Van der Spoel van Dijk, AnnekeRigauts, LeenMakhoahle, Pakiso Moses2018-07-202018-07-202009-11http://hdl.handle.net/11660/8902With TB still a major threat worldwide and South Africa (SA) being one of the countries with the highest TB incidence, the development in the field of epidemiology gained importance to elucidate the history and dynamics of the disease. The aim of the study was to elucidate the diversity and historic origin of Mycobacterium tuberculosis (MTB) strains in the FS by studying the molecular epidemiology of isolates in three high burden areas. During 2001-2003 MTB isolates were collected during two studies in the FS from consenting patients and DNA from these isolates was further investigated in this study. It involved the use of molecular methods such as spoligotyping and 12MIRU-VNTR typing that provides unique patterns for different highly transmissible genotypes, permitting historic relationships and the origin of circulating strains to be deciphered and to make predictions concerning their spread. Multiplex PCR was used to further characterise the Beijing lineage types and complex software packages including the SpolDB3 and 4, Excell 2007 and MIRU-VNTRplus (to draw phylogenetic trees) aided the analysis of the results. Strains of the FS were found to be extremely diverse with spoligo analysis resulting in an overall diversity of 73% and 12 MIRU-VNTR analyses a diversity of 50%. Nine lineages, namely Beijing, Haarlem, LAM, S, T, X, CAS, M. bovis and U were represented by the FS isolates with the three main families (T, LAM and X) respresenting 67.6%. Spoligopattern diversity within each of these three families varied substantially from 76%, 56% and 80% for T, LAM and X respectively. The T family was the most prominent, but phylogenetic tree analysis comparing the results of different typing methods, except for one closely related T1 (SIT53) cluster, showed little relationship between them as expected from reports globally. SIT 53 strains were the most prominent family found amongst the T isolates FS stains. The LAM3/SIT33 was the largest clonal group of FS strains and showed little diversity even by MIRU-VNTR code analyses. Only 8 Beijing type isolates were present, a family that is prominent in the Western Cape and many other countries. Comparison of all strains to international strains on the MIRU-VNTRplus database shows that FS strains can be linked to other countries such as Uganda, Ghana, Cameroon, China, Delhi counties, Zimbabwe and Tanzania. Nevertheless, it remains hard to determine the detailed history of MTBC strains in the FS province. It was not possible to determine unique pattern for the MTB strain using the 12-loci based MIRU-VNTR typing methods. Given the fact that both the X3 and Beijing strains - dominant in the Western Cape – are less important in the FS, it is more likely that MTB in the FS migrated down from the Gauteng province and Northern countries including Uganda, Ghana, Zimbabwe and Cameroon where similar lineages are present. This study served as a pilot as it contains isolates collected in the mid 2001. The incidence of legal and illegal immigrants entering the country plus global economic partnership allowing people free movement in and out of the country might have changed the dynamics of the disease. A need for follow up on current strains is urgently required to detect changes that influence TB TB management in the FS.enMolecular epidemiologyMycobacterium tuberculosis -- South Africa -- Free StateMycobacterium tuberculosisTuberculosis -- TransmissionDissertation (M.Med.Sc. (Medical Microbiology))--University of the Free State, 2009DissertationUniversity of the Free State