When “Leprosy” Is Not Leprosy by Polymerase Chain Reaction: Detection of Nontuberculous Mycobacterial Deoxyribonucleic Acid in Nasal Swabs from Patients with Chronic Skin Lesions in a Leprosy-endemic Area

Abstract

BACKGROUND: Leprosy remains a major cause of chronic dermatoneurological morbidity in endemic settings, and early etiologic confirmation is often challenging in primary care, where diagnosis may remain syndromic. Molecular testing can strengthen confirmation of Mycobacterium leprae , yet performance depends on specimen type and target selection, and leprosy-like phenotypes may overlap with cutaneous disease caused by nontuberculous mycobacteria (NTM). This study evaluated paired nasal versus buccal mucosal swabs from patients with chronic skin lesions and clinical suspicion of leprosy to characterize mycobacterial deoxyribonucleic acid (DNA) signals using a stepwise molecular workflow. METHODS: A cross-sectional study (September-November 2025) enrolled consecutive patients presenting to primary health centers (Puskesmas) in Palu City, Indonesia, with chronic cutaneous lesions (>2 weeks). Each participant contributed paired nasal and buccal swabs (140 specimens from 70 participants). DNA was extracted using a silica column method. Conventional polymerase chain reaction (PCR) targeting the M. leprae proline-rich antigen (PRA) gene was performed, followed - when indicated - by genus-level Mycobacterium 16S ribosomal ribonucleic acid (16S rRNA) PCR and additional species-associated targets; 16S rRNA-positive amplicons underwent Sanger sequencing with Basic Local Alignment Search Tool (BLAST)-based taxonomic assignment. Paired nasal-buccal positivity was compared using McNemar testing. RESULTS: All mucosal specimens were negative for M. leprae by PRA PCR (0/140). Genus-level 16S rRNA PCR detected Mycobacterium spp. DNA in 20/140 specimens (14.3%; 95% confidence interval [CI]: 9.4-21.0) and in 20/70 participants (28.6%; 95% CI: 19.3-40.1). Positivity was substantially higher in nasal swabs (18/70; 25.7%) than buccal swabs (2/70; 2.9%), with discordant paired results and no participants positive at both sites (McNemar exact P = 0.0004). Sequencing produced valid BLAST similarity outputs in 19/20 positive specimens; closest matches were most frequently to Mycobacterium parmense (13/19; 68.4%) and Mycobacterium kyogaense (6/19; 31.6%). CONCLUSIONS: In this endemic primary care cohort with chronic skin lesions, mucosal swab PCR targeting the single-gene PRA locus did not detect M. leprae , while a subset showed genus-level Mycobacterium DNA signals - predominantly from nasal swabs - with 16S rRNA sequences most closely aligned with uncommon NTM lineages. These findings support broadening diagnostic consideration beyond M. leprae when mucosal single-target PCR is uniformly negative. Because mucosal detection cannot establish lesion causality and partial 16S rRNA reads have limited species-level resolution, lesion-based sampling and higher-resolution confirmation (culture and/or multilocus sequencing) are warranted; escalation to more sensitive M. leprae targets (e.g., multicopy loci) may also be appropriate when clinical suspicion persists.

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