Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System

ABSTRACT Carbapenem-resistant Enterobacteriaceae (CRE) are an urgent public health concern. Rapid identification of the resistance genes, their mobilization capacity, and strains carrying them is essential to direct hospital resources to prevent spread and improve patient outcomes. Whole-genome sequ...

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Autores principales:	Nicole D. Pecora, Ning Li, Marc Allard, Cong Li, Esperanza Albano, Mary Delaney, Andrea Dubois, Andrew B. Onderdonk, Lynn Bry
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2015
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/47c8d8a888c44804b3bc4d4adcd949f5
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spelling	oai:doaj.org-article:47c8d8a888c44804b3bc4d4adcd949f52021-11-15T15:41:26ZGenomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System10.1128/mBio.01030-152150-7511https://doaj.org/article/47c8d8a888c44804b3bc4d4adcd949f52015-09-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01030-15https://doaj.org/toc/2150-7511ABSTRACT Carbapenem-resistant Enterobacteriaceae (CRE) are an urgent public health concern. Rapid identification of the resistance genes, their mobilization capacity, and strains carrying them is essential to direct hospital resources to prevent spread and improve patient outcomes. Whole-genome sequencing allows refined tracking of both chromosomal traits and associated mobile genetic elements that harbor resistance genes. To enhance surveillance of CREs, clinical isolates with phenotypic resistance to carbapenem antibiotics underwent whole-genome sequencing. Analysis of 41 isolates of Klebsiella pneumoniae and Enterobacter cloacae, collected over a 3-year period, identified K. pneumoniae carbapenemase (KPC) genes encoding KPC-2, −3, and −4 and OXA-48 carbapenemases. All occurred within transposons, including multiple Tn4401 transposon isoforms, embedded within more than 10 distinct plasmids representing incompatibility (Inc) groups IncR, -N, -A/C, -H, and -X. Using short-read sequencing, draft maps were generated of new KPC-carrying vectors, several of which were derivatives of the IncN plasmid pBK31551. Two strains also had Tn4401 chromosomal insertions. Integrated analyses of plasmid profiles and chromosomal single-nucleotide polymorphism (SNP) profiles refined the strain patterns and provided a baseline hospital mobilome to facilitate analysis of new isolates. When incorporated with patient epidemiological data, the findings identified limited outbreaks against a broader 3-year period of sporadic external entry of many different strains and resistance vectors into the hospital. These findings highlight the utility of genomic analyses in internal and external surveillance efforts to stem the transmission of drug-resistant strains within and across health care institutions. IMPORTANCE We demonstrate how detection of resistance genes within mobile elements and resistance-carrying strains furthers active surveillance efforts for drug resistance. Whole-genome sequencing is increasingly available in hospital laboratories and provides a powerful and nuanced means to define the local landscape of drug resistance. In this study, isolates of Klebsiella pneumoniae and Enterobacter cloacae with resistance to carbapenem antibiotics were sequenced. Multiple carbapenemase genes were identified that resided in distinct transposons and plasmids. This mobilome, or population of mobile elements capable of mobilizing drug resistance, further highlighted the degree of strain heterogeneity while providing a detailed timeline of carbapenemase entry into the hospital over a 3-year period. These surveillance efforts support effective targeting of infection control resources and the development of institution-specific repositories of resistance genes and the mobile elements that carry them.Nicole D. PecoraNing LiMarc AllardCong LiEsperanza AlbanoMary DelaneyAndrea DuboisAndrew B. OnderdonkLynn BryAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 6, Iss 4 (2015)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Nicole D. Pecora Ning Li Marc Allard Cong Li Esperanza Albano Mary Delaney Andrea Dubois Andrew B. Onderdonk Lynn Bry Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System
description	ABSTRACT Carbapenem-resistant Enterobacteriaceae (CRE) are an urgent public health concern. Rapid identification of the resistance genes, their mobilization capacity, and strains carrying them is essential to direct hospital resources to prevent spread and improve patient outcomes. Whole-genome sequencing allows refined tracking of both chromosomal traits and associated mobile genetic elements that harbor resistance genes. To enhance surveillance of CREs, clinical isolates with phenotypic resistance to carbapenem antibiotics underwent whole-genome sequencing. Analysis of 41 isolates of Klebsiella pneumoniae and Enterobacter cloacae, collected over a 3-year period, identified K. pneumoniae carbapenemase (KPC) genes encoding KPC-2, −3, and −4 and OXA-48 carbapenemases. All occurred within transposons, including multiple Tn4401 transposon isoforms, embedded within more than 10 distinct plasmids representing incompatibility (Inc) groups IncR, -N, -A/C, -H, and -X. Using short-read sequencing, draft maps were generated of new KPC-carrying vectors, several of which were derivatives of the IncN plasmid pBK31551. Two strains also had Tn4401 chromosomal insertions. Integrated analyses of plasmid profiles and chromosomal single-nucleotide polymorphism (SNP) profiles refined the strain patterns and provided a baseline hospital mobilome to facilitate analysis of new isolates. When incorporated with patient epidemiological data, the findings identified limited outbreaks against a broader 3-year period of sporadic external entry of many different strains and resistance vectors into the hospital. These findings highlight the utility of genomic analyses in internal and external surveillance efforts to stem the transmission of drug-resistant strains within and across health care institutions. IMPORTANCE We demonstrate how detection of resistance genes within mobile elements and resistance-carrying strains furthers active surveillance efforts for drug resistance. Whole-genome sequencing is increasingly available in hospital laboratories and provides a powerful and nuanced means to define the local landscape of drug resistance. In this study, isolates of Klebsiella pneumoniae and Enterobacter cloacae with resistance to carbapenem antibiotics were sequenced. Multiple carbapenemase genes were identified that resided in distinct transposons and plasmids. This mobilome, or population of mobile elements capable of mobilizing drug resistance, further highlighted the degree of strain heterogeneity while providing a detailed timeline of carbapenemase entry into the hospital over a 3-year period. These surveillance efforts support effective targeting of infection control resources and the development of institution-specific repositories of resistance genes and the mobile elements that carry them.
format	article
author	Nicole D. Pecora Ning Li Marc Allard Cong Li Esperanza Albano Mary Delaney Andrea Dubois Andrew B. Onderdonk Lynn Bry
author_facet	Nicole D. Pecora Ning Li Marc Allard Cong Li Esperanza Albano Mary Delaney Andrea Dubois Andrew B. Onderdonk Lynn Bry
author_sort	Nicole D. Pecora
title	Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System
title_short	Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System
title_full	Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System
title_fullStr	Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System
title_full_unstemmed	Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System
title_sort	genomically informed surveillance for carbapenem-resistant enterobacteriaceae in a health care system
publisher	American Society for Microbiology
publishDate	2015
url	https://doaj.org/article/47c8d8a888c44804b3bc4d4adcd949f5
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Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System

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