Identification of CTX-M Type ESBL E. coli from Sheep and Their Abattoir Environment Using Whole-Genome Sequencing

Widespread dissemination of extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) in animals, retail meats, and patients has been reported worldwide except for limited information on small ruminants. Our study focused on the genotypic characterizati...

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Autores principales:	Nigatu Aklilu Atlaw, Shivaramu Keelara, Maria Correa, Derek Foster, Wondwossen Gebreyes, Awa Aidara-Kane, Lyndy Harden, Siddhartha Thakur, Paula J. Fedorka Cray
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	abattoir environment antimicrobial resistance <i>E. coli</i> ESBL North Carolina sheep Medicine R
Acceso en línea:	https://doaj.org/article/b21dcaf4477c4673b2ae8f395c26a9e2
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spelling	oai:doaj.org-article:b21dcaf4477c4673b2ae8f395c26a9e22021-11-25T18:38:35ZIdentification of CTX-M Type ESBL <i>E. coli</i> from Sheep and Their Abattoir Environment Using Whole-Genome Sequencing10.3390/pathogens101114802076-0817https://doaj.org/article/b21dcaf4477c4673b2ae8f395c26a9e22021-11-01T00:00:00Zhttps://www.mdpi.com/2076-0817/10/11/1480https://doaj.org/toc/2076-0817Widespread dissemination of extended-spectrum beta-lactamase (ESBL) <i>Escherichia coli</i> (<i>E. coli</i>) in animals, retail meats, and patients has been reported worldwide except for limited information on small ruminants. Our study focused on the genotypic characterization of ESBL <i>E. coli</i> from healthy sheep and their abattoir environment in North Carolina, USA. A total of 113 ESBL <i>E. coli</i> isolates from sheep (n = 65) and their abattoir environment (n = 48) were subjected to whole-genome sequencing (WGS). Bioinformatics tools were used to analyze the WGS data. Multiple CTX-M-type beta-lactamase genes were detected, namely <i>bla</i><sub>CTX-M-1</sub>, <i>bla</i><sub>CTX-M-14</sub>, <i>bla</i><sub>CTX-M-15</sub>, <i>bla</i><sub>CTX-M-27</sub>, <i>bla</i><sub>CTX-M-32</sub>, <i>bla</i><sub>CTX-M-55</sub>, and <i>bla</i><sub>CTX-M-65</sub>. Other beta-lactamase genes detected included <i>bla</i><sub>CMY-2</sub>, <i>bla</i><sub>TEM-1A/B/C</sub>, and <i>bla</i><sub>CARB-2</sub>. In addition, antimicrobial resistance (AMR) genes and/or point mutations that confer resistance to quinolones, aminoglycosides, phenicols, tetracyclines, macrolides, lincosamides, and folate-pathway antagonists were identified. The majority of the detected plasmids were shared between isolates from sheep and the abattoir environment. Sequence types were more clustered around seasonal sampling but dispersed across sample types. In conclusion, our study reported wide dissemination of ESBL <i>E. coli</i> in sheep and the abattoir environment and associated AMR genes, point mutations, and plasmids. This is the first comprehensive AMR and WGS report on ESBL <i>E. coli</i> from sheep and abattoir environments in the United States.Nigatu Aklilu AtlawShivaramu KeelaraMaria CorreaDerek FosterWondwossen GebreyesAwa Aidara-KaneLyndy HardenSiddhartha ThakurPaula J. Fedorka CrayMDPI AGarticleabattoir environmentantimicrobial resistance<i>E. coli</i>ESBLNorth CarolinasheepMedicineRENPathogens, Vol 10, Iss 1480, p 1480 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	abattoir environment antimicrobial resistance <i>E. coli</i> ESBL North Carolina sheep Medicine R
