spatial and chemical variables and produce predictive models for future risk assessment. Sediment samples from 13 sites across the River Thames basin were taken at four time points across 2011 and 2012. Samples were analysed for class 1 integron prevalence and enumeration of third-generation cephalosporin-resistant bacteria. Class 1 integron prevalence was validated as a molecular marker of antibiotic resistance; levels of resistance showed significant geospatial and temporal variation. The main explanatory variables of resistance levels at each sample site were the number, proximity, size and type of surrounding wastewater-treatment plants. Model 1 revealed treatment plants accounted for 49.5% of the variance in resistance levels. Other contributing factors were extent of different surrounding land cover types (for example, Neutral Grassland), temporal patterns and prior rainfall; when modelling all variables the resulting model (Model 2) could explain 82.9% of variations in resistance levels in the whole catchment. Chemical analyses correlated with key indicators of treatment plant effluent and a model (Model 3) was generated based on water quality parameters (contaminant and macro- and micro-nutrient levels). Model 2 was beta tested on independent sites and explained over 78% of the variation in integron prevalence showing a significant predictive ability. We believe all models in this study are highly useful tools for informing and prioritising mitigation strategies to reduce the environmental resistome.
Abstract.
Author URL.
Dealtry S, Ding G-C, Weichelt V, Dunon V, Schlüter A, Martini MC, Del Papa MF, Lagares A, Amos GCA, Wellington EMH, et al (2014). Cultivation-independent screening revealed hot spots of IncP-1, IncP-7 and IncP-9 plasmid occurrence in different environmental habitats.
PLoS One,
9(2).
Abstract:
Cultivation-independent screening revealed hot spots of IncP-1, IncP-7 and IncP-9 plasmid occurrence in different environmental habitats.
IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC-DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are "hot spots" of plasmids potentially carrying catabolic genes.
Abstract.
Author URL.
Amos GCA, Zhang L, Hawkey PM, Gaze WH, Wellington EM (2014). Functional metagenomic analysis reveals rivers are a reservoir for diverse antibiotic resistance genes.
Vet Microbiol,
171(3-4), 441-447.
Abstract:
Functional metagenomic analysis reveals rivers are a reservoir for diverse antibiotic resistance genes.
The environment harbours a significant diversity of uncultured bacteria and a potential source of novel and extant resistance genes which may recombine with clinically important bacteria disseminated into environmental reservoirs. There is evidence that pollution can select for resistance due to the aggregation of adaptive genes on mobile elements. The aim of this study was to establish the impact of waste water treatment plant (WWTP) effluent disposal to a river by using culture independent methods to study diversity of resistance genes downstream of the WWTP in comparison to upstream. Metagenomic libraries were constructed in Escherichia coli and screened for phenotypic resistance to amikacin, gentamicin, neomycin, ampicillin and ciprofloxacin. Resistance genes were identified by using transposon mutagenesis. A significant increase downstream of the WWTP was observed in the number of phenotypic resistant clones recovered in metagenomic libraries. Common β-lactamases such as blaTEM were recovered as well as a diverse range of acetyltransferases and unusual transporter genes, with evidence for newly emerging resistance mechanisms. The similarities of the predicted proteins to known sequences suggested origins of genes from a very diverse range of bacteria. The study suggests that waste water disposal increases the reservoir of resistance mechanisms in the environment either by addition of resistance genes or by input of agents selective for resistant phenotypes.
Abstract.
Author URL.
Leonard AFC, Zhang L, Balfour AJ, Garside R, Gaze WH (2014). Human recreational exposure to antibiotic resistant bacteria in coastal bathing waters.
Environment InternationalAbstract:
Human recreational exposure to antibiotic resistant bacteria in coastal bathing waters
© 2015 Elsevier Ltd. Infections caused by antibiotic resistant bacteria (ARB) are associated with poor health outcomes and are recognised globally as a serious health problem. Much research has been conducted on the transmission of ARB to humans. Yet the role the natural environment plays in the spread of ARB and antibiotic resistance genes is not well understood. Antibiotic resistant bacteria have been detected in natural aquatic environments, and ingestion of seawater during water sports is one route by which many people could be directly exposed.The aim was to estimate the prevalence of resistance to one clinically important class of antibiotics (third-generation cephalosporins (3GCs)) amongst Escherichia coli in coastal surface waters in England and Wales. Prevalence data was used to quantify ingestion of 3GC-resistant E. coli (3GCREC) by people participating in water sports in designated coastal bathing waters. A further aim was to use this value to derive a population-level estimate of exposure to these bacteria during recreational use of coastal waters in 2012.The prevalence of 3GC-resistance amongst E. coli isolated from coastal surface waters was estimated using culture-based methods. This was combined with the density of E. coli reported in designated coastal bathing waters along with estimations of the volumes of water ingested during various water sports reported in the literature to calculate the mean number of 3GCREC ingested during different water sports.0.12% of E. coli isolated from surface waters were resistant to 3GCs. This value was used to estimate that in England and Wales over 6.3 million water sport sessions occurred in 2012 that resulted in the ingestion of at least one 3GCREC.Despite the low prevalence of resistance to 3GCs amongst E. coli in surface waters, there is an identifiable human exposure risk for water users, which varies with the type of water sport undertaken. The relative importance of this exposure is likely to be greater in areas where a large proportion of the population enjoys water sports. Millions of water sport sessions occurred in 2012 that were likely to have resulted in people ingesting E. coli resistant to a single class of antibiotics (3GCs). However, this is expected to be a significant underestimate of recreational exposure to all ARB in seawater.This is the first study to use volumes of water ingested during different water sports to estimate human exposure to ARB. Further work needs to be done to elucidate the health implications and clinical relevance of exposure to ARB in both marine and fresh waters in order to fully understand the risk to public health.
