Publications by year
Jones ML, Barnish MS, Hughes RR, Murray AK, Mansour O, Loni T, Vickery HM, Evans ML, Green L, Verdezoto N, et al
(2023). Exploring the potential of using simulation games for engaging with sheep farmers about lameness recognition. Front Vet Sci
Exploring the potential of using simulation games for engaging with sheep farmers about lameness recognition.
INTRODUCTION: Computer simulation games are increasingly being used in agriculture as a promising tool to study, support and influence real-life farming practices. We explored the potential of using simulation games to engage with sheep farmers on the ongoing challenge of reducing lameness. Working with UK stakeholders, we developed a game in which players are challenged with identifying all the lame sheep in a simulated flock. Here, we evaluate the game's potential to act as a tool to help assess, train and understand farmers' ability to recognize the early signs of lameness. METHODS: Participants in the UK were invited to play the game in an online study, sharing with us their in-game scores alongside information relating to their real-life farming experience, how they played the game, and feedback on the game. Mixed methods were used to analyze this information in order to evaluate the game. Quantitative analyses consisted of linear modeling to test for statistical relationships between participants' in-game recall (% of the total number of lame sheep that were marked as lame), and the additional information they provided. Qualitative analyses of participants' feedback on the game consisted of thematic analysis and a Likert Scale questionnaire to contextualize the quantitative results and identify additional insights from the study. RESULTS: Quantitative analyses identified no relationships between participants' (n = 63) recall scores and their real life farming experience, or the lameness signs they looked for when playing the game. The only relationship identified was a relationship between participants' recall score and time spent playing the game. Qualitative analyses identified that participants did not find the game sufficiently realistic or engaging, though several enjoyed playing it and saw potential for future development. Qualitative analyses also identified several interesting and less-expected insights about real-life lameness recognition practices that participants shared after playing the game. DISCUSSION: Simulation games have potential as a tool in livestock husbandry education and research, but achieving the desired levels of realism and/or engagingness may be an obstacle to realizing this. Future research should explore this potential further, aided by larger budgets and closer collaboration with farmers, stockpeople, and veterinarians. Abstract
. Author URL
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.
Murray A, Zhang L, Gaze W, Snape J (2023). Functional metagenomic libraries generated from anthropogenically impacted environments reveal importance of metabolic genes in biocide and antibiotic resistance (dataset).
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
Stanton IC, Tipper HJ, Chau K, Klümper U, Subirats J, Murray AK (2022). Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial‐Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes?. Environmental Toxicology and Chemistry
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
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. Abstract
. Author URL
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
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. Abstract
. Author URL
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 Chem
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. Abstract
. Author URL
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
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. 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
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
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).
(2020). Selection for antibiotic resistance in complex microbial communities.
Selection for antibiotic resistance in complex microbial communities
Measureable concentrations of antibiotics are released into the environment from anthropogenic sources. Environmental risk assessment investigates the risks these concentrations pose to aquatic life but does not determine whether selection for resistance is occurring. Recent studies suggest environmental concentrations of tetracycline, ciprofloxacin and cefotaxime may be able to select for resistance in complex microbial communities. Abstract
The aims of research presented in this thesis were to determine whether selection for resistance occurs at environmentally relevant concentrations of macrolide antibiotics; to understand how mixtures of antibiotics affect selective endpoints; to understand the effect of temperature on selective endpoints, and, finally, to compare the methods used with previously published methods.
Selective endpoints of macrolide antibiotics were found to be 1,000 µg/L of azithromycin and erythromycin and 750 µg/L of clarithromycin which is significantly higher than current environmental concentrations.
Mixing of antibiotics produces at least an additive, if not a synergistic, effect. The selective endpoints of sulfamethoxazole and trimethoprim decrease over 11 times and by a half, respectively, when used in combination. The selective endpoint of macrolides is reduced by a third when they are found in combination.
Selective endpoints of individual genes are affected by temperature but, as only preliminary data has been produced, overall effect concentrations have not been determined across the entire experimental resistome. Alternative gene targets associated with taxa favoured at low temperatures may be under selection.
Finally, the phenomenon of increased persistence has been described and the minimal increased persistence concentration has been defined for the first time.
Data presented here can be used by policy makers in environmental risk assessments, in conjunction with other ecotoxicological endpoints to determine safe release levels of antibiotic residues in wastewater. This will help minimise selection for antibiotic resistance in the environment and, therefore, exposure of humans to resistant bacteria through environmental transmission.
Murray AK (2020). The Novel Coronavirus COVID-19 Outbreak: Global Implications for Antimicrobial Resistance. Frontiers in Microbiology, 11
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).
