MICs and relative resistance of rifampicin and rifabutin in <i>M. tuberculosis.</i>

a<p>Twenty-five clinical isolates with unknown genotype plus one H37Rv strain were included as controls.</p>b<p>RR indicates relative resistance: Mutant MIC/Wild-type MIC.</p

Drug resistance mutation pattern in a convenience sample of 41 MDR Beijing isolates from the Western Cape.

<p>No data was available for the streptomycin resistance determining region in <i>rrs</i> (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070919#pone-0070919-t001" target="_blank">Table 1</a>). For more information see figure legend of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070919#pone-0070919-g003" target="_blank">Figure 3</a>.</p

Strain population structure of drug-sensitive (DS), mono-/poly-resistant (DR), <i>sensu stricto</i> multidrug-resistant (MDR <i>s.s.</i>; excluding identified pre-XDR and XDR isolates), pre-extensively drug-resistant (pre-XDR) and extensively drug resistant (XDR) isolates in three provinces of South Africa.

<p>The R220, R86 and F15/LAM4/KZN genotypes, respectively, represent a subgroup of the typical Beijing, “atypical” Beijing and LAM4 family <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070919#pone.0070919-Strauss1" target="_blank">[14]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070919#pone.0070919-Pillay1" target="_blank">[16]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070919#pone.0070919-Muller2" target="_blank">[22]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070919#pone.0070919-Gandhi2" target="_blank">[24]</a>. Based on similar IS<i>6110</i> RFLP patterns and whole genome sequencing data it was previously shown that “atypical” Beijing strains in the Western and Eastern Cape, unlike in other parts of the world, represent one single genotype herein referred to as R86 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070919#pone.0070919-Chihota1" target="_blank">[23]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070919#pone.0070919-Ioerger1" target="_blank">[25]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070919#pone.0070919-Klopper1" target="_blank">[27]</a>. The specific presence of R220 and F15/LAM4/KZN genotypes was only assessed in the Western Cape and KwaZulu-Natal, respectively, where these genotypes were known to be frequent among XDR-TB cases <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070919#pone.0070919-Muller2" target="_blank">[22]</a>.</p

Drug resistance mutation pattern in a random selection of 193 MDR R86 isolates from the Eastern Cape.

<p>Different colours indicate different drug resistance associated genes. The area of the circles is proportional to the number of isolates (indicated in the centre of each circle) harbouring an identical drug resistance mutation for the respective resistance gene as well as all circles connected to the left. Principal branches of the tree were defined by resistance mutations in <i>pncA</i>. Other first-line drug resistance mutations were connected by logical deduction to maximize clustering and were followed by second-line resistance mutations. However, the order of acquisition of resistance mutations may remain debatable in some cases.</p

Selection of study population.

<p>Grey boxes indicate sample sets used to analyze the strain population structures in the three South African provinces. Boxes with striped pattern indicate sample sets used to characterize drug resistance mutation patterns among XDR-TB associated genotypes. ^a) Computer-based random sampling was applied. ^b) Review of an extensive collection of data generated within multiple previous studies.</p

Geographical distribution of selected clusters of isolates.

<p>EC: Eastern Cape Province.</p><p>WC: Western Cape Province.</p><p>N_isolate: Number of isolates of a cluster detected in the municipal district indicated.</p><p>%: Proportion of isolates of a cluster detected in the municipal district indicated.</p

Drug resistance-associated genetic regions analyzed.

*<p>Genetic region covered by PCR with respect to nucleotide positions in H37Rv.</p><p>H: Isoniazid.</p><p>Eto: Ethionamide.</p><p>R: Rifampicin.</p><p>E: Ethambutol.</p><p>Z: Pyrazinamid.</p><p>S: Streptomycin.</p><p>Km: Kanamycin.</p><p>Am: Amikacin.</p><p>Cm: Capreomycin.</p><p>FQ: Fluoroquinolone.</p><p>Ofx: Ofloxacin.</p

Model for the evolution of XDR-TB associated strain families.

<p>Model for the evolution of XDR-TB associated strain families.</p

Geospatial distribution of <i>Mycobacterium tuberculosis</i> genotypes in Africa

<div><p>Objective</p><p>To investigate the distribution of <i>Mycobacterium tuberculosis</i> genotypes across Africa.</p><p>Methods</p><p>The SITVIT2 global repository and PUBMED were searched for spoligotype and published genotype data respectively, of <i>M</i>. <i>tuberculosis</i> from Africa. <i>M</i>. <i>tuberculosis</i> lineages in Africa were described and compared across regions and with those from 7 European and 6 South-Asian countries. Further analysis of the major lineages and sub-lineages using Principal Component analysis (PCA) and hierarchical cluster analysis were done to describe clustering by geographical regions. Evolutionary relationships were assessed using phylogenetic tree analysis.</p><p>Results</p><p>A total of 14727 isolates from 35 African countries were included in the analysis and of these 13607 were assigned to one of 10 major lineages, whilst 1120 were unknown. There were differences in geographical distribution of major lineages and their sub-lineages with regional clustering. Southern African countries were grouped based on high prevalence of LAM11-ZWE strains; strains which have an origin in Portugal. The grouping of North African countries was due to the high percentage of LAM9 strains, which have an origin in the Eastern Mediterranean region. East African countries were grouped based on Central Asian (CAS) and East-African Indian (EAI) strain lineage possibly reflecting historic sea trade with Asia, while West African Countries were grouped based on Cameroon lineage of unknown origin. A high percentage of the Haarlem lineage isolates were observed in the Central African Republic, Guinea, Gambia and Tunisia, however, a mixed distribution prevented close clustering.</p><p>Conclusions</p><p>This study highlighted that the TB epidemic in Africa is driven by regional epidemics characterized by genetically distinct lineages of <i>M</i>. <i>tuberculosis</i>. <i>M</i>. <i>tuberculosis</i> in these regions may have been introduced from either Europe or Asia and has spread through pastoralism, mining and war. The vast array of genotypes and their associated phenotypes should be considered when designing future vaccines, diagnostics and anti-TB drugs.</p></div

Clustering of countries according the proportion of <i>M</i>. <i>tuberculosis</i> isolates present in a specific lineage.

<p>Only data from the Beijing, Cameroon, CAS, EAI, H, LAM, Manu, and S lineages was included. Country codes according to (<a href="http://www.worldatlas.com/aatlas/ctycodes.htm" target="_blank">http://www.worldatlas.com/aatlas/ctycodes.htm</a>). (A) Principle component analysis: African countries in the PCA plot are coloured based on their most dominant lineage: CAS (red), Cameroon (green), H (purple), LAM (brown), Manu (blue), and EAI (yellow). European and Asian countries are shown in black. Overlapping country codes in the PCA plot indicate a similar distribution of <i>M</i>. <i>tuberculosis</i> lineages in the respective countries. (B) pvclust analysis: The clusters edges are numbered in grey and the AU p-values are shown in black. Strongly supported clusters with AU greater than 95% are highlighted with a dotted line.</p