Genomic characterization and SNP analysis connect respiratory infections caused by Mycobacterium intracellulare with a pool facility

Non-tuberculous mycobacteria are emerging respiratory pathogens that can persist in treated water systems. In 2018, a cluster of <i>Mycobacterium intracellulare</i> lung infections was linked to a pool facility in Australia, prompting an epidemiological and genomic investigation. <i>M. intracellulare</i> was isolated from five sputum samples across four clinical cases and from fourteen pool water samples across a total of five collection time points. All cases were resolved following exclusion from the pool facility, with only one patient requiring short-term steroids; none of the patients required anti-mycobacterial treatment. To test if this was a point-source outbreak, whole-genome sequencing of mycobacteria recovered from patients and the pool was implemented. Initial analysis confirmed all patient and water isolates were <i>M. intracellulare</i> with sequence type 210. A complete, circular genome was constructed from one of the isolates linked to this cluster and was used as a reference genome for high-resolution core genome SNP analysis. This analysis showed tight clustering of <i>M. intracellulare</i> genomes from patient and pool water isolates that were distinct from other <i>M. intracellulare</i>. Thus, epidemiological and comparative genome analysis strongly implicated the pool as the origin of these infections.