Additional file 1: Figure S1. of Phenotypic and genotypic monitoring of Schistosoma mansoni in Tanzanian schoolchildren five years into a preventative chemotherapy national control programme

Location of study sites in Tanzania. In order to collect S. mansoni miracidia, 7–11 year old children from two schools of Tanzania’s highly endemic Lake Victoria region were sampled. Bukindo Primary School is situated on Ukerewe Island inside Lake Victoria (Ukerewe District, Mwanza Region). The second school studied was Kisorya Primary School (Bunda District, Mara Region) which is located on the mainland. Both schools are in close proximity to the lakeshore. (TIFF 1924 kb

Geographical location of various study sites in Benin and Nigeria and the prevalence of <i>M. africanum</i> West Africa 1 (MAF1) and West Africa 2 (MAF2).

<p>Data from Benin was generated in the present study, the prevalence in Ibadan, Abuja and Nnewi was extracted and estimated from Lawson <i>et al.. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077000#pone.0077000-Lawson1" target="_blank">[9]</a>, whereas the prevalence in the Cross River State derived from Thumamo <i>et al.. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077000#pone.0077000-Thumamo1" target="_blank">[10]</a>.</p

Geographical distribution of identified <i>M. africanum</i> West Africa 1 (MAF1) sub-lineages.

<p>(CRS = Cross River State).</p

Population structure of <i>M. africanum</i> West Africa 1 (MAF1).

<p>A UPGMA tree was constructed including 141 MAF1 isolates from Benin, Sierra Leone and Nigeria. Ten sub-lineages were identified. Seven isolates could not be assigned to any of the defined sub-lineages.</p

Status of putative <i>M.</i> africanum operons essential for intracellular survival.

<p>Seven operons were previously defined as essential for growth within the macrophage <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002220#pntd.0002220-Rengarajan1" target="_blank">[13]</a>. Genes that are identical to the wildtype <i>M. tuberculosis</i> H37Rv gene homologue are displayed with a solid border line and white background. Genes, with a non-synonymous mutation are displayed in blue with dashed lines. Genes with a frameshift mutation, are displayed with striped background.</p

List of growth-attenuating genes with non-synonymous or frameshift mutations in <i>M. africanum</i>.

<p>List of growth-attenuating genes with non-synonymous or frameshift mutations in <i>M. africanum</i>.</p

A Mycobacterial Perspective on Tuberculosis in West Africa: Significant Geographical Variation of <i>M</i>. <i>africanum</i> and Other <i>M</i>. <i>tuberculosis</i> Complex Lineages

<div><p>Background</p><p>Phylogenetically distinct <i>Mycobacterium tuberculosis</i> lineages differ in their phenotypes and pathogenicity. Consequently, understanding mycobacterial population structures phylogeographically is essential for design, interpretation and generalizability of clinical trials. Comprehensive efforts are lacking to date to establish the West African mycobacterial population structure on a sub-continental scale, which has diagnostic implications and can inform the design of clinical TB trials.</p><p>Methodology/Principal Findings</p><p>We collated novel and published genotyping (spoligotyping) data and classified spoligotypes into mycobacterial lineages/families using TBLineage and Spotclust, followed by phylogeographic analyses using statistics (logistic regression) and lineage axis plot analysis in GenGIS, in which a phylogenetic tree constructed in MIRU-VNTRplus was analysed. Combining spoligotyping data from 16 previously published studies with novel data from The Gambia, we obtained a total of 3580 isolates from 12 countries and identified 6 lineages comprising 32 families. By using stringent analytical tools we demonstrate for the first time a significant phylogeographic separation between western and eastern West Africa not only of the two <i>M</i>. <i>africanum</i> (West Africa 1 and 2) but also of several major <i>M</i>. <i>tuberculosis sensu stricto</i> families, such as LAM10 and Haarlem 3. Moreover, in a longitudinal logistic regression analysis for grouped data we showed that <i>M</i>. <i>africanum</i> West Africa 2 remains a persistent health concern.</p><p>Conclusions/Significance</p><p>Because of the geographical divide of the mycobacterial populations in West Africa, individual research findings from one country cannot be generalized across the whole region. The unequal geographical family distribution should be considered in placement and design of future clinical trials in West Africa.</p></div

Longitudinal development of the <i>M</i>. <i>tuberculosis</i> complex in The Gambia between 2002–2010.

<p>1164 smear-positive pulmonary TB isolates were spoligotyped and assigned to lineages. We analyzed the longitudinal development of the six prevalent lineages over time, using logistic regression modelling for grouped data. As no lineage/time interaction or time as main effect was detected, the average prevalence and 95% confidence intervals for each lineage were estimated as follows: Euro-American: 57.2% (54.4%-60.0%); <i>M</i>. <i>africanum</i> West Africa 2 (MAF2): 35.4% (32.7%-38.2%); Indo-Oceanic: 4.3% (3.3%-5.6%); East Asian (Beijing): 2.5% (1.7%-3.6%); <i>M</i>. <i>africanum</i> West Africa 1 (MAF1): 1.0% (0.4%-2.4%); East African Indian 0.8% (0.2%-3.2%).</p

Phylogeographic analysis of major geographically restricted families using GenGIS.

<p><b>A.)</b> Phylogeography, in which an UPGMA tree that includes MAF1, MAF2, Haarlem 3 and LAM10 spoligotypes, is superimposed onto the geographical distribution map. Each spoligotype in the tree is linked to its actual location on the map and the crossing-overs of connecting lines can be counted. In case of no geographical separation crossings of the connecting lines would occur at random. If less crossings are observed than expected by chance geographical separation occurs, as for instance, at a geographic tree axis angle of 228.1° of these major four families. <b>B)</b> Linear axis plot scanning for axis angles of the superimposed phylogenetic tree onto the map, in which geographic separation occurs. The red line indicates the minimum number of crossings that would have been expected by chance at significance level p = 0.001. Every orientation of the tree onto the map that results in less crossings than expected by chance (9759.5) lies below the line and indicates significant geographical separation and can be observed between 110°-131°, 151°-170° and 217°- 270°. The most extreme geographical separation with the least crossings (9144) occurs at an angle of 228.1° (arrow) and is plotted in 2A.</p

<i>In vitro</i> growth curves from standardized inocula.

<p><i>M. tuberculosis</i> (solid line) and <i>M. africanum</i> (dashed line) were grown from standardized inocula in Bactec MGIT 960 and measured growth units (GU) are plotted versus time [days].</p