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NTM detection in a culture negative skin biopsy using bacterial sequencing: a case report

T Chin(1) M Vanhee(1) J Van Praet(1) A Muyldermans(1) K Floré(1) M Reynders(1)

1:General Hospital Sint-Jan Brugge

In our laboratory, we employ targeted sequencing when other diagnostic methods yield inconclusive results. While 16S sequencing can identify NTM species, its taxonomic resolution is limited. Subsequent hsp65 sequencing enhances species specificity. An important advantage of sequencing is its capacity to directly analyse samples without incubation, conserving crucial turnaround time. Following case illustrates its significant added value in NTM diagnostics.

A 51-year-old male presented with extensive skin lesions on all limbs and his trunk. He had undergone allogeneic stem cell transplantation for myelodysplastic syndrome two months prior. Initial differential diagnoses included acute graft-versus-host disease, erythema nodosum, soft tissue infection, and drug eruption. A skin biopsy revealed septal panniculitis with purulence. Tuberculosis PCR, Mucorales PCR, bacterial and fungal cultures  yielded no results. Although mycobacterial culture also remained negative, direct 16S sequencing of the sample complemented by hsp65 sequencing identified M. chelonae.

Two months later, a subsequent skin biopsy was cultured prior to initiating quadruple therapy comprising clarithromycin, doxycycline, moxifloxacin and amikacin. This time, mycobacterial culture (MGIT) grew acid-fast bacilli after 9 days of incubation. 16S and hsp65 sequencing on the MGIT medium confirmed M. chelonae once again. Antibiogram revealed no resistance, and the patient’s symptoms are steadily improving.

In conclusion, direct sequencing of samples expedites NTM detection, bypassing the need for culture growth, thus saving valuable time. In some cases, sequencing can detect NTM even when mycobacterial cultures remain negative, thus improving diagnostic sensitivity. Additionally, sequencing provides species identification, guiding further clinical management.

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