Clinical significance and simultaneous microevolution of two closely-related nontuberculous mycobacteria species

We aimed to investigate the clinical significance and in-host evolution of Mycobacterium septicum and Mycolicibacterium nivoides, two closely-related nontuberculous mycobacteria.

Using a detailed single-case study, we investigated pulmonary co-infection of M. septicum and M. nivoides by examining clinical data, conducting microbiological assays, performing genome sequencing for 20 colonies from each sample, and evaluating virulence using Galleria mellonella larva. We conducted a literature review to summarize M. septicum and M. nivoides clinical cases and curated all publicly-accessible genomes.

In the pulmonary co-infection, both M. septicum and M. nivoides were implicated as the causative agents and exhibited remarkable intra-strain genomic heterogeneity. We uncovered different putative in-host microevolution trajectories, via either α/β hydrolase variation for M. septicum or papA2 (trehalose-2-sulfate acyltransferase-encoding gene) mutation for M. nivoides. Intriguingly, both mutations were associated with enhanced virulence in the G. mellonella model. We identified 19 additional cases with M. septicum in literature, showing its multiple roles as a pathogen, a colonizer, or a contaminant. Re-analysis of 16 publicly-accessible genomes revealed misclassification of M. nivoides, potentially underestimating its clinical significance.

This study presents the first genomic evidence of co-infection of M. septicum and M. nivoides and divergent putative within-host evolution in a human patient. Simultaneously identifying multiple NTM colonies in chronic infection is needed for precise diagnosis. The observed convergence towards increased model virulence warrants further investigation as a potential adaptive strategy in NTM.