spellingShingle	abattoir environment antimicrobial resistance <i>E. coli</i> ESBL North Carolina sheep Medicine R Nigatu Aklilu Atlaw Shivaramu Keelara Maria Correa Derek Foster Wondwossen Gebreyes Awa Aidara-Kane Lyndy Harden Siddhartha Thakur Paula J. Fedorka Cray Identification of CTX-M Type ESBL <i>E. coli</i> from Sheep and Their Abattoir Environment Using Whole-Genome Sequencing
description	Widespread dissemination of extended-spectrum beta-lactamase (ESBL) <i>Escherichia coli</i> (<i>E. coli</i>) in animals, retail meats, and patients has been reported worldwide except for limited information on small ruminants. Our study focused on the genotypic characterization of ESBL <i>E. coli</i> from healthy sheep and their abattoir environment in North Carolina, USA. A total of 113 ESBL <i>E. coli</i> isolates from sheep (n = 65) and their abattoir environment (n = 48) were subjected to whole-genome sequencing (WGS). Bioinformatics tools were used to analyze the WGS data. Multiple CTX-M-type beta-lactamase genes were detected, namely <i>bla</i><sub>CTX-M-1</sub>, <i>bla</i><sub>CTX-M-14</sub>, <i>bla</i><sub>CTX-M-15</sub>, <i>bla</i><sub>CTX-M-27</sub>, <i>bla</i><sub>CTX-M-32</sub>, <i>bla</i><sub>CTX-M-55</sub>, and <i>bla</i><sub>CTX-M-65</sub>. Other beta-lactamase genes detected included <i>bla</i><sub>CMY-2</sub>, <i>bla</i><sub>TEM-1A/B/C</sub>, and <i>bla</i><sub>CARB-2</sub>. In addition, antimicrobial resistance (AMR) genes and/or point mutations that confer resistance to quinolones, aminoglycosides, phenicols, tetracyclines, macrolides, lincosamides, and folate-pathway antagonists were identified. The majority of the detected plasmids were shared between isolates from sheep and the abattoir environment. Sequence types were more clustered around seasonal sampling but dispersed across sample types. In conclusion, our study reported wide dissemination of ESBL <i>E. coli</i> in sheep and the abattoir environment and associated AMR genes, point mutations, and plasmids. This is the first comprehensive AMR and WGS report on ESBL <i>E. coli</i> from sheep and abattoir environments in the United States.
format	article
author	Nigatu Aklilu Atlaw Shivaramu Keelara Maria Correa Derek Foster Wondwossen Gebreyes Awa Aidara-Kane Lyndy Harden Siddhartha Thakur Paula J. Fedorka Cray
author_facet	Nigatu Aklilu Atlaw Shivaramu Keelara Maria Correa Derek Foster Wondwossen Gebreyes Awa Aidara-Kane Lyndy Harden Siddhartha Thakur Paula J. Fedorka Cray
author_sort	Nigatu Aklilu Atlaw
title	Identification of CTX-M Type ESBL <i>E. coli</i> from Sheep and Their Abattoir Environment Using Whole-Genome Sequencing
title_short	Identification of CTX-M Type ESBL <i>E. coli</i> from Sheep and Their Abattoir Environment Using Whole-Genome Sequencing
title_full	Identification of CTX-M Type ESBL <i>E. coli</i> from Sheep and Their Abattoir Environment Using Whole-Genome Sequencing
title_fullStr	Identification of CTX-M Type ESBL <i>E. coli</i> from Sheep and Their Abattoir Environment Using Whole-Genome Sequencing
title_full_unstemmed	Identification of CTX-M Type ESBL <i>E. coli</i> from Sheep and Their Abattoir Environment Using Whole-Genome Sequencing
title_sort	identification of ctx-m type esbl <i>e. coli</i> from sheep and their abattoir environment using whole-genome sequencing
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/b21dcaf4477c4673b2ae8f395c26a9e2
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Identification of CTX-M Type ESBL <i>E. coli</i> from Sheep and Their Abattoir Environment Using Whole-Genome Sequencing

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