A cross-environment comparison of nontuberculous mycobacterial diversity

Nontuberculous mycobacteria (NTM) are a group of environmental bacteria that encompass nearly 200 described species, some of which can cause chronic pulmonary and extrapulmonary infections in humans. What makes these infections unique is that they are environmentally acquired, yet there remains a limited understanding of how different environments contribute to potential pathogen exposure. Here, we use new and existing marker gene data sets to compare the amounts and types of NTM across three environments known to harbor mycobacteria, surface waters, soil, and household plumbing biofilms, to better understand potential pathogen occurrence in each environment. We used 16S rRNA gene sequencing, in tandem with mycobacterial-specific marker gene sequencing, to characterize variation in the relative abundances of the genus Mycobacterium and specific mycobacterial taxa across the three environments, with a focus on a clinically significant NTM. We found that household plumbing biofilms contained both the highest relative abundance of the genus Mycobacterium (on average, 13.7% of bacteria were members of the genus), as well as the highest occurrence of clinically relevant species detected (Mycobacterium avium and Mycobacterium abscessus), compared to surface waters and soil. Although mycobacteria are ubiquitous across many different environments, mycobacterial diversity is highly variable between environments with clinically relevant species largely restricted to household plumbing biofilms, information that is critical for understanding the ecology and epidemiology of NTM disease.IMPORTANCENontuberculous mycobacteria, or NTM, are a diverse group of bacteria within the genus Mycobacterium that are common in many environments. While most members of the genus pose little threat to human health, a handful of species, namely the Mycobacterium avium complex, M. abscessus, and M. kansasii, can cause severe and prolonged lung infections. These environmentally acquired infections are on the rise in the United States and around the world, yet we still do not have a good understanding of which environment types pose the greatest risk of infection to susceptible populations. Our study used cultivation-independent approaches to identify the specific NTM taxa found in over 1,000 samples from three potentially important environmental reservoirs-surface waters, soils, and household plumbing systems, to determine which of these environments are most likely to harbor NTM of clinical significance. Our results highlight the high degree of variability in the types of NTM taxa detected in different environments (including extensive novel diversity within the genus) and show that household plumbing biofilms are likely the most important reservoir and subsequent route of transmission for clinically significant NTM.