Enriched whole genome sequencing identified compensatory mutations in the RNA polymerase gene of rifampicin-resistant Mycobacterium leprae strains

Mallika Lavania,1 Itu Singh,1 Ravindra P Turankar,1 Anuj Kumar Gupta,2 Madhvi Ahuja,1 Vinay Pathak,1 Utpal Sengupta1 1Stanley Browne Laboratory, The Leprosy Mission Trust India, TLM Community Hospital Nand Nagari, 2Agilent Technologies India Pvt Ltd, Jasola District Centre, New Delhi, India Abstract: Despite more than three decades of multidrug therapy (MDT), leprosy remains a major public health issue in several endemic countries, including India. The emergence of drug resistance in Mycobacterium leprae (M. leprae) is a cause of concern and poses a threat to the leprosy-control program, which might ultimately dampen the achievement of the elimination program of the country. Rifampicin resistance in clinical strains of M. leprae are supposed to arise from harboring bacterial strains with mutations in the 81-bp rifampicin resistance determining region (RRDR) of the rpoB gene. However, complete dynamics of rifampicin resistance are not explained only by this mutation in leprosy strains. To understand the role of other compensatory mutations and transmission dynamics of drug-resistant leprosy, a genome-wide sequencing of 11 M. leprae strains – comprising five rifampicin-resistant strains, five sensitive strains, and one reference strain – was done in this study. We observed the presence of compensatory mutations in two rifampicin-resistant strains in rpoC and mmpL7 genes, along with rpoB, that may additionally be responsible for conferring resistance in those strains. Our findings support the role for compensatory mutation(s) in RNA polymerase gene(s), resulting in rifampicin resistance in relapsed leprosy patients. Keywords: leprosy, rifampicin resistance, compensatory mutations, next generation sequencing, relapsed, MDT, Indi

Detection of Mycobacterium lepromatosis in patients with leprosy in India

Madhvi Ahuja,1,* Mallika Lavania,1,* Itu Singh,1 Ravindra P Turankar,1 Seema Chhabra,2 Tarun Narang,3 Sunil Dogra,3 Utpal Sengupta1 1Department of Molecular Biology, Stanley Browne Laboratory, TLM Community Hospital, Delhi, India; 2Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India; 3Department of Dermatology Venereology and Leprology, Postgraduate Institute of Medical Education and Research, Chandigarh, India *These authors contributed equally to this work Introduction: The most commonly noted reactions in leprosy patients are type 1 reactions and erythema nodosum leprosum, with some rare phenomenon of host response known as Lucio phenomenon or leprosy of Lucio and Latapi which is caused by Mycobacterium lepromatosis. So far, no case of M. lepromatosis has been reported from India. Materials and methods: The main objective of this study was to detect any positive cases of M. lepromatosis in India with such a complication. We screened slit skin smear/biopsy samples from lepromatous leprosy (LL) patients reporting to The Leprosy Mission Community Hospitals across the country. Eighty-eight slit skin smears were collected from leprosy patients in 70% ethanol. DNA was extracted from all these samples. Polymerase chain reaction (PCR) was done for 2 genes; one set was for 16S rRNA and the other set was for coproporphyrinogen III oxidase (hemN) gene. Then, sequencing was done for all positive amplicons. Homology of the sequences was analyzed using the Basic Local Alignment Search Tool at the National Center of Biotechnology Information database. Results: Among 88 isolates, we found 4 positive cases for M. lepromatosis. All 4 were LL cases with a bacteriological index ranging from 2+ to 4+. On the basis of the National Center of Biotechnology Information Basic Local Alignment Search Tool analysis, the sequenced amplicons of both genes matched with the M. lepromatosis 16S rRNA and phosphofructokinase genes but not with hemN gene of lepromatosis. This is the first report for the presence of M. lepromatosis in LL cases from India.Conclusion: This new species M. lepromatosis exists beyond Mexico, Singapore and it is the cause of DLL in India also. It may cause dual infections along with M. leprae in endemic areas like India. Keywords: lepromatous leprosy, phosphofructokinase, M. lepromatosis, coproporphyrinogen III oxidase (hemN) gene, 16S rRNA gene

Detection of Mycobacterium lepromatosis in patients with leprosy in India [Retraction]

The Editor-in-Chief and Publisher of the Infection and Drug Resistance journal wishes to retract the published article.Concerns were raised about the data presented in the published article and a review was initiated. The review highlighted some potential issues relating to misinterpretation of results which led to the incorrect conclusions about the identity of Mycobacterium lepromatosis. Each of the four 16S rRNA sequences described in the study were supplied by the authors and reanalysed. None of the four sequences returned the highest match with M. lepromatosis and one sequence, CH4, returned a positive match for Corynebacterium casei. It was also observed that the three M. lepromatosis 16S rRNA sequences obtained from GenBank (EU203590, GQ900372, GQ900374) were homologous and shared the same phylogeny. However, this was not indicated in the article.Each of the three hemN sequences described in the study were also supplied by the authors and reanalyzed. None of the sequences returned the highest match with M. lepromatosis and two of the sequences (CH7 and CPH570) returned a close match with human DNA suggesting possible contamination of either the tissue sample or PCR reaction.The authors were asked to provide an explanation for these findings but were unable to provide a satisfactory response. It was therefore determined the findings and conclusions presented in the article were not supported. This retraction relates to this pape