dc.contributor.author |
Mbugi, Erasto V.
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dc.contributor.author |
Katale, Bugwesa Z.
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dc.contributor.author |
Streicher, Elizabeth M.
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dc.contributor.author |
Keyyu, Julius D.
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dc.contributor.author |
Kendall, Sharon L.
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dc.contributor.author |
Dockrell, Hazel M.
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dc.contributor.author |
Michel, Anita Luise
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dc.contributor.author |
Rweyemamu, Mark M.
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dc.contributor.author |
Warren, Robin M.
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dc.contributor.author |
Matee, Mecky I.
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dc.contributor.author |
Van Helden, Paul David
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dc.contributor.author |
Couvin, David
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dc.contributor.author |
Rastogi, Nalin
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dc.date.accessioned |
2016-07-07T07:26:22Z |
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dc.date.available |
2016-07-07T07:26:22Z |
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dc.date.issued |
2016-05-05 |
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dc.description |
S1 Fig. Spoligoforest tree drawn using the SpolTools software (available through http://
www.emi.unsw.edu.au/spolTools; 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 |
http://www.plosone.org |
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 |
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dc.identifier.other |
10.1371/journal.pone.0154571 |
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dc.identifier.uri |
http://hdl.handle.net/2263/54067 |
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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 |