Abstract.
Amos GCA, Hawkey PM, Gaze WH, Wellington EM (2014). Waste water effluent contributes to the dissemination of CTX-M-15 in the natural environment.
J Antimicrob Chemother,
69(7), 1785-1791.
Abstract:
Waste water effluent contributes to the dissemination of CTX-M-15 in the natural environment.
OBJECTIVES: Multidrug-resistant Enterobacteriaceae pose a significant threat to public health. We aimed to study the impact of sewage treatment effluent on antibiotic resistance reservoirs in a river. METHODS: River sediment samples were taken from downstream and upstream of a waste water treatment plant (WWTP) in 2009 and 2011. Third-generation cephalosporin (3GC)-resistant Enterobacteriaceae were enumerated. PCR-based techniques were used to elucidate mechanisms of resistance, with a new two-step PCR-based assay developed to investigate bla(CTX-M-15) mobilization. Conjugation experiments and incompatibility replicon typing were used to investigate plasmid ecology. RESULTS: We report the first examples of bla(CTX-M-15) in UK river sediment; the prevalence of bla(CTX-M-15) was dramatically increased downstream of the WWTP. Ten novel genetic contexts for this gene were identified, carried in pathogens such as Escherichia coli ST131 as well as indigenous aquatic bacteria such as Aeromonas media. The bla(CTX-M-15) -gene was readily transferable to other Gram-negative bacteria. We also report the first finding of an imipenem-resistant E. coli in a UK river. CONCLUSIONS: the high diversity and host range of novel genetic contexts proves that evolution of novel combinations of resistance genes is occurring at high frequency and has to date been significantly underestimated. We have identified a worrying reservoir of highly resistant enteric bacteria in the environment that poses a threat to human and animal health.
Abstract.
Author URL.
Ashbolt NJ, Amézquita A, Backhaus T, Borriello P, Brandt KK, Collignon P, Coors A, Finley R, Gaze WH, Heberer T, et al (2013). Human Health Risk Assessment (HHRA) for environmental development and transfer of antibiotic resistance.
Environ Health Perspect,
121(9), 993-1001.
Abstract:
Human Health Risk Assessment (HHRA) for environmental development and transfer of antibiotic resistance.
BACKGROUND: Only recently has the environment been clearly implicated in the risk of antibiotic resistance to clinical outcome, but to date there have been few documented approaches to formally assess these risks. OBJECTIVE: We examined possible approaches and sought to identify research needs to enable human health risk assessments (HHRA) that focus on the role of the environment in the failure of antibiotic treatment caused by antibiotic-resistant pathogens. METHODS: the authors participated in a workshop held 4-8 March 2012 in Québec, Canada, to define the scope and objectives of an environmental assessment of antibiotic-resistance risks to human health. We focused on key elements of environmental-resistance-development "hot spots," exposure assessment (unrelated to food), and dose response to characterize risks that may improve antibiotic-resistance management options. DISCUSSION: Various novel aspects to traditional risk assessments were identified to enable an assessment of environmental antibiotic resistance. These include a) accounting for an added selective pressure on the environmental resistome that, over time, allows for development of antibiotic-resistant bacteria (ARB); b) identifying and describing rates of horizontal gene transfer (HGT) in the relevant environmental "hot spot" compartments; and c) modifying traditional dose-response approaches to address doses of ARB for various health outcomes and pathways. CONCLUSIONS: We propose that environmental aspects of antibiotic-resistance development be included in the processes of any HHRA addressing ARB. Because of limited available data, a multicriteria decision analysis approach would be a useful way to undertake an HHRA of environmental antibiotic resistance that informs risk managers.
Abstract.
Author URL.
Gaze WH, Krone SM, Larsson DGJ, Li X-Z, Robinson JA, Simonet P, Smalla K, Timinouni M, Topp E, Wellington EM, et al (2013). Influence of humans on evolution and mobilization of environmental antibiotic resistome.
Emerg Infect Dis,
19(7).
Abstract:
Influence of humans on evolution and mobilization of environmental antibiotic resistome.
