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Characterisation of ESBL/ampC/ carbapenem resistant Escherichia coli from pigs and poultry to identify antimicrobial resistance genes, circulating plasmids and fitness attributes - VM0529

The emergence and spread of antimicrobial resistance (AMR) in bacteria pose a threat to human and animal health, and can have major economic consequences. In order to combat its spread the European Food Safety Authority (EFSA) has been involved in monitoring surveillance of AMR in important zoonotic bacteria from food animals. The most recent EU Decision requires increased annual AMR surveillance using phenotypic methods. Hence APHA has been involved in surveillance for AMR in Enterobacteriaceae isolated from poultry (2014) and pigs (2015). Although this is invaluable data there will be no information gathered on resistance mechanisms present and circulating in bacteria such as ESBL/ampC/carbapenem resistant E. coli that can pose problems in therapy. Therefore in this proposal we propose to perform detailed molecular characterization of E. coli collected through EU surveillance, so we can compare resistances present within animals and humans. For this we will use whole genome sequencing (WGS) to obtain detailed information on every gene present within the bacteria and plasmids, to determine the resistance profile (from AMR genes), the potential to cause disease (from virulence genes), and clonality (from multi-locus sequence typing genes). Whole genome sequencing methodologies proposed will be harmonised with a current WGS project funded through NIHR to University of Oxford (UoOx) and Public Health England (PHE) in which APHA are public sector partners. The results from the proposed project will be compared to profiles obtained from other projects including humans, to determine if the E. coli and/or plasmids have either been transferred along the food chain or circulate in other ways between animals and human.

Dissemination of AMR genes can be through clonal expansion of the host E. coli or horizontal gene transfer (HGT) of mobile elements to different hosts. To gain information on whether the same or different E. coli clones/plasmids may be circulating within these animals and to humans, selected plasmids, representative of conserved plasmids/clones (same or different MLST but same AMR profile), as well those with varied MLST and varied AMR profile, will be explored by plasmid genome sequencing as well as phenotypic characterization of plasmid bearing isolates (e.g. biocide, heavy metal resistance, Galleria melonella infection models). The genetic basis for these “fitness and survival” characteristics will be established, where possible, using the WGS data. Therefore, these experiments may help identify conditions, in addition to antimicrobial usage, that aid in co-selection of ESBL/ampC/carbapenem resistant E. coli and may be associated with their dissemination and possible adaptation in farm animals; it may help suggest modes of control in future. Assessment of virulence characteristics and pathogenesis will determine if these multi-drug resistant isolates are innocuous commensals or harbour virulence genes that are harmless for the healthy host but may contribute to a “disease state” and pose problems during therapy.

The whole genome sequencing pipeline that will be established at APHA in this project can be a standard scheme which is used, maintained and updated as required in future, to perform rapid genotypic characterization of isolates collected from surveillance and other relevant projects.
Objective 1: Whole genome sequencing and analysis of approximately 170 turkey and 170 broiler E.coli isolates collected from EU surveillance 2014.
Objective 2: Whole genome sequencing and analysis of E.coli isolates from pig caeca collected from EU surveillance 2015.
Objective 3: Survival in different stress modulators and pathogenesis of selected isolates.
Objective 4: Papers and final report.
Time-Scale and Cost
From: 2015

To: 2018

Cost: £66,663
Contractor / Funded Organisations
APHA (Animal and Plant Health Agency)
Antimicrobial Resistance