Comparison of clinical characteristics, species composition and antimicrobial resistance in extrapulmonary nontuberculous mycobacteria with or without HIV co-infection

Abstract Background Clinical nontuberculous mycobacteria (NTM) isolates are increasing annually. Extrapulmonary specimens lack typical imaging features, hampering differentiation from Mycobacterium tuberculosis . HIV infection influences NTM species composition, yet stratified data on extrapulmonary NTM isolates—particularly the drivers of resistance differences—remain limited. Methods We retrospectively analyzed mycobacterial culture records from Shenzhen Third People’s Hospital (2020–2025). A total of 135 extrapulmonary NTM isolates were stratified by HIV status. Demographics, susceptibility to eight antimicrobials, species distribution, and specimen types were compared. Within-species subgroup analysis identified the primary resistance driver. Results Annual NTM isolates increased from 496 in 2020 to 1,012 in 2025, while the overall proportion remained stable. HIV co-infection was common (65/135, 47.8%). Species composition differed markedly: Mycobacterium avium complex (MAC) dominated HIV-positive cases (>93%), while rapidly growing mycobacteria were frequent in HIV-negative cases (40.0%). Rifampin resistance was most prevalent (91.38%). Before species adjustment, the risk of levofloxacin resistance was significantly higher in the HIV-positive group (RR = 1.56, P = 0.005). However, within-species analysis revealed no significant differences after Bonferroni correction, confirming that the observed intergroup difference in resistance was driven by species composition shifts rather than by HIV-induced phenotypic changes. Conclusions Resistance differences in HIV-associated extrapulmonary NTM isolates are primarily driven by species composition shifts, not by direct HIV-induced changes in bacterial resistance. This finding highlights a critical methodological caveat for clinical microbiology laboratories: when interpreting resistance data from mixed NTM populations, failure to adjust for species composition may lead to biased conclusions regarding host-associated resistance. These findings provide a baseline reference for optimizing NTM identification and empirical therapy for extrapulmonary mycobacteria-positive specimens, and underscore the necessity of species-level stratification in routine susceptibility reporting.