The clinical failure of antimicrobial drugs that were previously effective in controlling infectious disease is a tragedy of increasing magnitude that gravely affects human health. This resistance by pathogens is often the endpoint of an evolutionary process that began billions of years ago in non-disease-causing microorganisms. This environmental resistome, its mobilization, and the conditions that facilitate its entry into human pathogens are at the heart of the current public health crisis in antibiotic resistance. Understanding the origins, evolution, and mechanisms of transfer of resistance elements is vital to our ability to adequately address this public health issue.
Abstract.
Author URL.
Wellington EMH, Boxall AB, Cross P, Feil EJ, Gaze WH, Hawkey PM, Johnson-Rollings AS, Jones DL, Lee NM, Otten W, et al (2013). The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria.
Lancet Infect Dis,
13(2), 155-165.
Abstract:
The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria.
During the past 10 years, multidrug-resistant Gram-negative Enterobacteriaceae have become a substantial challenge to infection control. It has been suggested by clinicians that the effectiveness of antibiotics is in such rapid decline that, depending on the pathogen concerned, their future utility can be measured in decades or even years. Unless the rise in antibiotic resistance can be reversed, we can expect to see a substantial rise in incurable infection and fatality in both developed and developing regions. Antibiotic resistance develops through complex interactions, with resistance arising by de-novo mutation under clinical antibiotic selection or frequently by acquisition of mobile genes that have evolved over time in bacteria in the environment. The reservoir of resistance genes in the environment is due to a mix of naturally occurring resistance and those present in animal and human waste and the selective effects of pollutants, which can co-select for mobile genetic elements carrying multiple resistant genes. Less attention has been given to how anthropogenic activity might be causing evolution of antibiotic resistance in the environment. Although the economics of the pharmaceutical industry continue to restrict investment in novel biomedical responses, action must be taken to avoid the conjunction of factors that promote evolution and spread of antibiotic resistance.
Abstract.
Author URL.
Finley RL, Collignon P, Larsson DGJ, McEwen SA, Li X-Z, Gaze WH, Reid-Smith R, Timinouni M, Graham DW, Topp E, et al (2013). The scourge of antibiotic resistance: the important role of the environment.
Clin Infect Dis,
57(5), 704-710.
Abstract:
The scourge of antibiotic resistance: the important role of the environment.
Antibiotic resistance and associated genes are ubiquitous and ancient, with most genes that encode resistance in human pathogens having originated in bacteria from the natural environment (eg, β-lactamases and fluoroquinolones resistance genes, such as qnr). The rapid evolution and spread of "new" antibiotic resistance genes has been enhanced by modern human activity and its influence on the environmental resistome. This highlights the importance of including the role of the environmental vectors, such as bacterial genetic diversity within soil and water, in resistance risk management. We need to take more steps to decrease the spread of resistance genes in environmental bacteria into human pathogens, to decrease the spread of resistant bacteria to people and animals via foodstuffs, wastes and water, and to minimize the levels of antibiotics and antibiotic-resistant bacteria introduced into the environment. Reducing this risk must include improved management of waste containing antibiotic residues and antibiotic-resistant microorganisms.
Abstract.
Author URL.
Iqbal M, Mast Y, Amin R, Hodgson DA, Wohlleben W, Burroughs NJ (2012). Extracting regulator activity profiles by integration of <i>de novo</i> motifs and expression data: characterizing key regulators of nutrient depletion responses in <i>Streptomyces coelicolor</i>.
NUCLEIC ACIDS RESEARCH,
40(12), 5227-5239.
Author URL.
Thomas L, Hodgson DA, Wentzel A, Nieselt K, Ellingsen TE, Moore J, Morrissey ER, Legaie R, Wohlleben W, Rodriguez-Garcia A, et al (2012). Metabolic Switches and Adaptations Deduced from the Proteomes of <i>Streptomyces coelicolor</i> Wild Type and <i>phoP</i> Mutant Grown in Batch Culture.
MOLECULAR & CELLULAR PROTEOMICS,
11(2).
Author URL.
Battke F, Herbig A, Wentzel A, Jakobsen OM, Bonin M, Hodgson DA, Wohlleben W, Ellingsen TE, Nieselt K (2011). A Technical Platform for Generating Reproducible Expression Data from <i>Streptomyces</i> <i>coelicolor</i> Batch Cultivations.
SOFTWARE TOOLS AND ALGORITHMS FOR BIOLOGICAL SYSTEMS,
696, 3-15.
Author URL.
Travis ER, Gaze WH, Pontiroli A, Sweeney FP, Porter D, Mason S, Keeling MJC, Jones RM, Sawyer J, Aranaz A, et al (2011). An inter-laboratory validation of a real time PCR assay to measure host excretion of bacterial pathogens, particularly of Mycobacterium bovis.
PLoS One,
6(11).
Abstract:
An inter-laboratory validation of a real time PCR assay to measure host excretion of bacterial pathogens, particularly of Mycobacterium bovis.
