Genomic Characterization of Mycobacterium leprae to Explore Transmission Patterns Identifies New Subtype in Bangladesh

Abstract

Mycobacterium leprae, the causative agent of leprosy, is an unculturable bacterium with a considerably reduced genome (3.27 Mb) compared to homologues mycobacteria from the same ancestry. In 2001, the genome of M. leprae was first described and subsequently four genotypes (1-4) and 16 subtypes (A-P) were identified providing means to study global transmission patterns for leprosy. In order to understand the role of asymptomatic carriers we investigated M. leprae carriage as well as infection in leprosy patients (n = 60) and healthy household contacts (HHC; n = 250) from Bangladesh using molecular detection of the bacterial element RLEP in nasal swabs (NS) and slit skin smears (SSS). In parallel, to study M. leprae genotype distribution in Bangladesh we explored strain diversity by whole genome sequencing (WGS) and Sanger sequencing. In the studied cohort in Bangladesh, M. leprae DNA was detected in 33.3% of NS and 22.2% of SSS of patients with bacillary index of 0 whilst in HHC 18.0% of NS and 12.3% of SSS were positive. The majority of the M. leprae strains detected in this study belonged to genotype 1D (55%), followed by 1A (31%). Importantly, WGS allowed the identification of a new M. leprae genotype, designated 1B-Bangladesh (14%), which clustered separately between the 1A and 1B strains. Moreover, we established that the genotype previously designated 1C, is not an independent subtype but clusters within the 1D genotype. Intraindividual differences were present between the M. leprae strains obtained including mutations in hypermutated genes, suggesting mixed colonization/infection or in-host evolution. In summary, we observed that M. leprae is present in asymptomatic contacts of leprosy patients fueling the concept that these individuals contribute to the current intensity of transmission. Our data therefore emphasize the importance of sensitive and specific tools allowing post-exposure prophylaxis targeted at M. leprae-infected or -colonized individuals.

Leprosy in wild chimpanzees

“…SNPs of the two newly sequenced genomes from chimpanzees were compared to the 263 publicly available M. leprae genomes (Supplementary Table 2) 25,60,62–64 and 21 new genomes from West African countries (Supplementary Information Note 5). Phylogenetic analyses were performed using a concatenated SNP alignment (Supplementary Table 3).…”

Blood RNA signature RISK4LEP predicts leprosy years before clinical onset

“…In the past years, several studies have searched for biomarkers to (early) detect leprosy either based on the host immune response [26] , [27] , [28] , [29] , [30] , [31] , the pathogen [32] , [33] , [34] , [35] , [36] , [37] , or a combination of both [38] , [39] , [40] , [41] , [42] , [43] , [44] , [45] . Molecular detection by identification of the repetitive element RLEP by (quantitative) PCR [ 33 , 46 , 47 ] as well as detection of anti- M. leprae phenolic glycolipid I (PGL-I) IgM in blood [ 28 , 29 ] are methods employed to assist leprosy diagnosis.…”

“…Molecular detection by identification of the repetitive element RLEP by (quantitative) PCR [ 33 , 46 , 47 ] as well as detection of anti- M. leprae phenolic glycolipid I (PGL-I) IgM in blood [ 28 , 29 ] are methods employed to assist leprosy diagnosis. Nevertheless, the sensitivity of these techniques to identify paucibacillary (PB) leprosy is not sufficient due to the low concentrations of bacilli in these patients [ 26 , 44 , 45 ]. On the other hand, PCR and anti-PGL-IgM, though useful to detect infection, are inadequate predictors of disease amongst HC of leprosy patients, as individuals remaining without disease may present positive PCR and/or PGL-I IgM [ 28 , 32 , 35 , 44 , 45 ].…”

“…Nevertheless, the sensitivity of these techniques to identify paucibacillary (PB) leprosy is not sufficient due to the low concentrations of bacilli in these patients [ 26 , 44 , 45 ]. On the other hand, PCR and anti-PGL-IgM, though useful to detect infection, are inadequate predictors of disease amongst HC of leprosy patients, as individuals remaining without disease may present positive PCR and/or PGL-I IgM [ 28 , 32 , 35 , 44 , 45 ]. In addition, combinations of other host proteins [ 24 , 27 ] have been shown to be useful to diagnose leprosy and detect M. leprae infection, but have not been studied prospectively yet.…”

In search of biomarkers for leprosy by unraveling the host immune response to Mycobacterium leprae

“…Biomarkers based on the host immune response to M leprae are thus ideally suited to aid in the diagnosis of leprosy patients, especially since the detection of M leprae is difficult in self-limited and preclinical stages of the disease. 8…”