Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Apr 15;231(4):902-912.
doi: 10.1093/infdis/jiae488.

Genomic Epidemiology of Extrapulmonary Nontuberculous Mycobacteria Isolates at Emerging Infections Program Sites-United States, 2019-2020

Thao L Masters  1   2 , Nadege Charles Toney  1 , Thomas O Ewing  1 , Gillian A McAllister  1 , Marsenia H Mathis  2 , Cheri Grigg  1 , Shelley S Magill  1 , Kelly A Jackson  1 , Rebecca Byram  1 , Isaac See  1 , Max Salfinger  3 , Devra Barter  4 , Helen Johnston  4 , Ruth Lynfield  5 , Paula Snippes Vagnone  5 , Laura Tourdot  5 , Bridget J Anderson  6 , Ghinwa Dumyati  7 , Rebecca Pierce  8 , Joseph D Lutgring  1 , Amy Gargis  1 , Susannah L McKay  1
Affiliations

Genomic Epidemiology of Extrapulmonary Nontuberculous Mycobacteria Isolates at Emerging Infections Program Sites-United States, 2019-2020

Thao L Masters et al. J Infect Dis. .

Abstract

Background: Nontuberculous mycobacteria (NTM) cause pulmonary and extrapulmonary infections. Although isolation of NTM from clinical specimens has increased nationally, few studies delineated the molecular characteristics of extrapulmonary NTM.

Methods: Extrapulmonary isolates were collected by 4 Emerging Infections Program sites from October 2019 to March 2020 and underwent laboratory characterization, including matrix-assisted laser desorption ionization-time of flight mass spectrometry, Sanger DNA sequencing, and whole genome sequencing. Bioinformatics analyses were employed to identify species, sequence types (STs), antimicrobial resistance (AR), and virulence genes; isolates were further characterized by phylogenetic analyses.

Results: Among 45 isolates, the predominant species were Mycobacterium avium (n = 20, 44%), Mycobacterium chelonae (n = 7, 16%), and Mycobacterium fortuitum (n = 6, 13%). The collection represented 31 STs across 10 species; the most common ST was ST11 (M. avium, n = 7). M. fortuitum and Mycobacterium abscessus isolates harbored multiple genes conferring resistance to aminoglycosides, β-lactams, and macrolides. No known AR mutations were detected in rpoB, 16S, or 23S rRNAs. Slow-growing NTM species harbored multiple virulence genes, including type VII secretion components, adhesion factors, and phospholipase C.

Conclusions: Continued active laboratory- and population-based surveillance will further inform the prevalence of NTM species and STs, monitor emerging clones, and allow AR characterization.

Keywords: antimicrobial resistance; extrapulmonary NTM; molecular epidemiology; public health bioinformatics; whole genome sequencing.

PubMed Disclaimer

Conflict of interest statement

Potential conflicts of interest. EIP site coauthors’ institutions received funding from the CDC. R. L. reports service on the program committee for IDWeek and receipt of travel support for conference planning and for the conference; service as associate editor for the American Academy of Pediatrics’ Red Book; receipt of fees for editorial work that were donated to the Minnesota Department of Health; receipt of support to attend the American Academy of Pediatrics’ Committee on Infectious Disease meetings; service on the Council of State and Territorial Epidemiologists’ Executive Board and receipt of travel support to attend its meetings; and service on the board of the National Foundation of Infectious Disease and receipt of travel support to attend its meetings. J. D. L. reports receiving travel support for attending the Clinical and Laboratory Standards Institute’s Antimicrobial Susceptibility Testing Subcommittee Meetings and the Society for Healthcare Epidemiology of America’s Spring Meetings and for serving as a member of the Clinical and Laboratory Standards Institute’s Antimicrobial Susceptibility Testing Subcommittee. S. S. M. reports receiving travel support to attend IDWeek from the Infectious Diseases Society of America. R. P. reports receiving honorarium from the Society for Healthcare Epidemiology of America. All other authors report no potential conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.

MeSH terms

LinkOut - more resources