Advances in the diagnosis of Mycobacterium bovis infection in wildlife hosts may benefit the development of sustainable approaches to the management of bovine tuberculosis in cattle. In the present study, three laboratories from two different countries participated in a validation trial to evaluate the reliability and reproducibility of a real time PCR assay in the detection and quantification of M. bovis from environmental samples. The sample panels consisted of negative badger faeces spiked with a dilution series of M. bovis BCG Pasteur and of field samples of faeces from badgers of unknown infection status taken from badger latrines in areas with high and low incidence of bovine TB (bTB) in cattle. Samples were tested with a previously optimised methodology. The experimental design involved rigorous testing which highlighted a number of potential pitfalls in the analysis of environmental samples using real time PCR. Despite minor variation between operators and laboratories, the validation study demonstrated good concordance between the three laboratories: on the spiked panels, the test showed high levels of agreement in terms of positive/negative detection, with high specificity (100%) and high sensitivity (97%) at levels of 10(5) cells g(-1) and above. Quantitative analysis of the data revealed low variability in recovery of BCG cells between laboratories and operators. On the field samples, the test showed high reproducibility both in terms of positive/negative detection and in the number of cells detected, despite low numbers of samples identified as positive by any laboratory. Use of a parallel PCR inhibition control assay revealed negligible PCR-interfering chemicals co-extracted with the DNA. This is the first example of a multi-laboratory validation of a real time PCR assay for the detection of mycobacteria in environmental samples. Field studies are now required to determine how best to apply the assay for population-level bTB surveillance in wildlife.
Abstract.
Author URL.
Laskaris P, Gaze WH, Wellington EMH (2011). Environmental Reservoirs of Resistance Genes in Antibiotic-Producing Bacteria and Their Possible Impact on the Evolution of Antibiotic Resistance. , 73-91.
Gaze WH, Zhang L, Abdouslam NA, Hawkey PM, Calvo-Bado L, Royle J, Brown H, Davis S, Kay P, Boxall ABA, et al (2011). Impacts of anthropogenic activity on the ecology of class 1 integrons and integron-associated genes in the environment.
ISME J,
5(8), 1253-1261.
Abstract:
Impacts of anthropogenic activity on the ecology of class 1 integrons and integron-associated genes in the environment.
The impact of human activity on the selection for antibiotic resistance in the environment is largely unknown, although considerable amounts of antibiotics are introduced through domestic wastewater and farm animal waste. Selection for resistance may occur by exposure to antibiotic residues or by co-selection for mobile genetic elements (MGEs) which carry genes of varying activity. Class 1 integrons are genetic elements that carry antibiotic and quaternary ammonium compound (QAC) resistance genes that confer resistance to detergents and biocides. This study aimed to investigate the prevalence and diversity of class 1 integron and integron-associated QAC resistance genes in bacteria associated with industrial waste, sewage sludge and pig slurry. We show that prevalence of class 1 integrons is higher in bacteria exposed to detergents and/or antibiotic residues, specifically in sewage sludge and pig slurry compared with agricultural soils to which these waste products are amended. We also show that QAC resistance genes are more prevalent in the presence of detergents. Studies of class 1 integron prevalence in sewage sludge amended soil showed measurable differences compared with controls. Insertion sequence elements were discovered in integrons from QAC contaminated sediment, acting as powerful promoters likely to upregulate cassette gene expression. On the basis of this data, >1 × 10(19) bacteria carrying class 1 integrons enter the United Kingdom environment by disposal of sewage sludge each year.
Abstract.
Author URL.
Byrne-Bailey KG, Gaze WH, Zhang L, Kay P, Boxall A, Hawkey PM, Wellington EMH (2011). Integron prevalence and diversity in manured soil.
Appl Environ Microbiol,
77(2), 684-687.
Abstract:
Integron prevalence and diversity in manured soil.
The levels of integron abundance and diversity in soil amended with pig slurry were studied. Real-time PCR illustrated a significant increase in class 1 integron prevalence after slurry application, with increased prevalence still evident at 10 months after application. Culture-dependent data revealed 10 genera, including putative human pathogens, carrying class 1 and 2 integrons.
Abstract.
Author URL.
Anukool U, O'Neill CE, Butr-Indr B, Hawkey PM, Gaze WH, Wellington EMH (2011). Meticillin-resistant Staphylococcus aureus in pigs from Thailand.
Int J Antimicrob Agents,
38(1), 86-87.
Author URL.
Gaze WH, Morgan G, Zhang L, Wellington EMH (2011). Mimivirus-like particles in acanthamoebae from Sewage Sludge.
Emerg Infect Dis,
17(6), 1127-1129.
Author URL.
Calvo-Bado LA, Oakley BB, Dowd SE, Green LE, Medley GF, Ul-Hassan A, Bateman V, Gaze W, Witcomb L, Grogono-Thomas R, et al (2011). Ovine pedomics: the first study of the ovine foot 16S rRNA-based microbiome.
