title: Genomic diversity in Mycobacterium leprae isolates from leprosy cases in South India.
abstract: The Objective of this study was to identify the strain diversity of Mycobacterium leprae in terms of SNP types and subtypes stratified as per genomic single nucleotide polymorphisms, in clinical isolates of leprosy patients from a tertiary care leprosy center in South India. Further, the associations of SNP types with clinical outcomes in leprosy were also investigated.
  
  
  
  DNA was extracted from excisional skin biopsies of a total of 172 newly diagnosed untreated leprosy patients from a clinic in Tamil Nadu, in south India, that also serves patients from neighboring states. All the leprosy patients were those who voluntarily reported at the clinic during the study period of one year i.e., 2015. Clinical and histopathological details were collected at diagnosis and leprosy was confirmed through bacteriological smear examination and PCR for M. leprae specific RLEP region. SNP types and subtypes were determined by PCR amplification and Sanger sequencing of PCR products.
  
  
  
  M. leprae specific RLEP gene amplification was achieved in 160 out of 172 patients. Among 160 specimens 118(73.75%) were type 1 and 42 (26.25%) were type 2 and on subtyping it was noted that 88/160 (55.00%) were 1D, 25/160 (15.62%) 1C, 5/160 (3.12%) 1A, 33/160 (20.62%) 2G and 9/160 (5.62%) were 2H.
  
  
  
  Our results indicated that subtype 1D is predominant in the south Indian population. We also noted 2G, 1C and 1A in the patient sample tested. Additionally we identified subtype 2H for the first time in India.
authors.affiliation: Molecular Biology Lab, Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC), Karigiri, Vellore, Tamil Nadu 632106, India. Electronic address: madhusmitadas21@gmail.com.
authors.forename: Madhusmita
authors.initials: M
authors.lastname: Das
authors.affiliation: Molecular Biology Lab, Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC), Karigiri, Vellore, Tamil Nadu 632106, India.
authors.forename: V Sundeep
authors.initials: VS
authors.lastname: Chaitanya
authors.affiliation: Molecular Biology Lab, Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC), Karigiri, Vellore, Tamil Nadu 632106, India.
authors.forename: K
authors.initials: K
authors.lastname: Kanmani
authors.affiliation: Molecular Biology Lab, Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC), Karigiri, Vellore, Tamil Nadu 632106, India.
authors.forename: Lakshmi
authors.initials: L
authors.lastname: Rajan
authors.affiliation: Molecular Biology Lab, Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC), Karigiri, Vellore, Tamil Nadu 632106, India.
authors.forename: Mannam
authors.initials: M
authors.lastname: Ebenezer
mesh_terms: D000293:Adolescent; D000328:Adult; D002648:Child; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D005260:Female; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D007194:India / Q000453:epidemiology; D007918:Leprosy / Q000453:epidemiology / Q000382:microbiology*; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D009166:Mycobacterium leprae / Q000235:genetics*; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D055815:Young Adult
chemical_list: D004269:DNA, Bacterial
keywords: Bacteriological index; Genetic diversity; Mycobacterium leprae; Ridley Jopling classification; Single nucleotide polymorphisms; Strain types