Evaluation of customised lineage-specific sets of MIRU-VNTR loci for genotyping Mycobacterium tuberculosis complex isolates in Ghana
Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana; Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland; Biochemistry Department, University of Ghana, Legon, Ghana; Genomics and Health Unit, Centre for Public Health Research, Valencia, Spain; CIBER (Centros de Investigación Biomédica en Red) in Epidemiology and Public Health, Madrid, Spain
Background: Different combinations of variable number of tandem repeat (VNTR) loci have been proposed for genotyping Mycobacterium tuberculosis complex (MTBC). Existing VNTR schemes show different discriminatory capacity among the six human MTBC lineages. Here, we evaluated the discriminatory power of a "customized MIRU12" loci format proposed previously by Comas et al. based on the standard 24 loci defined by Supply et al. for VNTR-typing of MTBC in Ghana. Method: One hundred and fifty-eight MTBC isolates classified into Lineage 4 and Lineage 5 were used to compare a customized lineage-specific panel of 12 MIRU-VNTR loci ("customized MIRU-12") to the standard MIRU-15 genotyping scheme. The resolution power of each typing method was determined based on the Hunter-Gaston- Discriminatory Index (HGDI). A minimal set of customized MIRU-VNTR loci for typing Lineages 4 (Euro-American) and 5 (M. africanum West African 1) strains from Ghana was defined based on the cumulative HGDI. Results and Conclusion: Among the 106 Lineage 4 strains, the customized MIRU-12 identified a total of 104 distinct genotypes consisting of 2 clusters of 2 isolates each (clustering rate 1.8%), and 102 unique strains while standard MIRU-15 yielded a total of 105 different genotypes, including 1 cluster of 2 isolates (clustering rate: 0.9%) and 104 singletons. Among, 52 Lineage 5 isolates, customized MIRU-12 genotyping defined 51 patterns with 1 cluster of 2 isolates (clustering rate: 0.9%) and 50 unique strains whereas MIRU-15 classified all 52 strains as unique. Cumulative HGDI values for customized MIRU-12 for Lineages 4 and 5 were 0.98 respectively whilst that of standard MIRU-15 was 0.99. A union of loci from the customised MIRU-12 and standard MIRU-15 revealed a set of customized eight highly discriminatory loci: 4052, 2163B, 40, 4165, 2165, 10,16 and 26 with a cumulative HGDI of 0.99 for genotyping Lineage 4 and 5 strains from Ghana. © 2014 Asante-Poku et al.
article; bacterial strain; bacterium isolation; controlled study; gene cluster; gene locus; genotype; Ghana; Hunter Gaston Discriminatory Index; Mycobacterium africanum; Mycobacterium tuberculosis; named inventories, questionnaires and rating scales; nonhuman; single nucleotide polymorphism; variable number of tandem repeat; clinical trial; epidemiology; genetics; genotype; human; isolation and purification; male; Mycobacterium tuberculosis; tuberculosis; Genotype; Ghana; Humans; Male; Minisatellite Repeats; Mycobacterium tuberculosis; Tuberculosis