Clinical utility of whole-genome sequencing in identifying a rare Mycobacterium species causing native joint infection
7 affiliations
- 1Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- 2Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
- 3Department of Infectious Diseases, Royal Children’s Hospital, Melbourne, Victoria, Australia
- 4Department of Infectious Diseases, University of Melbourne, Melbourne, Victoria, Australia
- 5Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- 6Department of Microbiology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- 7Department of Infectious Diseases, Royal Melbourne Hospital, Melbourne, Victoria, Australia
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.
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BibTeX
@article{globan2026clinical,
title = {{Clinical utility of whole-genome sequencing in identifying a rare Mycobacterium species causing native joint infection}},
author = {M. Globan and J. Moselen and N. Wang and E. Steinig and Y. Nong and L. Viberg and L. Caly and K. A. Bond},
journal = {ASM case reports},
year = {2026},
month = sep,
doi = {10.1128/asmcr.00062-26},
url = {https://europepmc.org/article/PMC/PMC13729740},
note = {CC BY},
}
RIS
TY - JOUR
TI - Clinical utility of whole-genome sequencing in identifying a rare Mycobacterium species causing native joint infection
AU - M. Globan
AU - J. Moselen
AU - N. Wang
AU - E. Steinig
AU - Y. Nong
AU - L. Viberg
AU - L. Caly
AU - K. A. Bond
PY - 2026
DA - 2026/09/23
JO - ASM case reports
DO - 10.1128/asmcr.00062-26
UR - https://europepmc.org/article/PMC/PMC13729740
AB - 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.
SN - 2996-2684
ER -