ISME J,
5(9), 1426-1437.
Abstract:
Ovine pedomics: the first study of the ovine foot 16S rRNA-based microbiome.
We report the first study of the bacterial microbiome of ovine interdigital skin based on 16S rRNA by pyrosequencing and conventional cloning with Sanger-sequencing. Three flocks were selected, one a flock with no signs of footrot or interdigital dermatitis, a second flock with interdigital dermatitis alone and a third flock with both interdigital dermatitis and footrot. The sheep were classified as having either healthy interdigital skin (H) and interdigital dermatitis (ID) or virulent footrot (VFR). The ovine interdigital skin bacterial community varied significantly by flock and clinical condition. The diversity and richness of operational taxonomic units was greater in tissue from sheep with ID than H or VFR-affected sheep. Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria were the most abundant phyla comprising 25 genera. Peptostreptococcus, Corynebacterium and Staphylococcus were associated with H, ID and VFR, respectively. Sequences of Dichelobacter nodosus, the causal agent of ovine footrot, were not amplified because of mismatches in the 16S rRNA universal forward primer (27F). A specific real-time PCR assay was used to demonstrate the presence of D. nodosus, which was detected in all samples including the flock with no signs of ID or VFR. Sheep with ID had significantly higher numbers of D. nodosus (10(4)-10(9) cells per g tissue) than those with H or VFR feet.
Abstract.
Author URL.
Pontiroli A, Travis ER, Sweeney FP, Porter D, Gaze WH, Mason S, Hibberd V, Holden J, Courtenay O, Wellington EMH, et al (2011). Pathogen quantitation in complex matrices: a multi-operator comparison of DNA extraction methods with a novel assessment of PCR inhibition.
PLoS One,
6(3).
Abstract:
Pathogen quantitation in complex matrices: a multi-operator comparison of DNA extraction methods with a novel assessment of PCR inhibition.
BACKGROUND: Mycobacterium bovis is the aetiological agent of bovine tuberculosis (bTB), an important recrudescent zoonosis, significantly increasing in British herds in recent years. Wildlife reservoirs have been identified for this disease but the mode of transmission to cattle remains unclear. There is evidence that viable M. bovis cells can survive in soil and faeces for over a year. METHODOLOGY/PRINCIPAL FINDINGS: We report a multi-operator blinded trial for a rigorous comparison of five DNA extraction methods from a variety of soil and faecal samples to assess recovery of M. bovis via real-time PCR detection. The methods included four commercial kits: the QIAamp Stool Mini kit with a pre-treatment step, the FastDNA® Spin kit, the UltraClean™ and PowerSoil™ soil kits and a published manual method based on phenol:chloroform purification, termed Griffiths. M. bovis BCG Pasteur spiked samples were extracted by four operators and evaluated using a specific real-time PCR assay. A novel inhibition control assay was used alongside spectrophotometric ratios to monitor the level of inhibitory compounds affecting PCR, DNA yield, and purity. There were statistically significant differences in M. bovis detection between methods of extraction and types of environmental samples; no significant differences were observed between operators. Processing times and costs were also evaluated. To improve M. bovis detection further, the two best performing methods, FastDNA® Spin kit and Griffiths, were optimised and the ABI TaqMan environmental PCR Master mix was adopted, leading to improved sensitivities. CONCLUSIONS: M. bovis was successfully detected in all environmental samples; DNA extraction using FastDNA® Spin kit was the most sensitive method with highest recoveries from all soil types tested. For troublesome faecal samples, we have used and recommend an improved assay based on a reduced volume, resulting in detection limits of 4.25×10(5) cells g(-1) using Griffiths and 4.25×10(6) cells g(-1) using FastDNA® Spin kit.
Abstract.
Author URL.
Tsibidis GD, Burroughs NJ, Gaze W, Wellington EMH (2011). Semi-automated Acanthamoeba polyphaga detection and computation of Salmonella typhimurium concentration in spatio-temporal images.
Micron,
42(8), 911-920.
Abstract:
Semi-automated Acanthamoeba polyphaga detection and computation of Salmonella typhimurium concentration in spatio-temporal images.
Interaction between bacteria and protozoa is an increasing area of interest, however there are a few systems that allow extensive observation of the interactions. A semi-automated approach is proposed to analyse a large amount of experimental data and avoid a time demanding manual object classification. We examined a surface system consisting of non nutrient agar with a uniform bacterial lawn that extended over the agar surface, and a spatially localised central population of amoebae. Location and identification of protozoa and quantification of bacteria population are performed by the employment of image analysis techniques in a series of spatial images. The quantitative tools are based on intensity thresholding, or on probabilistic models. To accelerate organism identification, correct classification errors and attain quantitative details of all objects a custom written Graphical User Interfaces has also been developed.
Abstract.
Author URL.
