Clinical utility of whole-genome sequencing in identifying a rare Mycobacterium species causing native joint infection

ABSTRACT Background The gold standard for identifying non-tuberculous mycobacteria (NTM) is partial sequencing of one or more distinct gene loci and determining the closest match through reference database matching. The advent of whole-genome sequencing (WGS) allows for higher accuracy in resolving Mycobacterium species, by matching a larger genome, although at increased cost. Determining when to employ WGS for NTM identification in diagnostic laboratories is a challenge, particularly when only a minority of isolated NTM are clinically significant. Case Summary A 5-year-old patient with inflammatory arthritis, previously responsive to intra-articular glucocorticoid injections, presented with a chronic, painful, hot, swollen left knee. An NTM isolated from synovial fluid was initially reported as Mycobacterium intracellulare subsp. chimaera , based on gene-loci 16S rRNA and internal transcribed spacer (rRNA 16S-23S ITS) PCR and sequencing. WGS subsequently determined the NTM to best match a single, novel Mycobacterium species collected from a patient with lung disease from South Korea, 2018 (NCBI upload 2022). Phylogenetic analysis determined the isolate from our case to share the most recent ancestry with Mycobacterium nebraskense , and clustered in a sister clade to that of Mycobacterium avium intracellulare complex. The patient’s symptoms improved after a prolonged course of rifabutin, azithromycin, and moxifloxacin, with samples culture-negative 7 months following treatment. Conclusion We describe a rare NTM as the cause of a significant joint infection in a 5-year-old child. WGS was instrumental in defining the diagnosis and should be considered early for accurate NTM identification in significant infections, those non-responsive to treatment, or where iatrogenic or outbreak-related cases are a consideration.