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

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.