Alam MT, Merlo ME, Hodgson DA, Wellington EMH, Takano E, Breitling R (2010). Metabolic modeling and analysis of the metabolic switch in <i>Streptomyces coelicolor</i>.
BMC GENOMICS,
11 Author URL.
Nieselt K, Battke F, Herbig A, Bruheim P, Wentzel A, Jakobsen ØM, Sletta H, Alam MT, Merlo ME, Moore J, et al (2010). The dynamic architecture of the metabolic switch in Streptomyces coelicolor.
BMC Genomics,
11Abstract:
The dynamic architecture of the metabolic switch in Streptomyces coelicolor.
BACKGROUND: During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene expression patterns during this switch, using a specifically designed Affymetrix genechip and a high-resolution time-series of fermenter-grown samples. RESULTS: Surprisingly, we find that the metabolic switch actually consists of multiple finely orchestrated switching events. Strongly coherent clusters of genes show drastic changes in gene expression already many hours before the classically defined transition phase where the switch from primary to secondary metabolism was expected. The main switch in gene expression takes only 2 hours, and changes in antibiotic biosynthesis genes are delayed relative to the metabolic rearrangements. Furthermore, global variation in morphogenesis genes indicates an involvement of cell differentiation pathways in the decision phase leading up to the commitment to antibiotic biosynthesis. CONCLUSIONS: Our study provides the first detailed insights into the complex sequence of early regulatory events during and preceding the major metabolic switch in S. coelicolor, which will form the starting point for future attempts at engineering antibiotic production in a biotechnological setting.
Abstract.
Author URL.
Byrne-Bailey KG, Gaze WH, Kay P, Boxall ABA, Hawkey PM, Wellington EMH (2009). Prevalence of sulfonamide resistance genes in bacterial isolates from manured agricultural soils and pig slurry in the United Kingdom.
Antimicrob Agents Chemother,
53(2), 696-702.
Abstract:
Prevalence of sulfonamide resistance genes in bacterial isolates from manured agricultural soils and pig slurry in the United Kingdom.
The prevalences of three sulfonamide resistance genes, sul1, sul2, and sul3 and sulfachloropyridazine (SCP) resistance were determined in bacteria isolated from manured agricultural clay soils and slurry samples in the United Kingdom over a 2-year period. Slurry from tylosin-fed pigs amended with SCP and oxytetracycline was used for manuring. Isolates positive for sul genes were further screened for the presence of class 1 and 2 integrons. Phenotypic resistance to SCP was significantly higher in isolates from pig slurry and postapplication soil than in those from preapplication soil. of 531 isolates, 23% carried sul1, 18% sul2, and 9% sul3 only. Two percent of isolates contained all three sul genes. Class 1 and class 2 integrons were identified in 5% and 11.7%, respectively, of sul-positive isolates. In previous reports, sul1 was linked to class 1 integrons, but in this study only 8% of sul1-positive isolates carried the intI1 gene. Sulfonamide-resistant pathogens, including Shigella flexneri, Aerococcus spp. and Acinetobacter baumannii, were identified in slurry-amended soil and soil leachate, suggesting a potential environmental reservoir. Sulfonamide resistance in Psychrobacter, Enterococcus, and Bacillus spp. is reported for the first time, and this study also provides the first description of the genotypes sul1, sul2, and sul3 outside the Enterobacteriaceae and in the soil environment.
Abstract.
Author URL.
Gaze W, O'Neill C, Wellington E, Hawkey P (2008). Antibiotic resistance in the environment, with particular reference to MRSA.
Adv Appl Microbiol,
63, 249-280.
Author URL.
Gaze W (2008). Is pollution driving antibiotic resistance?.
Planet Earth(WINTER), 14-15.
Abstract:
Is pollution driving antibiotic resistance?
The current problem with the bacterias being resistant to antibiotics is being blamed by the media over prescription of antibiotics and poor hygiene standards. However, they may not be the sole reason. One explanation is that since bacteria are primitive asexual organisms that reproduce by simple division, they instead exchange genetic material on a huge scale. This transfer can be assisted by viruses or by passing bacteria latching on to strands of naked DNA lying around in soil or water. This gene transfer is capable of driving the spread of resistance genes when bacteria are faced with antibiotics, disinfectants or other pollutants in waste. On the one hand, loose antibiotics and other chemicals could drive antibiotic resistance that enter rivers and soils.
Abstract.
Burroughs NJ, Tsibidis GD, Gaze W, Wellington L (2008). Study of Spatial Biological Systems Using a Graphical User Interface.
Proceedings of the Tenth International Conference on. Human-Computer Interaction 2003, pp. 48-52Abstract:
Study of Spatial Biological Systems Using a Graphical User Interface
In this paper, we describe a Graphical User Interface (GUI) designed to
manage large quantities of image data of a biological system. After setting the
design requirements for the system, we developed an ecology quantification GUI
that assists biologists in analysing data. We focus on the main features of the
interface and we present the results and an evaluation of the system. Finally,
we provide some directions for some future work.
