<i>Salmonella</i> serovars detected from various sources in Kampala, Uganda.

<p><i>Salmonella</i> serovars detected from various sources in Kampala, Uganda.</p

Antimicrobial resistance structure in <i>Salmonella</i> from various sources revealed by Latent class analysis.

<p>Antimicrobial resistance structure in <i>Salmonella</i> from various sources revealed by Latent class analysis.</p

Archived <i>Salmonella</i> isolates collected from Uganda between 2003 and 2010.

<p>Archived <i>Salmonella</i> isolates collected from Uganda between 2003 and 2010.</p

Plots of the posterior distributions of the proportion of <i>Salmonella</i> from human wastewater (black), poultry (red) and Nakivubo Channel (green) that were resistant to eight antimicrobials: A, ampicillin; C, chloramphenicol; S, streptomycin; Su, sulfisoxazole; Sx, trimethoprim/sulfamethoxazole; T, tetracycline; Na, nalidixic acid and Cip, ciprofloxacin.

<p>Plots of the posterior distributions of the proportion of <i>Salmonella</i> from human wastewater (black), poultry (red) and Nakivubo Channel (green) that were resistant to eight antimicrobials: A, ampicillin; C, chloramphenicol; S, streptomycin; Su, sulfisoxazole; Sx, trimethoprim/sulfamethoxazole; T, tetracycline; Na, nalidixic acid and Cip, ciprofloxacin.</p

PFGE patterns in isolates of common <i>Salmonella</i> serovars.

<p>PFGE patterns in isolates of common <i>Salmonella</i> serovars.</p

Map of Kampala showing the 14 sampling sites.

<p>M1–M4: live poultry markets; N1–N3: sampling sites along Nakivubo Channel; S1–S2: ruminant slaughterhouses; S3: swine slaughterhouse; WTP: wastewater treatment plant; W1–W3: waste stabilization pond systems.</p

VP6 gene (segment 6).

<p>Maximum Likelihood phylogenetic trees of nucleotide sequences of rotavirus genome segment 6 of human and animal RVA strains circulating in Uganda, 2012–2014. Bootstrap values above 70 are shown for 1000 replicates. The Ugandan human strains are labelled with blue circles and the Ugandan animal strains with red triangles. Chicken strain RVA/Chicken-tc/GBR/Ch-2/1979/G3P[30] served as the outgroup. The scale bar at the bottom of the tree calibrates the genetic distance expressed as nucleotide substitution per site.</p

The maps of Uganda, Kampala and Masaka districts showing the hospitals and households at which the study children and animals (rotavirus positives that were sequenced) were recruited respectively.

<p>The maps of Uganda, Kampala and Masaka districts showing the hospitals and households at which the study children and animals (rotavirus positives that were sequenced) were recruited respectively.</p

NSP2 gene (segment 8).

<p>Maximum Likelihood phylogenetic trees of nucleotide sequences of genome segment 8 of human and animal RVA strains circulating in Uganda, 2012–2014. Bootstrap values above 70 are shown for 1000 replicates. The Ugandan human strains are labelled with blue circles and the Ugandan animal strains with red triangles. Pigeon strain RVA/Pigeon-tc/PN/PO-13/1983/G18P[17] served as the outgroup. The scale bar at the bottom of the tree calibrates the genetic distance expressed as nucleotide substitution per site.</p

VP4 gene (segment 4).

<p>Maximum Likelihood phylogenetic trees of nucleotide sequences of rotavirus genome segment 4 of human and animal RVA strains circulating in Uganda, 2012–2014. Bootstrap values above 70 are shown for 1000 replicates. The Ugandan human strains are labelled with blue circles and the Ugandan animal strains with red triangles. Chicken strain, RVA/Chicken-tc/GBR/Ch-2/1979/G3P[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178855#pone.0178855.ref030" target="_blank">30</a>] served as the outgroup. The scale bar at the bottom of the tree calibrates the genetic distance expressed as nucleotide substitution per site.</p