Host Environment, Genetics, and Behaviors That Contribute to Nontuberculous Mycobacterial Pulmonary Disease in Hawai'i

Abstract RATIONALE: The reasons why some people develop nontuberculous mycobacterial (NTM) pulmonary disease (PD) while others do not is likely due to a complex interplay of underlying host risk factors, NTM virulence, and exposures. Our goal was to begin to disentangle the contributions of the environment, host genetics, and behaviors for people with NTMPD in the hot spot of Hawai'i. This study was undertaken to genetically match respiratory NTM to patient home environmental samples, identify genomic signatures associated with disease, and elucidate lifestyle behaviors that predispose to NTMPD. METHODS: A case-control study was performed consisting of 35 people with NTMPD and 28 controls within the Kaiser Permanente Hawai'i system who collected household samples and completed a questionnaire providing their demographics, behaviors, and lifestyle activities. Respiratory and environmental NTM isolates were subjected to whole genome sequencing and core genome comparisons and phylogenomic analysis methods were used to compare and determine respiratory and environmental matches. DNA was extracted from the blood of 27 NTMPD patients, whole exome libraries constructed, and Illumina sequencing performed.Sequences were compared to >98K controls analyzed from NCBI's Allele Frequency Aggregator pipeline to elucidate candidate genes associated with NTMPD. A hierarchical logistic regression that accounted for NTM prevalence in natural and built environments was used to interrogate behaviors more common among cases vs. controls. RESULTS: Demographics between cases and controls were closely matched. Mycobacterium intracellulare subsp. chimaera and Mycobacterium abscessus were the most frequently identified NTM from respiratory specimens. Using comparative phylogenomics, in some cases, respiratory M. chimaera and M. abscessus isolates had high genomic similarity to isolates from kitchen sinks of the same household. A genome wide association study identified 59 genes linked to NTMPD (p<1e-08) compared to controls. Two top-ranked genes significantly associated with NTMPD were PPP3CA (calcineurin phosphatase, role in mycobacteria clearance) and PLCG2 (phospholipase Cγ2, role in modulating mycobacteria survival) (Figure). Natural and built environmental predictors were soil moisture, soil expansive ability, evapotranspiration, and population size of Asian ethnicity, respectively. Environmental NTM colonization did not predict whether a person had NTMPD rather, cases were older and had more indoor plants. Lower odds of NTMPD were found for homes with pet dogs and frequent outdoor activity. CONCLUSIONS: We discovered the combination of host aging and lifestyle choices contribute to NTMPD as well as genes PPP3CA and PLCG2 which may be involved in host response to NTM infection and should be investigated as future therapeutic targets.