Abstract.
Author URL.
Sweeney FP, Courtenay O, Hibberd V, Hewinson RG, Reilly LA, Gaze WH, Wellington EMH (2007). Environmental monitoring of Mycobacterium bovis in badger feces and badger sett soil by real-time PCR, as confirmed by immunofluorescence, immunocapture, and cultivation.
Appl Environ Microbiol,
73(22), 7471-7473.
Abstract:
Environmental monitoring of Mycobacterium bovis in badger feces and badger sett soil by real-time PCR, as confirmed by immunofluorescence, immunocapture, and cultivation.
Real-time PCR was used to detect and quantify Mycobacterium bovis cells in naturally infected soil and badger feces. Immunomagnetic capture, immunofluorescence, and selective culture confirmed species identification and cell viability. These techniques will prove useful for monitoring M. bovis in the environment and for elucidating transmission routes between wildlife and cattle.
Abstract.
Author URL.
Gaze WH, Abdouslam N, Hawkey PM, Wellington EMH (2005). Incidence of class 1 integrons in a quaternary ammonium compound-polluted environment.
Antimicrob Agents Chemother,
49(5), 1802-1807.
Abstract:
Incidence of class 1 integrons in a quaternary ammonium compound-polluted environment.
Samples of effluent and soil were collected from a reed bed system used to remediate liquid waste from a wool finishing mill with a high use of quaternary ammonium compounds (QACs) and were compared with samples of agricultural soils. Resistance quotients of aerobic gram-negative and gram-positive bacteria to ditallowdimethylammomium chloride (DTDMAC) and cetyltrimethylammonium bromide (CTAB) were established by plating onto nutrient agar containing 5 microg/ml or 50 microg/ml DTDMAC or CTAB. Approximately 500 isolates were obtained and screened for the presence of the intI1 (class 1 integrase), qacE (multidrug efflux), and qacE Delta1 (attenuated qacE) genes. QAC resistance was higher in isolates from reed bed samples, and class 1 integron incidence was significantly higher for populations that were preexposed to QACs. This is the first study to demonstrate that QAC selection in the natural environment has the potential to coselect for antibiotic resistance, as class 1 integrons are well-established vectors for cassette genes encoding antibiotic resistance.
Abstract.
Author URL.
Anukool U, Gaze WH, Wellington EMH (2004). In situ monitoring of streptothricin production by Streptomyces rochei F20 in soil and rhizosphere.
Appl Environ Microbiol,
70(9), 5222-5228.
Abstract:
In situ monitoring of streptothricin production by Streptomyces rochei F20 in soil and rhizosphere.
The onset of streptothricin (ST) biosynthesis in Streptomyces rochei F20 was studied by using reverse transcription-PCR (RT-PCR) to detect transcripts of ST genes during growth in liquid medium, soil, and the rhizosphere. In situ results correlated with those obtained in vitro, illustrating the growth phase-dependent manner of ST production by F20. Maximal transcription of ST resistance (sttR) and biosynthesis (sttA) genes occurred during the transition between the exponential and stationary phases of growth, when the specific growth rate (micro) started to decline. A higher level of gene expression of sttR versus sttA was observed in all experiments. In liquid culture, maximal transcript accumulation of the sttA gene was only ca. 40% that of the sttR gene. sttA and sttR mRNAs were detected in soil containing approximately 10(6) CFU of growing cells g of soil(-1). sttR mRNA was detected in sterile and nonsterile rhizosphere colonized with growing mycelium of F20 at 1.2 x 10(6) and 4.0 x 10(5) CFU g of soil(-1), respectively. However, neither sttR nor sttA transcripts were detected by RT-PCR in the rhizoplane, which supported a lower population density of F20 than the rhizosphere.
Abstract.
Author URL.
Gaze WH, Burroughs N, Gallagher MP, Wellington EMH (2003). Interactions between Salmonella typhimurium and Acanthamoeba polyphaga, and observation of a new mode of intracellular growth within contractile vacuoles.
Microb Ecol,
46(3), 358-369.
Abstract:
Interactions between Salmonella typhimurium and Acanthamoeba polyphaga, and observation of a new mode of intracellular growth within contractile vacuoles.
Acanthamoeba polyphaga feeding on Salmonella typhimurium in a simple model biofilm were observed by light microscopy and a detailed record of interactions kept by digital image capture and image analysis. A strain of S. typhimurium SL1344 carrying a fis: gfp reporter construct (pPDT105) was used to assess intracellular growth in A. polyphaga on non-nutrient agar (NNA) plates. Invasion of the contractile vacuole (CV) was observed at a frequency of 1:100-1000 acanthamoebae at 35 degrees C. The salmonellae contained in CVs illustrated significant up-regulation of fis relative to extracellular bacteria, indicating that they were in the early stages of logarithmic growth, and reached numbers of 100-200 cells per vacuole after 4 days. This is the first report of this mode of intracellular growth. Up-regulation of fis was also observed in a proportion of S. typhimurium cells contained within food vacuoles. Filamentation of S. typhimurium and E. coli cells was frequently observed in coculture with A. polyphaga on NNA plates, with bacterial cells reaching lengths of up to 500 microm after 10 days' incubation at 35 degrees C. A. polyphaga was also seen to mediate bacterial translocation over the agar surface; egested salmonellae subsequently formed microcolonies along amoebal tracks. This illustrated intracellular survival of a fraction of the S. typhimurium population. These phenomena suggest that protozoa such as A. polyhaga may play an important role in the ecology of S. typhimurium in soil and aquatic environments.
