Table 1.
Antimicrobial susceptibility testing of Salmonella UGA isolates by disk diffusion.
Table 2.
Whole genome sequencing analysis.
Fig 1.
A maximum likelihood single-nucleotide polymorphism (SNP)–based phylogeny of S. Typhimurium isolates from Kenya between 2000 and 2011 associated with invasive disease.
The strains that were sequenced as part of this study are represented as UGA followed by a number, and all other strains were previously reported by the publications indicated in the “Reference” column. Names of genomes from this study are colored in pink, isolates from lineage 1 and lineage 2 identified previously by Okoro et al. [24] are colored in cyan and purple respectively, and all other genomes are colored in gray. The tree was rooted using the midpoint method in iTOL. The scale bar indicates number of substitutions per site. Bootstrap support are labeled on branches with black dots whose size correspond to bootstrap support values.
Fig 2.
Circular representation of the S. Typhimurium UGA14 genome including the chromosome and four plasmids.
The outermost four circles indicate start sites of genes. Starting on the outside, circles 1–2 consist of forward-strand gene products; circles 3–4 consist of reverse-strand gene products (colors represent the following categories: CDS, blue; tRNA, brown; rRNA; magenta; other, grey); circle 5 shows AMR genes; circle 6 shows mobile gene elements (insertion sequences and prophage genes); circles 7–9 show homologous regions of blastn search against near neighbors in GenBank (highly similar regions are shown in darker color); circle 8 shows GC content; circle 9 shows GC bias (G-C/G+C where green indicates values >1 and purple <1).
Table 3.
Non-typhoidal Salmonella clinical isolates.
Table 4.
UGA14 plasmid characteristics.
Fig 3.
Plasmid synteny between S. Typhimurium UGA14 plasmid pKST313-UGA14 and reference plasmids.
Comparisons were made using the Artemis Comparison Tool (ACT) [62]. (A) pKST313-UGA14 compared to reference plasmid pKST313 [21] with regions of homology indicated in red or blue (inversion), an AMR gene island indicated with a blue circle (dashed line), direct repeats in pKST313 highlighted in yellow, and loci of insertion and its target site duplication labeled with triangles. (B) Two inserted regions of pKST313-UGA14 are compared with potential donor organisms, Enterobacter hormaechei strain 34983 and Escherichia coli strain S43.
Fig 4.
Heatmaps of selected Biolog phenotypic array profiles for S. Typhimurium strains.
Data are grouped into categories based on their biological roles as either (A) chemicals and antimicrobials or (B) nutrients. S. Typhimurium reference strain ATCC 13311 (antibiotic susceptible and non-invasive) was compared to isolates UGA10 and UGA14. Each column represents the area under the curve (AUC) values computed by adding all OmniLog values at all time points. All raw AUC data is available in S1 Data. Blue represents low relative growth in a given condition while yellow represents high growth.
Fig 5.
S. Typhimurium isolates UGA14 and UGA10 displayed altered membrane permeability and zeta potential compared to the antimicrobial sensitive and non-invasive ATCC 13311 strain.
Both UGA14 and UGA10 displayed reduced (A) membrane permeability and a (B) more positive zeta potential compared to the reference strain ATCC 13311. Alterations in zeta potential were independent of growth conditions comprised of either Mueller Hinton Broth (MHB, unaltered at pH 7) or minimal media made with M9 salts supplemented as described in the Materials and Methods section (M9 Minimal) adjusted to either pH 5.5 or 7. (C) The minimum inhibitory concentration (MIC) of colistin is significantly reduced in minimal media conditions as compared to standard MHB susceptibility testing conditions. Uniquely for a Salmonella strain, UGA14 (D) displays growth on brilliant green agar indicating fermentation of lactose and/or sucrose, (E) contains an intact lac operon, and (F) contains a plasmid-mediated sucrose regulon. S. Typhimurium ATCC 14028 (labeled “14028” in (D)) is a highly virulent reference strain [113] that lacks the ability to ferment lactose and sucrose. Values plotted are mean ± standard deviation. Membrane permeability represent the average of nine independent experiments each recording 10,000 events. Zeta potential represent the average of triplicates from three independent experiments. MIC determinations represent the average of 2–4 independent experiments. Statistical significance was determined for UGA10 and UGA14 values compared to the reference strain ATCC 13311 with *P < 0.05, **P < 0.01 and ***P < 0.001.