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One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock.

Published version
Peer-reviewed

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Authors

Ludden, Catherine 
Raven, Kathy E 
Jamrozy, Dorota 
Gouliouris, Theodore 
Blane, Beth 

Abstract

Livestock have been proposed as a reservoir for drug-resistant Escherichia coli that infect humans. We isolated and sequenced 431 E. coli isolates (including 155 extended-spectrum β-lactamase [ESBL]-producing isolates) from cross-sectional surveys of livestock farms and retail meat in the East of England. These were compared with the genomes of 1,517 E. coli bacteria associated with bloodstream infection in the United Kingdom. Phylogenetic core genome comparisons demonstrated that livestock and patient isolates were genetically distinct, suggesting that E. coli causing serious human infection had not directly originated from livestock. In contrast, we observed highly related isolates from the same animal species on different farms. Screening all 1,948 isolates for accessory genes encoding antibiotic resistance revealed 41 different genes present in variable proportions in human and livestock isolates. Overall, we identified a low prevalence of shared antimicrobial resistance genes between livestock and humans based on analysis of mobile genetic elements and long-read sequencing. We conclude that within the confines of our sampling framework, there was limited evidence that antimicrobial-resistant pathogens associated with serious human infection had originated from livestock in our region.IMPORTANCE The increasing prevalence of E. coli bloodstream infections is a serious public health problem. We used genomic epidemiology in a One Health study conducted in the East of England to examine putative sources of E. coli associated with serious human disease. E. coli from 1,517 patients with bloodstream infections were compared with 431 isolates from livestock farms and meat. Livestock-associated and bloodstream isolates were genetically distinct populations based on core genome and accessory genome analyses. Identical antimicrobial resistance genes were found in livestock and human isolates, but there was limited overlap in the mobile elements carrying these genes. Within the limitations of sampling, our findings do not support the idea that E. coli causing invasive disease or their resistance genes are commonly acquired from livestock in our region.

Description

Keywords

ESBL, Escherichia coli, antimicrobial resistance, genomics, livestock, Animals, Computational Biology, Cross-Sectional Studies, Drug Resistance, Bacterial, England, Epidemiological Monitoring, Escherichia coli, Escherichia coli Infections, Genes, Bacterial, Genetic Variation, Genomics, Humans, Interspersed Repetitive Sequences, Livestock, Meat, One Health, Prevalence, Sequence Analysis, DNA, Whole Genome Sequencing

Journal Title

mBio

Conference Name

Journal ISSN

2161-2129
2150-7511

Volume Title

10

Publisher

American Society for Microbiology
Sponsorship
Wellcome Trust (098600/Z/12/Z)
Medical Research Council (G1001787)
Medical Research Council (MR/K021133/1)
Medical Research Council (MR/N002660/1)
Wellcome Trust (103387/Z/13/Z)