Fig 1.
Maximum-likelihood phylogeny of 270 S. Typhimurium and monophasic S. Typhimurium isolates from Colombia.
Maximum likelihood phylogeny demonstrating the population structure of S. Typhimurium ST19, ST34, ST313 and other sequence types. Twenty-three contextual S. Typhimurium genomes are shown as red branches with red labels for each. The coloured rings indicate, from inside to outside, the clusters (defined at the HC100 level), sub-clusters (defined at the HC50 level), serovars (defined by the presence or absence of fljAB genes), sequence types, and year of sampling. The monophasic S. Typhimurium lineages are numbered 1, 2, 3 and 4. The scale bar represents the number of SNPs per branch. The isolate names and the position of outgroup Salmonella Typhi strain CT18 are shown in the S1 Fig.
Fig 2.
Linking genotypes with the antimicrobial resistance phenotypes of Colombian S. Typhimurium isolates.
The maximum-likelihood tree is a linear version of the circular tree shown in Fig 1. On the phylogenetic tree, three highlighted clusters are shaded by coloured backgrounds and the eight cluster designations are indicated with coloured strips. In the vertical columns to the right, the number of AMR genes from 0 to 11 are shown in different shades of red. The AMR profiles are visualised as heatmaps. The results of phenotypic antibiotic susceptibility tests are highlighted with a blue bar above the relevant columns. The red, pink, blue and grey results of the antibiotic susceptibility tests are detailed in the key. In other columns, the genome-predicted presence and absence of AMR genes are indicated in red and grey, respectively. Antibiotics abbreviation: Amp, ampicillin; Chl, chloramphenicol; Str, streptomycin; Tet, tetracycline; Gen, gentamicin; Amk, amikacin; Nal, nalidixic acid; Tmp, trimethoprim; Cip, ciprofloxacin; Caz, ceftazidime; Cxm, cefotaxime. The 11 antibiotics are classified into six groups by the ResFinder database according to the drug family [33]. There are six AMR genes associated with antimicrobials that were not phenotypically tested in this study.
Fig 3.
The prevalence of the pSLT virulence plasmid and the distribution of small plasmids in the Colombian S. Typhimurium isolates.
The maximum-likelihood tree is the linear version of the circular tree shown in Fig 1. Clusters 2, 3 and sub-cluster 7.3 are highlighted on the tree. All clusters are shown as a vertical colour strip, as described in the key. The sequence coverage of the S. Typhimurium LT2 pSLT plasmid and 14 other small plasmids in the S. Typhimurium isolates is shown in gradations of Red. Only small plasmids with sequence coverage of >80% are shown in the figure. The names of the small plasmids were derived from either an identical reference plasmid from PLSDB or according to their plasmid-derived pMLST designation [40].
Fig 4.
Temporal and geographic transmission history of the global S. Typhimurium isolates belonging to three Colombian clades.
Global transmission events inferred from the Bayesian evolutionary analysis by BactDating v1.1.0 [47]. Three Colombian S. Typhimurium clades from Figs 2 and 3 are highlighted with coloured backgrounds. The colours of tips and nodes represent geographic locations. When a node has two colours, the percentage of the colours represents the inferred likelihood of the node being associated with two geographic locations. Geographic transmission routes were determined with Make.simmap, as described in the Methods. When the MRCA of a clade had >50% possibility of being located in Colombia, the clade was designated as being transmitted in Colombia shown by coloured backgrounds on the tree. The date range of the introduction events is estimated from the year of the MRCAs before and after transmission to Colombia. (A) Three introduction events (T1, T2 and T3) of Colombian HC100_305 isolates. (B) A global HC100_20801 (ST313) lineage and two introduction events (T1, T2) to Colombia. The analysis suggests that ST313 L3 was introduced to Malawi from South Africa. The representative isolate of ST313 L3 (BKQZM9) is labelled. (C) HC50_64733 originated from Colombia and was introduced to Ecuador and sporadically transmitted to North America and Europe. The important evolutionary events are labelled in white boxes.
Fig 5.
Inferred international transmission routes of three Colombian clades.
The sample size of S. Typhimurium genomes from each country is shown as coloured bubbles. The lines show the likely transmission routes. The inferred years of introduction to Colombia are labelled with red text boxes. The dotted lines show sporadic transmissions. The base layer of the map was sourced from Natural Earth in GeoJSON format, available at https://geojson-maps.kyd.au/, and is provided under the public domain terms outlined at Natural Earth Terms of Use.
Fig 6.
The invasiveness index of 7 major Colombian HC100 clusters.
Box plot representing the distribution of invasiveness index values for the genome sequences included in this study, summarized by lineage assignment. The 7 Colombian HC100 clusters are defined in Fig 1. Number of isolates in each group: Cluster 1 (n = 10), Cluster 2 (n = 75), Cluster 3 (n = 5), Cluster 4 (n = 14), Cluster 5 (n = 7), Cluster 6 (n = 31), and Cluster 7 (n = 70). The central line in the box plot represents the median value (50th percentile), the box limits denote the 25th and 75th percentiles, the whiskers extend by 1.5 times the interquartile range and individual points represent outliers. For comparative purposes, the median invasiveness indices of African S. Typhimurium ST19, ST313 L1, L2 and L3 (reported in [12]) are plotted as horizontal lines on the right side of the figure. The plot was made with R package ggplot2 [52].