One Health Genomic Surveillance of <named-content content-type="genus-species">Escherichia coli</named-content> Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock

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 E...

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Autores principales:	Catherine Ludden, Kathy E. Raven, Dorota Jamrozy, Theodore Gouliouris, Beth Blane, Francesc Coll, Marcus de Goffau, Plamena Naydenova, Carolyne Horner, Juan Hernandez-Garcia, Paul Wood, Nazreen Hadjirin, Milorad Radakovic, Nicholas M. Brown, Mark Holmes, Julian Parkhill, Sharon J. Peacock
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	ESBL Escherichia coli antimicrobial resistance genomics livestock Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/55cfd36ef5c548999da394a6a634db21
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spelling	oai:doaj.org-article:55cfd36ef5c548999da394a6a634db212021-11-15T15:55:14ZOne Health Genomic Surveillance of <named-content content-type="genus-species">Escherichia coli</named-content> Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock10.1128/mBio.02693-182150-7511https://doaj.org/article/55cfd36ef5c548999da394a6a634db212019-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02693-18https://doaj.org/toc/2150-7511ABSTRACT 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.Catherine LuddenKathy E. RavenDorota JamrozyTheodore GouliourisBeth BlaneFrancesc CollMarcus de GoffauPlamena NaydenovaCarolyne HornerJuan Hernandez-GarciaPaul WoodNazreen HadjirinMilorad RadakovicNicholas M. BrownMark HolmesJulian ParkhillSharon J. PeacockAmerican Society for MicrobiologyarticleESBLEscherichia coliantimicrobial resistancegenomicslivestockMicrobiologyQR1-502ENmBio, Vol 10, Iss 1 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	ESBL Escherichia coli antimicrobial resistance genomics livestock Microbiology QR1-502
spellingShingle	ESBL Escherichia coli antimicrobial resistance genomics livestock Microbiology QR1-502 Catherine Ludden Kathy E. Raven Dorota Jamrozy Theodore Gouliouris Beth Blane Francesc Coll Marcus de Goffau Plamena Naydenova Carolyne Horner Juan Hernandez-Garcia Paul Wood Nazreen Hadjirin Milorad Radakovic Nicholas M. Brown Mark Holmes Julian Parkhill Sharon J. Peacock One Health Genomic Surveillance of <named-content content-type="genus-species">Escherichia coli</named-content> Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock
description	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.
format	article
author	Catherine Ludden Kathy E. Raven Dorota Jamrozy Theodore Gouliouris Beth Blane Francesc Coll Marcus de Goffau Plamena Naydenova Carolyne Horner Juan Hernandez-Garcia Paul Wood Nazreen Hadjirin Milorad Radakovic Nicholas M. Brown Mark Holmes Julian Parkhill Sharon J. Peacock
author_facet	Catherine Ludden Kathy E. Raven Dorota Jamrozy Theodore Gouliouris Beth Blane Francesc Coll Marcus de Goffau Plamena Naydenova Carolyne Horner Juan Hernandez-Garcia Paul Wood Nazreen Hadjirin Milorad Radakovic Nicholas M. Brown Mark Holmes Julian Parkhill Sharon J. Peacock
author_sort	Catherine Ludden
title	One Health Genomic Surveillance of <named-content content-type="genus-species">Escherichia coli</named-content> Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock
title_short	One Health Genomic Surveillance of <named-content content-type="genus-species">Escherichia coli</named-content> Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock
title_full	One Health Genomic Surveillance of <named-content content-type="genus-species">Escherichia coli</named-content> Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock
title_fullStr	One Health Genomic Surveillance of <named-content content-type="genus-species">Escherichia coli</named-content> Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock
title_full_unstemmed	One Health Genomic Surveillance of <named-content content-type="genus-species">Escherichia coli</named-content> Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock
title_sort	one health genomic surveillance of <named-content content-type="genus-species">escherichia coli</named-content> demonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/55cfd36ef5c548999da394a6a634db21
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One Health Genomic Surveillance of <named-content content-type="genus-species">Escherichia coli</named-content> Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock

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