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Mycobacterium immunogenum acquisition from hospital tap water: a genomic and epidemiologic analysis.

Publication ,  Journal Article
Baker, AW; Nick, SE; Jia, F; Graves, AM; Warren, BG; Zavala, S; Stout, JE; Lee, MJ; Alexander, BD; Davidson, RM; Anderson, DJ
Published in: J Clin Microbiol
May 1, 2024

We identified 23 cases of Mycobacterium immunogenum respiratory acquisition linked to a colonized plumbing system at a new hospital addition. We conducted a genomic and epidemiologic investigation to assess for clonal acquisition of M. immunogenum from hospital water sources and improve understanding of genetic distances between M. immunogenum isolates. We performed whole-genome sequencing on 28 M. immunogenum isolates obtained from August 2013 to July 2021 from patients and water sources on four intensive care and intermediate units at an academic hospital. Study hospital isolates were recovered from 23 patients who experienced de novo respiratory isolation of M. immunogenum and from biofilms obtained from five tap water outlets. We also analyzed 10 M. immunogenum genomes from previously sequenced clinical (n = 7) and environmental (n = 3) external control isolates. The 38-isolate cohort clustered into three clades with pairwise single-nucleotide polymorphism (SNP) distances ranging from 0 to 106,697 SNPs. We identified two clusters of study hospital isolates in Clade 1 and one cluster in Clade 2 for which clinical and environmental isolates differed by fewer than 10 SNPs and had less than 0.5% accessory genome variation. A less restrictive combined threshold of 40 SNPs and 5% accessory genes reliably captured additional isolates that met clinical criteria for hospital acquisition, but 12 (4%) of 310 epidemiologically unrelated isolate pairs also met this threshold. Core and accessory genome analyses confirmed respiratory acquisition of multiple clones of M. immunogenum from hospital water sources to patients. When combined with epidemiologic investigation, genomic thresholds accurately distinguished hospital acquisition.

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Published In

J Clin Microbiol

DOI

EISSN

1098-660X

Publication Date

May 1, 2024

Start / End Page

e0014924

Location

United States

Related Subject Headings

  • Whole Genome Sequencing
  • Water Microbiology
  • Polymorphism, Single Nucleotide
  • Mycobacterium Infections, Nontuberculous
  • Mycobacterium
  • Middle Aged
  • Microbiology
  • Male
  • Humans
  • Hospitals
 

Citation

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Baker, A. W., Nick, S. E., Jia, F., Graves, A. M., Warren, B. G., Zavala, S., … Anderson, D. J. (2024). Mycobacterium immunogenum acquisition from hospital tap water: a genomic and epidemiologic analysis. J Clin Microbiol, e0014924. https://doi.org/10.1128/jcm.00149-24
Baker, Arthur W., Sophie E. Nick, Fan Jia, Amanda M. Graves, Bobby G. Warren, Sofia Zavala, Jason E. Stout, et al. “Mycobacterium immunogenum acquisition from hospital tap water: a genomic and epidemiologic analysis.J Clin Microbiol, May 1, 2024, e0014924. https://doi.org/10.1128/jcm.00149-24.
Baker AW, Nick SE, Jia F, Graves AM, Warren BG, Zavala S, et al. Mycobacterium immunogenum acquisition from hospital tap water: a genomic and epidemiologic analysis. J Clin Microbiol. 2024 May 1;e0014924.
Baker, Arthur W., et al. “Mycobacterium immunogenum acquisition from hospital tap water: a genomic and epidemiologic analysis.J Clin Microbiol, May 2024, p. e0014924. Pubmed, doi:10.1128/jcm.00149-24.
Baker AW, Nick SE, Jia F, Graves AM, Warren BG, Zavala S, Stout JE, Lee MJ, Alexander BD, Davidson RM, Anderson DJ. Mycobacterium immunogenum acquisition from hospital tap water: a genomic and epidemiologic analysis. J Clin Microbiol. 2024 May 1;e0014924.

Published In

J Clin Microbiol

DOI

EISSN

1098-660X

Publication Date

May 1, 2024

Start / End Page

e0014924

Location

United States

Related Subject Headings

  • Whole Genome Sequencing
  • Water Microbiology
  • Polymorphism, Single Nucleotide
  • Mycobacterium Infections, Nontuberculous
  • Mycobacterium
  • Middle Aged
  • Microbiology
  • Male
  • Humans
  • Hospitals