Abstract.
Author URL.
Hutchens E, Valsami-Jones E, McEldowney S, Gaze W, McLean J (2003). The role of heterotrophic bacteria in feldspar dissolution - an experimental approach.
Mineralogical Magazine,
67(6), 1157-1170.
Abstract:
The role of heterotrophic bacteria in feldspar dissolution - an experimental approach
This paper presents the results of a laboratory study on the influence of heterotrophic bacteria on dissolution of a silicate mineral (K-feldspar) under a variety of growth conditions. Twenty seven strains of heterotrophic bacteria were isolated from a feldspar-rich soil (Shap, NW England). Liquid and solid minimal aerobic media (C/N-sufficient, K-limited, Fe-limited, N-limited and glucose/NH4Cl only) at 26°C were used for isolation of the bacteria. The media selected bacterial isolates that were fast-growing aerobic heterotrophs able to use glucose as the sole source of carbon and energy. The extent of mineral dissolution (in the presence of the isolates) was assessed after 48 h of incubation by measuring the release of Al from the K-feldspar by ICP-AES. More detailed dissolution experiments were carried out with one of the strains, Serratia macescens, an isolate that was very effective in enhancing feldspar dissolution. The main conclusions of this study are: (1) the degree of enhancement of K-feldspar dissolution varied with bacterial isolate and growth conditions; (2) enhancement of dissolution began during stationary phase growth; (3) the production of chelating compounds (exopolymers, siderophores, pigments) during the stationary phase might be a possible mechanism for bacterially enhanced K-feldspar dissolution; (4) the frequent sub-culturing of isolates can have a significant effect on their physiological characteristics and may possibly influence their capacity to enhance mineral dissolution. © 2003 the Mineralogical Society.
Abstract.
Gaze WH, Wootten R (1999). An SEM study of adhesive disc skeletal structures isolated from trichodinids (Ciliophora: Peritrichida) of the genera Trichodina Ehrenberg, 1838 and Paratrichodina Lom, 1963.
Syst Parasitol,
43(3), 167-174.
Abstract:
An SEM study of adhesive disc skeletal structures isolated from trichodinids (Ciliophora: Peritrichida) of the genera Trichodina Ehrenberg, 1838 and Paratrichodina Lom, 1963.
Specimens of Trichodina domerguei Wallengren, 1897, T. intermedia (Lom, 1961) and Paratrichodina incissa (Lom, 1959) were sonicated to liberate skeletal components of the adhesive disc. This enabled SEM observation of the taxonomically important structures obscured in preparations of complete cells. A previously undescribed peg-like structure on the centrifugal surface of the central part of the denticles is revealed in T. domerguei. In P. incissa the ray apophysis and its supporting apophysis appear to be absent, providing an additional characteristic to discriminate it from species of the genus Trichondina Ehrenberg, 1838. From silver stained and SEM preparations of T. intermedia and P. incissa important differences in denticle blade form are apparent, underlining the value of observation of isolated skeletal structures by electron microscopy.
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Gaze WH, Wootten R (1998). Ectoparasitic species of the genus Trichodina (Ciliophora: Peritrichida) parasitising British freshwater fish.
Folia Parasitol (Praha),
45(3), 177-190.
Abstract:
Ectoparasitic species of the genus Trichodina (Ciliophora: Peritrichida) parasitising British freshwater fish.
Seven species of the genus Trichodina Ehrenberg, 1838 were identified during a sampling programme of twenty freshwater fish species from approximately sixty sites in Scotland, England and Wales. Species found include: Trichodina acuta Lom, 1961 from Cyprinus carpio L. Carassius auratus L. Oncorhynchus mykiss (Walbaum), Salmo trutta L. and Phoxinus phoxinus L.; Trichodina domerguei Wallengren, 1897 from Gasterosteus aculeatus L.; Trichodina tenuidens Faure-Fremiet, 1944 from Gasterosteus aculeatus; Trichodina pediculus Ehrenberg, 1838 from Gasterosteus aculeatus; Trichodina modesta Lom, 1970 from Abramis brama L.; Trichodina nigra Lom, 1960 from Cyprinus carpio, Salmo trutta and Oncorhynchus mykiss; and Trichodina intermedia Lom, 1960 from Phoxinus. Morphological variation within and between host populations and host specificity of the Trichodina species recovered are described.
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