Murray AK, Zhang L, Snape J, Gaze WH
(2019). Comparing the selective and co-selective effects of different antimicrobials in bacterial communities. International Journal of Antimicrobial Agents
Comparing the selective and co-selective effects of different antimicrobials in bacterial communities
Bacterial communities are exposed to a cocktail of antimicrobial agents, including antibiotics, heavy metals and biocidal antimicrobials such as quaternary ammonium compounds (QACs). The extent to which these compounds may select or co-select for antimicrobial resistance (AMR) is not fully understood. In this study, human-associated, wastewater-derived bacterial communities were exposed to either benzalkonium chloride (BAC), ciprofloxacin or trimethoprim at sub-point-of-use concentrations for one week to determine selective and co-selective potential. Metagenome analyses were performed to determine effects on bacterial community structure and prevalence of antibiotic resistance genes (ARGs) and metal or biocide resistance genes (MBRGS). Ciprofloxacin had the greatest co-selective potential, significantly enriching for resistance mechanisms to multiple antibiotic classes. Conversely, BAC exposure significantly reduced relative abundance of ARGs and MBRGS, including the well characterised qac efflux genes. However, BAC exposure significantly impacted bacterial community structure. Therefore BAC, and potentially other QACs, did not play as significant a role in co-selection for AMR as antibiotics such as ciprofloxacin at sub-point-of-use concentrations in this study. This approach can be used to identify priority compounds for further study, to better understand evolution of AMR in bacterial communities exposed to sub-point-of-use concentrations of antimicrobials. Abstract
Zhang L, Calvo-Bado L, Murray AK, Amos GCA, Hawkey PM, Wellington EM, Gaze WH
(2019). Novel clinically relevant antibiotic resistance genes associated with sewage sludge and industrial waste streams revealed by functional metagenomic screening. Environment International
Novel clinically relevant antibiotic resistance genes associated with sewage sludge and industrial waste streams revealed by functional metagenomic screening
A growing body of evidence indicates that anthropogenic activities can result in increased prevalence of antimicrobial resistance genes (ARGs) in bacteria in natural environments. Many environmental studies have used next-generation sequencing methods to sequence the metagenome. However, this approach is limited as it does not identify divergent uncharacterized genes or demonstrate activity. Characterization of ARGs in environmental metagenomes is important for understanding the evolution and dissemination of resistance, as there are several examples of clinically important resistance genes originating in environmental species. The current study employed a functional metagenomic approach to detect genes encoding resistance to extended spectrum β-lactams (ESBLs) and carbapenems in sewage sludge, sludge amended soil, quaternary ammonium compound (QAC) impacted reed bed sediment and less impacted long term curated grassland soil. ESBL and carbapenemase genes were detected in sewage sludge, sludge amended soils and QAC impacted soil with varying degrees of homology to clinically important β-lactamase genes. The flanking regions were sequenced to identify potential host background and genetic context. Novel β-lactamase genes were found in Gram negative bacteria, with one gene adjacent to an insertion sequence ISPme1, suggesting a recent mobilization event and/ the potential for future transfer. Sewage sludge and quaternary ammonium compound (QAC) rich industrial effluent appear to disseminate and/or select for ESBL genes which were not detected in long term curated grassland soils. This work confirms the natural environment as a reservoir of novel and mobilizable resistance genes, which may pose a threat to human and animal health. Abstract
Djenadi K, Zhang L, Murray AK, Gaze WH
(2018). Carbapenem resistance in bacteria isolated from soil and water environments in Algeria. Journal of Global Antimicrobial Resistance
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 > 64 μg/mL) and cefotaxime-resistant (MIC > 8 μg/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
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). Environment International
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
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. mBio
Novel insights into selection for antibiotic resistance in complex microbial communities
Recent research has demonstrated that 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 that the strength of selection for naturally occurring resistance alleles in a complex community remains constant from low subinhibitory to above clinically relevant concentrations. Selection increases with antibiotic concentration before reaching a plateau where selection remains constant over a 2-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 of sewage-derived bacterial communities evolved under cefotaxime exposure show preferential enrichment for bla CTX-M genes 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. IMPORTANCE Antibiotic resistance is one of the greatest global issues facing society. Still, comparatively little is known about selection for resistance at very low antibiotic concentrations. We show that the strength of selection for clinically important resistance genes within a complex bacterial community can remain constant across a large antibiotic concentration range (wide selective space). Therefore, largely understudied ecological compartments could be just as important as clinical environments for selection of antibiotic resistance. Abstract
Murray AK, Lee J, Bendall R, Zhang L, Sunde M, Slettemeås JS, Gaze W, Page AJ, Vos M
(2018). Staphylococcus cornubiensis sp. nov. a member of the staphylococcus intermedius group (SIG). International Journal of Systematic and Evolutionary Microbiology
Staphylococcus cornubiensis sp. nov. a member of the staphylococcus intermedius group (SIG)
We here describe a novel species in the Staphylococcus intermedius Group (SIG) which is phenotypically similar to Staphylococcus pseudintermedius but is genomically distinct from it and other SIG members, with an average nucleotide identity of 90.2% with its closest relative S. intermedius. The description of Staphylococcus cornubiensis sp. nov. is based on strain NW1 T (=NCTC 13950 T =DSM 105366 T ) isolated from a human skin infection in Cornwall, UK. Although pathogenic, NW1 T carries no known virulence genes or mobilizable antibiotic resistance genes and further studies are required to assess the prevalence of this species in humans as well as its potential presence in companion animals. 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. Journal of Clinical Microbiology
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. Abstract