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Transmission patterns of Mycobacterium leprae in the Comoros

S M Braet(1,4,10) A Jouet(2) M Ronse(4) W Mulders(4) M Van Dyck-Lippens(4) Y Assoumani(5) A Mzembaba(6) S H Grillone(6) N Attoumane(6) A Baco(6) C J Meehan(7) E Hasker(4) M Jackson(3) L Rigouts(4) P N Suffys(8) C Avanzi(3) P Supply(9) B C De Jong(4)

1:University of Antwerp; 2:Genoscreen; 3:Colorado State University; 4:Institute of Tropical Medicine, Antwerp; 5:Damien Foundation; 6:National Tuberculosis and Leprosy control Program, Moroni, Union of the Comoros; 7:Nottingham Trent University, Nottingham, UK; 8:Fiocruz, Rio de Janeiro, Brazil; 9:Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL (Center for Infection and Immunity of Lille), Lille, France; 10:Research Foundation Flanders, Brussels, Belgium

Despite a strong control program since 2008, leprosy remains highly endemic in the Comoros, with ongoing transmission. This study investigates the effectiveness of using multiple-locus variable number of tandem repeats (VNTR) analysis (MLVA) and SNP-typing on a targeted deep sequencing platform, (Deeplex Myc-Lep) to study Mycobacterium leprae transmission in the island.

A total of 1403 leprosy patients were enrolled, of which 290 biopsies with the highest bacterial load were processed using Deeplex Myc-Lep. From 256 biopsies, a VNTR-based phylogenetic tree was constructed based on their complete profiles (11 VNTR markers). SNP subtypes 1D (85.9%) and 1A (13.3%) were detected, correlating closely with VNTR-based branches. Two VNTR markers (6-3a and 12-5) lacked variability within the population. Among 97 distinct profiles, 45 (46%) VNTR profiles were clustered and 52 unique, with most of clustered patients living in proximity or self-reporting contact. However, only 50% of known contacts shared the same genotype. In 30 strains from 5 clusters with identical VNTR profiles, we performed whole-genome sequencing (WGS) to get deeper resolution at SNP level. The results showed a median of 5 SNPs (range 2-12) between strains from the same cluster. In this high burden setting, self-reported epidemiological links had low specificity for a transmission link relative to genotyping by VNTR profiling and/or whole genome sequencing. The proportion of leprosy due to recent transmission is underestimated, and improving the limit of detection for genotyping will allow for better transmission cluster definitions and develop new tools to track M. leprae spread between communities.

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