Nontuberculous Mycobacteria in the Biofilm Microbiome of Private Well and Premise Plumbing

Abstract

Household plumbing biofilms can harbor and transmit bacterial pathogens. Pulmonary infections by nontuberculous mycobacteria (NTM) can occur from this transmission route. NTM infections are increasing around the world and in New Jersey (NJ), where this field study was performed. Plumbing biofilm samples were collected from sinks and showerheads in homes using private wells (n = 19) and in homes of NTM patients (n = 5). DNA extracts were analyzed by quantitative polymerase chain reaction (qPCR) to quantify mycobacterial marker genes and by amplicon sequencing to describe the microbiomes where NTM were observed. Water samples were analyzed for basic water quality parameters and fecal indicator organisms. Participants completed surveys about their wells and home water systems to enable testing of potential relationships between these environmental factors and the microbial communities. NTM were observed in more than half of private well biofilm samples using qPCR and in all of the selected samples analyzed by amplicon sequencing (n = 29/70), even when below detection by qPCR. Samples from patient homes, most of whom used public water supply, had similar abundances of NTM as samples from private wells. Physiography and within-home location (e.g., kitchen sink) explained some variation in concentrations of mycobacteria genes. One microbial family with no known human pathogens, Rikenellaceae, was identified as a potential antagonist to mycobacteria using linear discriminant analysis effect size (LEfSe). This study illuminates the widespread nature of NTM in private well water systems without disinfection selection pressures, and works toward understanding ecological interactions that may aid or slow the growth of NTM toward ecological engineering of healthy plumbing microbiomes.