Carbapenem resistance in bacteria isolated from soil and water environments in Algeria.

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordOBJECTIVES: Recent research has demonstrated that natural populations of bacteria carry large numbers of mobile genetic elements which may harbour antibiotic resistance determinants. The aim of this study was to investigate carbapenem resistance in Gram negative bacteria isolated from natural environments in Bejaia (Algeria), and determine the horizontal gene transfer potential of a subset of these resistance genes. METHODS: Resistant bacteria were isolated and host identified with MALDI-TOF/16S rRNA sequencing. Resistance gene carriage was investigated using double disc synergy, metallo-β-lactamase (MBL) production tests and PCR screening for carbapenemase resistance genes. To determine potential mobility, conjugation experiments were performed. To identify resistance genes, genomic libraries were constructed, functionally screened; then inserts were sequenced. RESULTS: From soil and water samples, 62 resistant strains were classified as belonging to the Enterobacteriaceae, Pseudomonadaceae, Xanthomonadaceae and Aeromonadaceae families. Four highly imipenem and cefotaxime resistant (MICs >64μg/ml and >8μg/ml, respectively), clinically relevant strains were selected for further characterization. All four strains produced extended spectrum β-lactamases, but MBL production was not confirmed. Imipenem and cefotaxime resistance was transferable to E. coli strains 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 which conferred clinical resistance to cefotaxime. CONCLUSIONS: The environment is a reservoir of carbapenem resistant bacteria. Further investigation of evolution and dissemination of antibiotic resistance in environmental bacteria is required, to understand and prevent the emergence of resistance in clinical environment

A coliform-targeted metagenomic method facilitating human exposure estimates to Escherichia coli-borne antibiotic resistance genes.

This is the author accepted manuscript. The final version is available from Oxford University Press via the DOI in this record.Background: 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. Aim: 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. Approach: 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. Findings: 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.This work was supported by the University of Exeter and the Chinese University of Hong Kong

CRISPR-Cas antimicrobials: Challenges and future prospects

This is the final version. Available from PLoS via the DOI in this record.Antimicrobial resistance (AMR) poses a serious threat to modern medicine and may render common infections untreatable. The discovery of new antibiotics has come to a relative standstill during the last decade [1], and developing novel approaches to tackle the spread of AMR genes will require significant efforts in the coming years [2]. In 2014, several groups independently demonstrated how CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR–associated), a bacterial immune system now widely used for genome editing, can selectively remove AMR genes from bacterial populations. Here, we discuss the current state of the field of CRISPR-Cas antimicrobials, the challenges ahead, and how they may be overcome.Biotechnology & Biological Sciences Research Council (BBSRC)Medical Research CouncilNatural Environment Research CouncilWellcome TrustEuropean Research CouncilPeople Programme (Marie Curie Actions) of the European Union’s Horizon 202

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

This is the final version of the article. Available from the publisher via the DOI in this record.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.MRG is supported by the Australian Research Council, AP is supported by the Alfred P Sloan Foundation Microbiology of the Built Environment program and the National Science Foundation RAPID award no. 1402651, KS is supported by the Deutsche Forschungsgemeinschaft (DFG) funding the Research Unit FOR 566 ‘Veterinary Medicines in Soil: Basic Research for Risk Analysis’ (Grant No. SM59/5-3) and by the Umweltbundesamt (3713 63 402), JMT is supported by the US National Science Foundation and Y-GZ is supported by the National Science Foundation of China

Dawning of a new ERA: Environmental Risk Assessment of antibiotics and their potential to select for antimicrobial resistance

This is the final version. Available on open access from Elsevier via the DOI in this recordAntibiotics 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

Natural recreational waters and the risk that exposure to antibiotic resistant bacteria poses to human health

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordAntimicrobial 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.Natural Environment Research CouncilMedical Research CouncilNatural Environment Research CouncilNatural Environment Research CouncilEnvironmental Protection Agenc

Why don't the British eat locally harvested shellfish? The role of misconceptions and knowledge gaps

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record 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.European Regional Development Fund ProgrammeEuropean Social Fund Convergence Programme for Cornwall and the Isles of Scill

Functional metagenomic libraries generated from anthropogenically impacted environments reveal importance of metabolic genes in biocide and antibiotic resistance (article)

This is the final version. Available from Elsevier via the DOI in this record.The research data supporting this publication are provided within this paper and the supplementary information accompanying this publication. The sequence data are openly available from the University of Exeter's institutional repository Open Research Exeter (ORE) at https://doi.org/10.24378/exe.4524.Anthropogenic activities result in the release of antimicrobial resistant bacteria and a cocktail of antimicrobial compounds into the environment that may directly select or indirectly co-select for antimicrobial resistance (AMR). Many studies use metagenome sequencing or qPCR-based approaches to study the environmental resistome but these methods are limited by a priori knowledge. In this study, a functional metagenomic approach was used to explore biocide resistance mechanisms in two contaminated environments and a pristine site, and to identify whether potentially novel genes conferring biocide resistance also conferred resistance or reduced susceptibility to antibiotics. Resistance was predominately mediated through novel mechanisms exclusive of the well-known qac efflux genes. UDP-galactose 4-epimerase (galE) –like genes were identified in both contaminated environments and were shown to confer cross-resistance to biocides and clinically important antibiotics for the first time (to our knowledge), compared to knockout mutants. GalE -like genes were also co-located with transposons, suggesting mobilisation potential. These results show that housekeeping genes may play a significant yet underappreciated role in AMR in environmental microbiomes.Biotechnology & Biological Sciences Research Council (BBSRC)Natural Environment Research Council (NERC