One Health genomic surveillance ofEscherichia colidemonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock

Abstract

Running title: One Health genomic surveillance of Escherichia coli 25 2 ABSTRACT 26 Livestock have been proposed as a reservoir for drug-resistant Escherichia coli that infect 27 humans. We isolated and sequenced 431 E. coli (including 155 ESBL-producing isolates) 28 from cross-sectional surveys of livestock farms and retail meat in the East of England. These 29 were compared with the genomes of 1517 E. coli associated with bloodstream infection in the 30 United Kingdom. Phylogenetic core genome comparisons demonstrated that livestock and 31 patient isolates were genetically distinct, indicating that E. coli causing serious human 32 infection do not directly originate from livestock. By contrast, we observed highly related 33 isolates from the same animal species on different farms. Analysis of accessory (variable) 34 genomes identified a virulence cassette associated previously with cystitis and neonatal 35 meningitis that was only present in isolates from humans. Screening all 1948 isolates for 36 accessory genes encoding antibiotic resistance revealed 41 different genes present in variable 37proportions of humans and livestock isolates. We identified a low prevalence of shared 38 antimicrobial resistance genes between livestock and humans based on analysis of mobile 39 genetic elements and long-read sequencing. We conclude that in this setting, there was 40 limited evidence to support the suggestion that antimicrobial resistant pathogens that cause 41 serious infection in humans originate from livestock. 42 43 44 45 46 47 48 Importance 51The increasing prevalence of E. coli bloodstream infections is a serious public health 52 problem. We used genomic epidemiology in a One Health study conducted in the East of 53England to examine putative sources of E. coli associated with serious human disease. E. 54 coli from 1517 patients with bloodstream infection were compared with 431 isolates from 55 livestock farms and meat. Livestock-associated and bloodstream isolates were genetically 56 distinct populations based on core genome and accessory genome analyses. Identical 57 antimicrobial resistance genes were found in livestock and human isolates, but there was little 58 overlap in the mobile elements carrying these genes. In addition, a virulence cassette found in 59 humans isolates was not identified in any livestock-associated isolate. Our findings do not 60 support the idea that E. coli causing invasive disease or their resistance genes are commonly 61 acquired from livestock. 62 128 Genomic comparison of E. coli from patients with bloodstream infection, livestock, and 129 retail meat. We combined and compared the 1517 human invasive with the 431 livestock-130 associated genomes. Analysis of the 1948 genomes identified 331 multilocus sequence types 131 (STs), 44 clonal complexes (CCs) and 149 singletons (STs that did not share alleles at six out 132 of seven loci with any other STs). Most STs were host-specific, with 192 human-specific STs 133 (1261/1517 isolates, 83%), 98 livestock-specific STs (225/411 isolates, ...

Reduced antibacterial drug resistance and blaCTX-M β-lactamase gene carriage in cattle-associated Escherichia coli at low temperatures, at sites dominated by older animals and on pastureland: implications for surveillance

“…Whilst unpublished, the other plasmid (pTC_N40607) has been identified in E. coli in the USA so is likely to be similarly widespread. Accordingly, whilst there is some evidence of shared circulating plasmids, as reported in a number of recent studies (35–37), the overall level of overlap between farm and human bla CTX-M E. coli identified in this study was very small and not suggestive of any novel or recent transmission events.…”

Molecular epidemiology of Escherichia coli producing CTX-M and plasmid AmpC-type β-lactamases from dairy farms identifies a dominant plasmid encoding CTX-M-32 but no evidence for transmission to humans in the same geographical region

“…13 However, recent reports suggest that such transmission is very limited, at least in the UK. 14 In dairy farming, antibiotics are used both therapeutically in the treatment of common infections such as mastitis, and preventatively e.g. in so-called dry cow therapy, an antibacterial preparation inserted into a cow’s udder between lactations to prevent against mastitis.…”

Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer

“…One-Health studies applying massive-parallel and single-molecule sequencing conform a good approximation to try to understand how antibiotic resistances flow between human-animal-environment scenario. There are different One-Health studies were Illumina 64 and Nanopore 65 or PacBio 66 sequencing are used together to characterize bacteria isolated from different sources and try to unveil if there is relation amongst them. For example, in 2018, Ludden et al 64 performed a study in which concluded that there were similar antibiotic resistances between livestock and human E. coli, conferring resistance to 4 type of antibiotics, but on the other hand there was not a close relation between E. coli isolated from livestock and E. coli causing infection in human.…”