Whole genome sequencing of Nontuberculous Mycobacterium (NTM) isolates from sputum specimens of co-habiting patients with NTM pulmonary disease and NTM isolates from their environment

• Published in: BMC genomics Vol. 21; no. 1; p. 322
• Main Authors: Yoon, Jung-Ki, Kim, Taek Soo, Kim, Jong-Il, Yim, Jae-Joon
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 23-04-2020; BioMed Central; BMC
• Subjects: Aged; Aged, 80 and over; Analysis; Chromosomes; Cloning; Cystic fibrosis; Cystic Fibrosis - microbiology; Disease control; Disease transmission; DNA sequencing; Environmental Microbiology; Female; Gene sequencing; Genetic aspects; Genetic distance; Genomes; Genomics; Households; Humans; Infections; Lung diseases; Lung Diseases - microbiology; Male; Medical research; Microorganisms; Middle Aged; Mycobacterium avium Complex - genetics; Mycobacterium avium Complex - isolation & purification; Mycobacterium Infections, Nontuberculous - microbiology; Mycobacterium Infections, Nontuberculous - transmission; Next-generation sequencing; Non-tuberculosis mycobacterium; Non-tuberculous mycobacterial pulmonary disease; Nontuberculous Mycobacteria - classification; Nontuberculous Mycobacteria - genetics; Nontuberculous Mycobacteria - physiology; Nucleotides; Patients; Phylogenetics; Phylogenomics; Phylogeny; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Sputum; Sputum - microbiology; Studies; Transmission; Tuberculosis; Urban areas; Whole genome sequencing; Whole Genome Sequencing - methods; Non-tuberculous mycobacterial pulmonary disease; Whole genome sequencing; Non-tuberculosis mycobacterium; Transmission; Phylogenomics
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-020-6738-2

Nontuberculous mycobacterium (NTM) species are ubiquitous microorganisms. NTM pulmonary disease (NTM-PD) is thought to be caused not by human-to-human transmission but by independent environmental acquisition. However, recent studies using next-generation sequencing (NGS) have reported trans-continental spread of Mycobacterium abscessus among patients with cystic fibrosis.
We investigated NTM genomes through NGS to examine transmission patterns in three pairs of co-habiting patients with NTM-PD who were suspected of patient-to-patient transmission. Three pairs of patients with NTM-PD co-habiting for at least 15 years were enrolled: a mother and a daughter with M. avium-PD, a couple with M. intracellulare-PD, and a second couple, one of whom was infected with M. intracellulare and the other of whom was infected with M. abscessus. Whole genome sequencing was performed using patients' NTM isolates as well as environmental specimens. Genetic distances were estimated based on single nucleotide polymorphisms (SNPs). By comparison with the genetic distances among 78 publicly available NTM genomes, NTM isolates derived from the two pairs of patients infected with the same NTM species were not closely related to each other. In phylogenetic analysis, the NTM isolates from patients with M. avium-PD clustered with isolates from different environmental sources.
In conclusion, considering the genetic distances between NTM strains, the likelihood of patient-to-patient transmission in pairs of co-habiting NTM-PD patients without overt immune deficiency is minimal.