Mapping of Mycobacterium tuberculosis complex genetic diversity profiles in Tanzania and other African countries

Show simple item record Mbugi, Erasto V. Katale, Bugwesa Z. Streicher, Elizabeth M. Keyyu, Julius D. Kendall, Sharon L. Dockrell, Hazel M. Michel, Anita Luise Rweyemamu, Mark M. Warren, Robin M. Matee, Mecky I. Van Helden, Paul David Couvin, David Rastogi, Nalin 2016-07-07T07:26:22Z 2016-07-07T07:26:22Z 2016-05-05
dc.description S1 Fig. Spoligoforest tree drawn using the SpolTools software (available through http://; Reyes et al. [27], Tang et al. [26]), and shown as a Hierarchical Layout. The Figure was drawn on all patterns including orphan patterns (n = 293). Each spoligotype pattern from the study is represented by a node with area size being proportional to the total number of isolates with that specific pattern. Changes (loss of spacers) are represented by directed edges between nodes, with the arrowheads pointing to descendant spoligotypes. In this representation, the heuristic used selects a single inbound edge with a maximum weight using a Zipf model. Solid black lines link patterns that are very similar, i.e., loss of one spacer only (maximum weight being 1.0), while dashed lines represent links of weight comprised between 0.5 and 1, and dotted lines a weight less than 0.5. (PDF) en_ZA
dc.description S1 Table. Detailed demographic, epidemiologic and genotyping information on Tanzanian M. tuberculosis isolates. Note that all strains were pansusceptible, and were isolated from newly diagnosed, sputum smear/culture positive pulmonary TB patients. NEW SITs are followed by an asterisk ( ) and highlighted in yellow. Orphan spoligotypes are highlighted in blue. (PDF) en_ZA
dc.description.abstract The aim of this study was to assess and characterize Mycobacterium tuberculosis complex (MTBC) genotypic diversity in Tanzania, as well as in neighbouring East and other several African countries. We used spoligotyping to identify a total of 293 M. tuberculosis clinical isolates (one isolate per patient) collected in the Bunda, Dar es Salaam, Ngorongoro and Serengeti areas in Tanzania. The results were compared with results in the SITVIT2 international database of the Pasteur Institute of Guadeloupe. Genotyping and phylogeographical analyses highlighted the predominance of the CAS, T, EAI, and LAM MTBC lineages in Tanzania. The three most frequent Spoligotype International Types (SITs) were: SIT21/ CAS1-Kili (n = 76; 25.94%), SIT59/LAM11-ZWE (n = 22; 7.51%), and SIT126/EAI5 tentatively reclassified as EAI3-TZA (n = 18; 6.14%). Furthermore, three SITs were newly created in this study (SIT4056/EAI5 n = 2, SIT4057/T1 n = 1, and SIT4058/EAI5 n = 1). We noted that the East-African-Indian (EAI) lineage was more predominant in Bunda, the Manu lineage was more common among strains isolated in Ngorongoro, and the Central-Asian (CAS) lineage was more predominant in Dar es Salaam (p-value<0.0001). No statistically significant differences were noted when comparing HIV status of patients vs. major lineages (p-value = 0.103). However, when grouping lineages as Principal Genetic Groups (PGG), we noticed that PGG2/3 group (Haarlem, LAM, S, T, and X) was more associated with HIVpositive patients as compared to PGG1 group (Beijing, CAS, EAI, and Manu) (p-value = 0.03). This study provided mapping of MTBC genetic diversity in Tanzania (containing information on isolates from different cities) and neighbouring East African and other several African countries highlighting differences as regards to MTBC genotypic distribution between Tanzania and other African countries. This work also allowed underlining of spoligotyping patterns tentatively grouped within the newly designated EAI3-TZA lineage (remarkable by absence of spacers 2 and 3, and represented by SIT126) which seems to be specific to Tanzania. However, further genotyping information would be needed to confirm this specificity. en_ZA
dc.description.department Veterinary Tropical Diseases en_ZA
dc.description.librarian am2016 en_ZA
dc.description.sponsorship The Wellcome Trust Grant [WT087546MA] to EVM, MMR and MIM and by MUHAS Sida Sarec Small Grant [000/3177] to EVM, MIM and BZK. The Southern African Centre for Infectious Disease Surveillance (SACIDS) provided a Postdoctoral Research Fellowship to EVM and PhD candidacy for BZK. en_ZA
dc.description.uri en_ZA
dc.identifier.citation Mbugi EV, Katale BZ, Streicher EM, Keyyu JD, Kendall SL, Dockrell HM, et al. (2016) Mapping of Mycobacterium tuberculosis Complex Genetic Diversity Profiles in Tanzania and Other African Countries. PLoS ONE 11(5): e0154571. DOI: 10.1371/journal.pone.0154571. en_ZA
dc.identifier.issn 1932-6203
dc.identifier.other 10.1371/journal.pone.0154571
dc.language.iso en en_ZA
dc.publisher Public Library of Science en_ZA
dc.rights © 2016 Mbugi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License. en_ZA
dc.subject Tanzania en_ZA
dc.subject Pasteur Institute of Guadeloupe en_ZA
dc.subject Mycobacterium tuberculosis complex (MTBC) en_ZA
dc.subject Mycobacterium tuberculosis (MTB) en_ZA
dc.subject African countries en_ZA
dc.title Mapping of Mycobacterium tuberculosis complex genetic diversity profiles in Tanzania and other African countries en_ZA
dc.type Article en_ZA

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