Source and location of <i>Salmonella</i> Weltevreden isolates contributing to this study.

<p>Source and location of <i>Salmonella</i> Weltevreden isolates contributing to this study.</p

Confocal fluorescence microscopy image of S. Typhimurium SL1344 and S. Weltevreden in epithelial cells.

<p>Image shows S. Typhimurium SL1344 (a; two hours and b; six hours) and S. Weltevreden (c; two hours and d; six hours) interacting with Hep-2 cells at two and six hours post exposure. Cell nuclei are stained with DAPI (blue), common surface antigens (CSA) on extracellular Salmonella bacteria are stained in red and the Salmonella (pSsaG) where GFP expressing and are visible in green (GFP).</p

Viable Salmonella recovered in gentamicin killing assay with epithelial cells.

<p>a) Plots showing viable Salmonella (CFU/mL) recovered two (black) and six hours (grey) post infection after an invasion assay with Hep-2 cells infected with S. Typhimurium SL1344, S. Weltevreden SW C2346, SW 10259 SW98_11262 and SW99_3134 (MOI, 50); error bars indicate standard deviation. b) Plot of six hour time point only. Two-way ANOVA multiple comparisons were performed, significance is highlight by the symbols (* p<0.05, **** p<0.0001).</p

The phylogenetic positioning of Salmonella Weltevreden within Salmonella enterica.

<p>Maximum likelihood phylogenetic tree showing S. Weltevreden in the context of 14 additional serovars of Salmonella enterica. 3,269 core genes from whole genome sequences, representing 3,161,517 bps, were used to construct this tree; SNPs were detected at 134,485 positions. S. Weltevreden is highlighted in red and the scale is shown.</p

Murine challenge with S. Weltevreden in comparison to S. Typhimurium SL1344.

<p>a) Survival plot showing percentage survival of C57bl/6 mice challenged with S. Typhimurium SL1344, S. Weltevreden C2346 and S. Weltevreden 10259 following intravenous infection. Assays were performed in triplicate. b) Plots showing colonization of the murine caecum by S. Typhimurium SL1344, S. Weltevreden C2346 or S. Weltevreden 10259 in C57bl/6 mice at four days post infection. Differences in bacterial load were determined using the Mann Whitney Test identified (* p<0.05) Assays were performed in triplicate.</p

The population structure of Salmonella Weltevreden.

<p>a) The locations of sampling in which the 115 S. Weltevreden isolates included in the study were isolated. Each colored marker (red for ‘Continental cluster’ and yellow for ‘Island cluster’) represents the phylogenetic cluster present in the location and the number of organisms isolated in each sampled location. b) Maximum likelihood phylogenetic tree constructed using 2,601 SNPs showing the population structure of S. Weltevreden isolates with key metadata. The outer most ring shows isolates with predicted resistance against antimicrobials. The second ring shows isolates with laboratory confirmed resistance against antimicrobials. The third ring shows clusters (defined by BAPS) and the fourth ring shows the sub-cluster. Nodes are colored by geographical region.</p

Summary of antimicrobial resistance genes identified in <i>Salmonella</i> Weltevreden and their nearest plasmid matches.

<p>Summary of antimicrobial resistance genes identified in <i>Salmonella</i> Weltevreden and their nearest plasmid matches.</p

Acquired multidrug-resistance in Nigerian <i>S</i>. Typhi isolates.

<p>Maximum likelihood tree of 128 Nigerian <i>S</i>. Typhi isolates from 2,541 SNPs is shown on the left. On the right is a heatmap which shows, for each isolate, its multidrug-resistant (MDR) status (purple), the presence of <i>gyrA</i> mutations (dark green S83Y; light green S83F), resistance genes <i>cat</i>, <i>blaTEM</i>, <i>dfrA</i>, <i>sul1/2</i>, <i>strAB</i>, <i>tetB/AR</i>, <i>qnr</i> (red) and plasmids, including IncHI1 (dark blue), Kpn3 (light blue), IncY (orange), IncQ1 (light pink), IncFIIs (yellow) and Col(RNAI) (magenta). Different colored bars within the plasmid column show isolates that harbor multiple plasmids with each bar representing a plasmid type. The absence of a genotype or plasmid was displayed in grey. Branch lengths are indicative of the estimated substitution rate per variable site.</p

Presence of antimicrobial resistance of <i>S</i>. Typhi in the study areas.

<p>The proportion of <i>S</i>. Typhi isolates that were resistant to one or more antimicrobials (red line) and were multidrug-resistant (MDR; defined as resistance to ampicillin, chloramphenicol and trimethoprim-sulfamethoxazole, blue line) are shown. Percentages are of the total <i>S</i>. Typhi isolated per year.</p

Distribution of Nigerian <i>S</i>. Typhi isolates in Africa in this study.

<p>A maximum likelihood tree of 366 <i>S</i>. Typhi isolates constructed using 9,352 SNPs from whole genome sequence from 128 Nigerian isolates and 238 isolates from other regions of Africa is shown on the left. The geographical location of isolation is highlighted on the maps of Africa displayed on the right (<a href="http://microreact.org/showcase/" target="_blank">http://microreact.org/showcase/</a>). <i>S</i>. Typhi isolates from Abuja (122 isolates) and Kano (6) are denoted using red and orange squares, respectively. Colored circles on both the tree and maps represent isolates from other regions of Africa. The common genotypes of the Nigerian isolate are highlighted by a grey ring surrounding the tree with the corresponding geographical location marked on the map. Branch lengths are indicative of the estimated substitution rate per variable site.</p