Mycobacterium leprae in Colombia described by SNP7614 in gyrA, two minisatellites and geography

• Published in: Infection, genetics and evolution genetics and evolution, 2013-03, Vol.14, p.375-382
• Main Authors: Cardona-Castro, Nora, Beltrán-Alzate, Juan Camilo, Romero-Montoya, Irma Marcela, Li, Wei, Brennan, Patrick J., Vissa, Varalakshmi
• Format: Article
• Language: English
• Subjects: agarose; alleles; cities; Colombia - epidemiology; DNA; DNA Gyrase - genetics; drug resistance; ecology; gel electrophoresis; genetic markers; Genotype; geographic information systems; gyrA; Humans; latitude; Leprosy; Leprosy - epidemiology; loci; longitude; minisatellite repeats; Minisatellite Repeats - genetics; monitoring; Mycobacterium leprae; Mycobacterium leprae - genetics; patients; polymerase chain reaction; Polymorphism, Single Nucleotide; restriction fragment length polymorphism; rivers; single nucleotide polymorphism; SNP; SNP7614; Topography, Medical; VNTR; World Health Organization
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2012.12.015

•Affordable geographic and molecular tools to map leprosy strains in Colombia. • With only three markers, multiple Mycobacterium leprae genotypes were detected; two were predominant. • The dominant genotype in Atlantic region is gyrA SNP7614 (C)/27-5(5)/12-5(4) [C54]. • The dominant genotype is gyrA SNP7614 (T)/27-5(4)/12-5(5) [T45] in the Andean region. New cases of leprosy are still being detected in Colombia after the country declared achievement of the WHO defined ‘elimination’ status. To study the ecology of leprosy in endemic regions, a combination of geographic and molecular tools were applied for a group of 201 multibacillary patients including six multi-case families from eleven departments. The location (latitude and longitude) of patient residences were mapped. Slit skin smears and/or skin biopsies were collected and DNA was extracted. Standard agarose gel electrophoresis following a multiplex PCR-was developed for rapid and inexpensive strain typing of Mycobacterium leprae based on copy numbers of two VNTR minisatellite loci 27-5 and 12-5. A SNP (C/T) in gyrA (SNP7614) was mapped by introducing a novel PCR-RFLP into an ongoing drug resistance surveillance effort. Multiple genotypes were detected combining the three molecular markers. The two frequent genotypes in Colombia were SNP7614(C)/27-5(5)/12-5(4) [C54] predominantly distributed in the Atlantic departments and SNP7614 (T)/27-5(4)/12-5(5) [T45] associated with the Andean departments. A novel genotype SNP7614 (C)/27-5(6)/12-5(4) [C64] was detected in cities along the Magdalena river which separates the Andean from Atlantic departments; a subset was further characterized showing association with a rare allele of minisatellite 23-3 and the SNP type 1 of M. leprae. The genotypes within intra-family cases were conserved. Overall, this is the first large scale study that utilized simple and rapid assay formats for identification of major strain types and their distribution in Colombia. It provides the framework for further strain type discrimination and geographic information systems as tools for tracing transmission of leprosy.