title: Diverse Molecular Genotypes of Mycobacterium tuberculosis Complex Isolates Circulating in the Free State, South Africa.
abstract: Tuberculosis is a serious public health concern especially in Africa and Asia. Studies describing strain diversity are lacking in the Free State region of South Africa. The aim of the study was to describe the diversity of Mycobacterium tuberculosis (M. tuberculosis) strain families in the Free State province of South Africa. A total of 86 M. tuberculosis isolates were genotyped using spoligotyping. A 12-locus mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTRs) typing was used to further characterize the resulting spoligotyping clusters. SITVITWEB identified 49 different patterns with allocation to six lineages including Latin-American-Mediterranean (LAM) (18 isolates), T (14 isolates), Beijing (five isolates), S (six isolates), Haarlem (one isolate), and X (five isolates), while 37 (43.0%) orphans were identified. Eight clusters included 37 isolates with identical spoligotypes (2 to 13/cluster). MIRU-VNTR typing further differentiated three spoligotyping clusters: SIT1/Beijing/MIT17, SIT33/LAM3/MIT213, and confirmed one SIT34/S/MIT311. In addition, SpolDB3/RIM assignment of the orphan strains resulted in a further 10 LAM and 13 T families. In total, LAM (28 isolates) and T (27 isolates) cause 63% of the individual cases of MTB in our study. The Free State has a highly diverse TB population with LAM being predominant. Further studies with inclusion of multidrug-resistant strains with larger sample size are warranted.
authors.affiliation: Department of Medical Microbiology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa; National Health Laboratory Service, Universitas Academic Laboratory, Bloemfontein 9301, South Africa.
authors.forename: Anneke
authors.identifier: 0000-0003-3892-8499
authors.initials: A
authors.lastname: Van der Spoel van Dijk
authors.affiliation: Unit for Drug Discovery Research, Department of Health Sciences, Biomedical Technology, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, South Africa.
authors.forename: Pakiso M
authors.identifier: 0000-0001-6131-9419
authors.initials: PM
authors.lastname: Makhoahle
authors.affiliation: Mycobacteriology Unit, Institute of Tropical Medicine, Nationalestraat 155, 2000 Antwerp, Belgium; University of Antwerp, 2000 Antwerp, Belgium.
authors.forename: Leen
authors.initials: L
authors.lastname: Rigouts
authors.affiliation: Department of Medical Microbiology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa; National Health Laboratory Service, Universitas Academic Laboratory, Bloemfontein 9301, South Africa.
authors.forename: Kamaldeen
authors.identifier: 0000-0001-8270-8683
authors.initials: K
authors.lastname: Baba