Diverse Commensal <named-content content-type="genus-species">Escherichia coli</named-content> Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador

ABSTRACT The increased prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae has had major clinical and economic impacts on human medicine. Many of the multidrug-resistant (multiresistant) Enterobacteriaceae found in humans are community acquired, and some of them are possibly linked...

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Autores principales:	Liseth Salinas, Paúl Cárdenas, Timothy J. Johnson, Karla Vasco, Jay Graham, Gabriel Trueba
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	Escherichia coli antibiotic resistance clonality plasmid analysis Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/1cf14387d9fd42929f2ef96ae369ddcc
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spelling	oai:doaj.org-article:1cf14387d9fd42929f2ef96ae369ddcc2021-11-15T15:22:20ZDiverse Commensal <named-content content-type="genus-species">Escherichia coli</named-content> Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador10.1128/mSphere.00316-192379-5042https://doaj.org/article/1cf14387d9fd42929f2ef96ae369ddcc2019-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00316-19https://doaj.org/toc/2379-5042ABSTRACT The increased prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae has had major clinical and economic impacts on human medicine. Many of the multidrug-resistant (multiresistant) Enterobacteriaceae found in humans are community acquired, and some of them are possibly linked to food animals (i.e., livestock raised for meat and dairy products). In this study, we examined whether numerically dominant commensal Escherichia coli strains from humans (n = 63 isolates) and domestic animals (n = 174 isolates) in the same community and with matching phenotypic AMR patterns were clonally related or shared the same plasmids. We identified 25 multiresistant isolates (i.e., isolates resistant to more than one antimicrobial) that shared identical phenotypic resistance patterns. We then investigated the diversity of E. coli clones, AMR genes, and plasmids carrying the AMR genes using conjugation, replicon typing, and whole-genome sequencing. All of the multiresistant E. coli isolates (from children and domestic animals) analyzed had at least 90 or more whole-genome SNP differences between one another, suggesting that none of the strains was recently transferred. While the majority of isolates shared the same antimicrobial resistance genes and replicons, DNA sequencing indicated that these genes and replicons were found on different plasmid structures. We did not find evidence of the clonal spread of AMR in this community: instead, AMR genes were carried on diverse clones and plasmids. This presents a significant challenge for understanding the movement of AMR in a community. IMPORTANCE Even though Escherichia coli strains may share nearly identical phenotypic AMR profiles and AMR genes and overlap in space and time, the diversity of clones and plasmids challenges research that aims to identify sources of AMR. Horizontal gene transfer appears to play a more significant role than clonal expansion in the spread of AMR in this community.Liseth SalinasPaúl CárdenasTimothy J. JohnsonKarla VascoJay GrahamGabriel TruebaAmerican Society for MicrobiologyarticleEscherichia coliantibiotic resistanceclonalityplasmid analysisMicrobiologyQR1-502ENmSphere, Vol 4, Iss 3 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Escherichia coli antibiotic resistance clonality plasmid analysis Microbiology QR1-502
spellingShingle	Escherichia coli antibiotic resistance clonality plasmid analysis Microbiology QR1-502 Liseth Salinas Paúl Cárdenas Timothy J. Johnson Karla Vasco Jay Graham Gabriel Trueba Diverse Commensal <named-content content-type="genus-species">Escherichia coli</named-content> Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador
description	ABSTRACT The increased prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae has had major clinical and economic impacts on human medicine. Many of the multidrug-resistant (multiresistant) Enterobacteriaceae found in humans are community acquired, and some of them are possibly linked to food animals (i.e., livestock raised for meat and dairy products). In this study, we examined whether numerically dominant commensal Escherichia coli strains from humans (n = 63 isolates) and domestic animals (n = 174 isolates) in the same community and with matching phenotypic AMR patterns were clonally related or shared the same plasmids. We identified 25 multiresistant isolates (i.e., isolates resistant to more than one antimicrobial) that shared identical phenotypic resistance patterns. We then investigated the diversity of E. coli clones, AMR genes, and plasmids carrying the AMR genes using conjugation, replicon typing, and whole-genome sequencing. All of the multiresistant E. coli isolates (from children and domestic animals) analyzed had at least 90 or more whole-genome SNP differences between one another, suggesting that none of the strains was recently transferred. While the majority of isolates shared the same antimicrobial resistance genes and replicons, DNA sequencing indicated that these genes and replicons were found on different plasmid structures. We did not find evidence of the clonal spread of AMR in this community: instead, AMR genes were carried on diverse clones and plasmids. This presents a significant challenge for understanding the movement of AMR in a community. IMPORTANCE Even though Escherichia coli strains may share nearly identical phenotypic AMR profiles and AMR genes and overlap in space and time, the diversity of clones and plasmids challenges research that aims to identify sources of AMR. Horizontal gene transfer appears to play a more significant role than clonal expansion in the spread of AMR in this community.
format	article
author	Liseth Salinas Paúl Cárdenas Timothy J. Johnson Karla Vasco Jay Graham Gabriel Trueba
author_facet	Liseth Salinas Paúl Cárdenas Timothy J. Johnson Karla Vasco Jay Graham Gabriel Trueba
author_sort	Liseth Salinas
title	Diverse Commensal <named-content content-type="genus-species">Escherichia coli</named-content> Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador
title_short	Diverse Commensal <named-content content-type="genus-species">Escherichia coli</named-content> Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador
title_full	Diverse Commensal <named-content content-type="genus-species">Escherichia coli</named-content> Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador
title_fullStr	Diverse Commensal <named-content content-type="genus-species">Escherichia coli</named-content> Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador
title_full_unstemmed	Diverse Commensal <named-content content-type="genus-species">Escherichia coli</named-content> Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador
title_sort	diverse commensal <named-content content-type="genus-species">escherichia coli</named-content> clones and plasmids disseminate antimicrobial resistance genes in domestic animals and children in a semirural community in ecuador
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/1cf14387d9fd42929f2ef96ae369ddcc
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Diverse Commensal <named-content content-type="genus-species">Escherichia coli</named-content> Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador

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