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Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly

Mycobacterium chelonae is a rapidly growing nontuberculous mycobacterium that is a common cause of nosocomial infections. Here we describe investigation of a possible nosocomial transmission of M. chelonae at the Hospital of the University of Pennsylvania (HUP). M. chelonae strains with similar high...

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Autores principales: Gu, Christopher H., Zhao, Chunyu, Hofstaedter, Casey, Tebas, Pablo, Glaser, Laurel, Baldassano, Robert, Bittinger, Kyle, Mattei, Lisa M., Bushman, Frederic D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7652343/
https://www.ncbi.nlm.nih.gov/pubmed/33166284
http://dx.doi.org/10.1371/journal.pone.0236533
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author Gu, Christopher H.
Zhao, Chunyu
Hofstaedter, Casey
Tebas, Pablo
Glaser, Laurel
Baldassano, Robert
Bittinger, Kyle
Mattei, Lisa M.
Bushman, Frederic D.
author_facet Gu, Christopher H.
Zhao, Chunyu
Hofstaedter, Casey
Tebas, Pablo
Glaser, Laurel
Baldassano, Robert
Bittinger, Kyle
Mattei, Lisa M.
Bushman, Frederic D.
author_sort Gu, Christopher H.
collection PubMed
description Mycobacterium chelonae is a rapidly growing nontuberculous mycobacterium that is a common cause of nosocomial infections. Here we describe investigation of a possible nosocomial transmission of M. chelonae at the Hospital of the University of Pennsylvania (HUP). M. chelonae strains with similar high-level antibiotic resistance patterns were isolated from two patients who developed post-operative infections at HUP in 2017, suggesting a possible point source infection. The isolates, along with other clinical isolates from other patients, were sequenced using the Illumina and Oxford Nanopore technologies. The resulting short and long reads were hybrid assembled into draft genomes. The genomes were compared by quantifying single nucleotide variants in the core genome and assessed using a control dataset to quantify error rates in comparisons of identical genomes. We show that all M. chelonae isolates tested were highly dissimilar, as indicated by high pairwise SNV values, consistent with environmental acquisition and not a nosocomial point source. Our control dataset determined a threshold for evaluating identity between strains while controlling for sequencing error. Finally, antibiotic resistance genes were predicted for our isolates, and several single nucleotide variants were identified that have the potential to modulated drug resistance.
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spelling pubmed-76523432020-11-18 Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly Gu, Christopher H. Zhao, Chunyu Hofstaedter, Casey Tebas, Pablo Glaser, Laurel Baldassano, Robert Bittinger, Kyle Mattei, Lisa M. Bushman, Frederic D. PLoS One Research Article Mycobacterium chelonae is a rapidly growing nontuberculous mycobacterium that is a common cause of nosocomial infections. Here we describe investigation of a possible nosocomial transmission of M. chelonae at the Hospital of the University of Pennsylvania (HUP). M. chelonae strains with similar high-level antibiotic resistance patterns were isolated from two patients who developed post-operative infections at HUP in 2017, suggesting a possible point source infection. The isolates, along with other clinical isolates from other patients, were sequenced using the Illumina and Oxford Nanopore technologies. The resulting short and long reads were hybrid assembled into draft genomes. The genomes were compared by quantifying single nucleotide variants in the core genome and assessed using a control dataset to quantify error rates in comparisons of identical genomes. We show that all M. chelonae isolates tested were highly dissimilar, as indicated by high pairwise SNV values, consistent with environmental acquisition and not a nosocomial point source. Our control dataset determined a threshold for evaluating identity between strains while controlling for sequencing error. Finally, antibiotic resistance genes were predicted for our isolates, and several single nucleotide variants were identified that have the potential to modulated drug resistance. Public Library of Science 2020-11-09 /pmc/articles/PMC7652343/ /pubmed/33166284 http://dx.doi.org/10.1371/journal.pone.0236533 Text en © 2020 Gu et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Gu, Christopher H.
Zhao, Chunyu
Hofstaedter, Casey
Tebas, Pablo
Glaser, Laurel
Baldassano, Robert
Bittinger, Kyle
Mattei, Lisa M.
Bushman, Frederic D.
Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly
title Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly
title_full Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly
title_fullStr Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly
title_full_unstemmed Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly
title_short Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly
title_sort investigating hospital mycobacterium chelonae infection using whole genome sequencing and hybrid assembly
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7652343/
https://www.ncbi.nlm.nih.gov/pubmed/33166284
http://dx.doi.org/10.1371/journal.pone.0236533
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