# Non-tuberculous mycobacteria isolates from patients with chronic pulmonary disease and no epidemiological relationship show sequence clusters through whole-genome sequencing

## TL;DR

This study used whole-genome sequencing to find clusters of non-tuberculous mycobacteria from patients with lung disease, suggesting infections may come from shared sources.

## Contribution

The study demonstrates that WGS can identify clusters of mycobacteria isolates from unrelated patients, suggesting environmental sources rather than patient-to-patient transmission.

## Key findings

- M. intracellulare subsp. intracellulare and M. intracellulare subsp. chimaera isolates formed clusters from unrelated patients.
- M. avium subsp. avium isolates did not form clusters across patients.
- Three clustering methods confirmed close genetic relationships among isolates from different patients.

## Abstract

This study aimed to investigate the genomic epidemiology of slow-growing mycobacteria (SGM) isolates from patients with bronchiectasis through whole-genome sequencing (WGS) and assess various bioinformatic tools to establish relationships between the isolates.

A total of 46 SGM isolates from 37 patients with underlying chronic pulmonary disease, previously identified as Mycobacterium avium, Mycobacterium intracellulare, or Mycobacterium chimaera through polymerase chain reaction, were analyzed using WGS and three different clustering methods, namely rPinecone, Split K-mer analysis (SKA), and custom single nucleotide variant threshold calculation.

The three analyses revealed one cluster of M. intracellulare subsp. intracellulare isolates and one cluster of M. intracellulare subsp. chimaera isolates from different patients. The analyses did not indicate any clusters formed by M. avium subsp. avium isolates from different patients.

M. intracellulare subsp. chimaera and M. intracellulare subsp. intracellulare form clusters of very closely related isolates from patients with no epidemiological relationship. This absence of an epidemiological relationship indicated that the infections were likely acquired from common sources rather than through direct transmission between patients. The use of three methodologies is an adequate strategy for an in-depth study of the relationship between isolates of very closely related species and subspecies.