Classic and new candidate markers for drug resistance in a large cohort of leprosy patients from the Amazon state, Brazil.

Multidrug therapy for leprosy is highly effective and the recommended standard of care for leprosy worldwide. However, reports of antimicrobial resistance (AMR) have emerged globally. This study aimed to estimate the frequency of primary and secondary AMR associated with leprosy in patients treated at the Alfredo da Matta Foundation, Manaus, Amazonas, Brazil, as well as to determine the circulating subtypes of Mycobacterium leprae in this population. A total of 315 biopsy samples were investigated for variants in leprosy AMR-associated genes (rpoB, folP1, gyrA); a subset of 163 samples was also investigated for 5 additional candidate genes: gyrB, ctpC, ctpI, ribD, and fadD9. Patients were categorized into new cases, relapses, and suspected treatment failures. For statistical analysis, Pearson's chi-square or Fisher's exact test was employed for categorical variables, while mean and SD were calculated for continuous variables, with a significance level of 5%. Variant analysis detected 10 resistant M. leprae isolates displaying mutations in the rpoB (2, 0.6%) and folP1 (8, 2.5%) genes. In addition, variants in gyrB (1, 0.6%), ctpC (6, 3.7%), ribD (4, 2.4%), and fadD9 (15, 9.2%) were detected. Nine out of 10 resistant isolates were observed in the relapse group (P = 0,0014). Despite the low variant frequencies observed, variant detection highlights the need for expanded antimicrobial monitoring and surveillance. The impact of mutations in ribD and fadD9 on therapeutic response remains unclear, underscoring the need for further research. Genotyping revealed subtype-4 predominance (79.6%). Our findings highlight the importance of comprehensive AMR monitoring, particularly in relapse cases.