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Variation among human, veterinary and environmental Mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns

Mycobacterium chelonae is a member of the Mycobacterium chelonae-abscessus complex and a cause of opportunistic disease in fish, reptiles, birds, and mammals including humans. Isolates in the complex are often difficult to identify and have differing antimicrobial susceptibilities. Thirty-one previo...

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Autores principales: Fogelson, Susan B., Camus, Alvin C., Lorenz, W. Walter, Vasireddy, Ravikiran, Vasireddy, Sruthi, Smith, Terry, Brown-Elliott, Barbara A., Wallace, Richard J., Hasan, Nabeeh A., Reischl, Udo, Sanchez, Susan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6433289/
https://www.ncbi.nlm.nih.gov/pubmed/30908517
http://dx.doi.org/10.1371/journal.pone.0214274
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author Fogelson, Susan B.
Camus, Alvin C.
Lorenz, W. Walter
Vasireddy, Ravikiran
Vasireddy, Sruthi
Smith, Terry
Brown-Elliott, Barbara A.
Wallace, Richard J.
Hasan, Nabeeh A.
Reischl, Udo
Sanchez, Susan
author_facet Fogelson, Susan B.
Camus, Alvin C.
Lorenz, W. Walter
Vasireddy, Ravikiran
Vasireddy, Sruthi
Smith, Terry
Brown-Elliott, Barbara A.
Wallace, Richard J.
Hasan, Nabeeh A.
Reischl, Udo
Sanchez, Susan
author_sort Fogelson, Susan B.
collection PubMed
description Mycobacterium chelonae is a member of the Mycobacterium chelonae-abscessus complex and a cause of opportunistic disease in fish, reptiles, birds, and mammals including humans. Isolates in the complex are often difficult to identify and have differing antimicrobial susceptibilities. Thirty-one previously identified rapidly-growing, non-tuberculous Mycobacterium sp. isolates cultured from biofilms, fish, reptiles, mammals, including humans, and three ATCC reference strains were evaluated with nine M. chelonae-abscessus complex whole genome sequences from GenBank by phylogenomic analysis, targeted gene comparisons, and in-vitro antimicrobial susceptibility patterns to assess strain variation among isolates from different sources. Results revealed minimal genetic variation among the M. chelonae strains. However, the core genomic alignment and SNP pattern of the complete 16S rRNA sequence clearly separated the turtle type strain ATCC 35752(T) from the clinical isolates and human reference strain “M. chelonae chemovar niacinogenes” ATCC 19237, providing evidence of two distinct subspecies. Concatenation of the partial rpoB (752 bp) and complete hsp65 (1,626 bp) sequence produced the same species/subspecies delineations as the core phylogeny. Partial rpoB and hsp65 sequences identified all the clinical isolates to the appropriate species level when respective cut-offs of 98% and 98.4% identity to the M. chelonae type strain ATCC 35752(T) were employed. The human strain, ATCC19237, was the most representative strain for the evaluated human, veterinary, and environmental strains. Additionally, two isolates were identified as Mycobacterium saopaulense, its first identification in a non-fish or non-human host.
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spelling pubmed-64332892019-04-08 Variation among human, veterinary and environmental Mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns Fogelson, Susan B. Camus, Alvin C. Lorenz, W. Walter Vasireddy, Ravikiran Vasireddy, Sruthi Smith, Terry Brown-Elliott, Barbara A. Wallace, Richard J. Hasan, Nabeeh A. Reischl, Udo Sanchez, Susan PLoS One Research Article Mycobacterium chelonae is a member of the Mycobacterium chelonae-abscessus complex and a cause of opportunistic disease in fish, reptiles, birds, and mammals including humans. Isolates in the complex are often difficult to identify and have differing antimicrobial susceptibilities. Thirty-one previously identified rapidly-growing, non-tuberculous Mycobacterium sp. isolates cultured from biofilms, fish, reptiles, mammals, including humans, and three ATCC reference strains were evaluated with nine M. chelonae-abscessus complex whole genome sequences from GenBank by phylogenomic analysis, targeted gene comparisons, and in-vitro antimicrobial susceptibility patterns to assess strain variation among isolates from different sources. Results revealed minimal genetic variation among the M. chelonae strains. However, the core genomic alignment and SNP pattern of the complete 16S rRNA sequence clearly separated the turtle type strain ATCC 35752(T) from the clinical isolates and human reference strain “M. chelonae chemovar niacinogenes” ATCC 19237, providing evidence of two distinct subspecies. Concatenation of the partial rpoB (752 bp) and complete hsp65 (1,626 bp) sequence produced the same species/subspecies delineations as the core phylogeny. Partial rpoB and hsp65 sequences identified all the clinical isolates to the appropriate species level when respective cut-offs of 98% and 98.4% identity to the M. chelonae type strain ATCC 35752(T) were employed. The human strain, ATCC19237, was the most representative strain for the evaluated human, veterinary, and environmental strains. Additionally, two isolates were identified as Mycobacterium saopaulense, its first identification in a non-fish or non-human host. Public Library of Science 2019-03-25 /pmc/articles/PMC6433289/ /pubmed/30908517 http://dx.doi.org/10.1371/journal.pone.0214274 Text en © 2019 Fogelson 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
Fogelson, Susan B.
Camus, Alvin C.
Lorenz, W. Walter
Vasireddy, Ravikiran
Vasireddy, Sruthi
Smith, Terry
Brown-Elliott, Barbara A.
Wallace, Richard J.
Hasan, Nabeeh A.
Reischl, Udo
Sanchez, Susan
Variation among human, veterinary and environmental Mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns
title Variation among human, veterinary and environmental Mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns
title_full Variation among human, veterinary and environmental Mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns
title_fullStr Variation among human, veterinary and environmental Mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns
title_full_unstemmed Variation among human, veterinary and environmental Mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns
title_short Variation among human, veterinary and environmental Mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns
title_sort variation among human, veterinary and environmental mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6433289/
https://www.ncbi.nlm.nih.gov/pubmed/30908517
http://dx.doi.org/10.1371/journal.pone.0214274
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