A. Localization of the genotypes.

<p>Eleven repeated genotypes, which were observed in four or more isolates, are represented with colored squares on the map of the endemic areas of Alpes-Maritimes and Provence. The two endemic areas are separated by a blue line. The remaining genotypes are represented by light brown squares. The area in the black rectangle is shown in further detail in Fig 3B. B. Detailed localization of isolates in the Alpes-Maritimes endemic area and more precisely the surrounding region of Nice. Isolates were localized at the city level. The black line represents the delimitation of Nice.</p

Repeated genotypes.

<p>Arbitrary numbers assigned to the 30 repeated genotypes in (x-axis) and number of isolates belonging to each genotype (y-axis). The origin of each isolates is indicated by the different colors.</p

Geographical distribution of isolates from Southeastern France.

<p>Isolates clustered into four endemic areas. The geographic areas where samples were isolated from Cévennes (blue), Provence (green), Alpes-Maritimes (red) and Corsica (violet) are indicated. The Alpes-Maritimes and Provence endemic areas are located in the PACA region.</p

Temporal distribution of the 11 genotypes represented by more than four isolates.

<p>Temporal distribution of the 11 genotypes represented by more than four isolates.</p

Estimated population structure for <i>L</i>. <i>infantum</i> from Southeastern France assessed using STRUCTURE software based on the analysis of the 270 <i>L</i>. <i>infantum</i> DNA samples at 12 microsatellite markers.

<p><b>A</b>: The plots show the estimated membership coefficient (Q) of each isolates. Each isolate is represented by a single vertical line divided into K colors, in which K is the number of populations assumed. Each color represents one population, and the length of the colored segment shows the estimated proportion of isolates membership in that population. The derived graph for delta K shows K = 2, thereby indicating the presence of two populations in the investigated sample set. <b>B</b>: Isolates of the sub-populations A and B with delta K values for each sub-population. Two close values were observed for K in sub-population A: K = 4 and K = 6. For sub-population B, K = 2.</p

Unrooted neighbor-joining tree inferred from genetic distances derived from the proportion of alleles shared among the 270 isolates of <i>L</i>. <i>infantum</i> based on 12 microsatellite markers.

<p>The two populations defined using STRUCTURE are highlighted. The blue stars correspond to the non-MON-1 strains. At the end of each branche of the network, the first three characters correspond to the arbitrarily assigned number for each genotype, the following two characters (AM, P, Ce, Co) correspond to the endemic area of sample collection, and then the last two characters correspond to the number of isolates with the given genotype. The orange rectangles represent the isolates with mixed genotypes. The sub populations are represented with colored ovals at K = 6 for A sub-populations and K = 2 for B sub-populations. The isolates with no color are those with mixed genotypes within A sub-populations at K = 6. MEGA 4 software was used to visualize the neighbor-joining tree.</p

UPGMA tree based on the MIRU-VNTR (26 loci) and spoligotyping data.

<p>1, SB number = name of spoligotype based on <a href="http://www.Mbovis.org" target="_blank">http://www.Mbovis.org</a> database nomenclature; 2, RDAf1 = Genomic deletion specific to Af1 clonal complex; 3, The MIRU-VNTR patterns are detailed in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003142#pntd-0003142-t002" target="_blank">table 2</a>.</p

Spoligotypes, MIRU-VNTR patterns and clonal complex identification of the <i>M. bovis</i> strains isolated in Burkina Faso.

1<p><b>▪</b>, presence of spacer; <b>□</b>, absence of spacer.</p>2<p>MIRU-VNTR loci: ETR A, ETR B, ETR C, ETR D, ETR E, QUB-11a, QUB-11b, QUB-3232, QUB-26, QUB-4156, MIRU 2, MIRU 10, MIRU 16, MIRU 20, MIRU 23, MIRU 24, MIRU 26, MIRU 27, MIRU 39, MIRU 40, Mtub 04, Mtub 21, Mtub 29, Mtub 30, Mtub 34, Mtub 39. NA = Not Available.</p>3<p>Af1 = African 1 clonal complex, Af5 = putative African 5 clonal complex.</p><p>Spoligotypes, MIRU-VNTR patterns and clonal complex identification of the <i>M. bovis</i> strains isolated in Burkina Faso.</p

Allelic diversity of the 26 MIRU-VNTR loci in <i>M. bovis</i> isolates from humans and livestock in Burkina Faso.^*

<p>*Excluding one strain of the putative African 5 clonal complex that hasn't MIRU-VNTR data.</p><p>Af1 = African 1 clonal complex, Af5 = putative African 5 clonal complex.</p><p>Allelic diversity of the 26 MIRU-VNTR loci in <i>M. bovis</i> isolates from humans and livestock in Burkina Faso.^{<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003142#nt108" target="_blank">*</a>}</p

Socio-demographic informations about hosts and <i>M. bovis</i> isolates.

a<p>specific to human hosts,</p>b<p>bovine study,</p>c<p>nationwide survey,</p>d<p>regional study.</p><p>Socio-demographic informations about hosts and <i>M. bovis</i> isolates.</p