Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

Abstract

Salmonella enterica serotype Kentucky can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S.enterica serotype Kentucky sequence type 198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug-resistant (MDR) S.enterica serotype Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island (SGI) 1 (variant SGI1-K) conferring resistance to ampicillin, streptomycin, gentamicin, sulfamethoxazole and tetracycline. Phylogeographical analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone-resistance-determining regions (QRDRs) of DNA gyrase (gyrA) and DNA topoisomerase IV (parC), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the S. enterica serotype Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome of the MDR clone carried a different SGI1-K derivative structure; this variation could be attributed to IS26-mediated insertions and deletions, which appear to have hampered previous attempts to trace the clone's evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems and/or azithromycin. These results indicate that most MDR S. enterica serotype Kentucky circulating globally result from the clonal expansion of a single lineage that acquired chromosomal AMR genes 30 years ago, and has continued to diversify and accumulate additional resistances to last-line oral antimicrobials. This article contains data hosted by Microreact.

Keywords: Kentucky; MDR; SGI; ST198; Salmonella; phylogenomics.

Fig. 1.

Phylogeographical analysis of S. e nterica serotype Kentucky ST198 based on whole-genome SNV data. Bayesian maximum clade credibility tree inferred using beast, with the MDR lineage shaded orange. The dark orange box indicates three isolates from the same patient. Major internal nodes are labelled with circles indicating branch support (black, ≥95 % posterior support; red, >70 % posterior support; unfilled, >30 % posterior support); divergence date estimates (95 % higher posterior density values) are provided for key points in the evolution of the MDR lineage. Leaf nodes are coloured by region of origin (see inset map). Coloured branches indicate inferred geographical distribution of internal branches, inferred using maximum-likelihood ancestral trait reconstruction. Data columns indicate country of origin; source of isolate (H for human, N for non-human, ? for unknown); SGI type (see inset legend); quinolone resistance-related codons, with resistance-associated alleles highlighted. Reference genome 201001922 is marked with red arrow. Red and black vertical lines indicate clades that are mentioned in the text.

Fig. 2.

SGI variation in S. e nterica serotype Kentucky ST198. (a) Backbone of SGI, with arrows pointing to the different insertion sites of the resistance region in SGI1 and SGI2. (b) Different examples of SGI1 types in S. e nterica serotype Kentucky ST198. Arrows show ORFs of the SGI backbone and MDR region with arrowheads indicating direction of transcription; colour indicates gene class. Coloured blocks indicate regions of homology between sequences in the same orientation: green, same orientation; orange, inverse orientation.

Fig. 3.

Horizontally acquired AMR genes in the S. e nterica serotype Kentucky ST198 MDR lineage. (a) Dated Bayesian (beast) phylogeny for the MDR lineage, extracted from the tree shown in Fig. 1. Leaf nodes are coloured by region of origin (see the key); the orange box highlights three isolates recovered from the same patient over 3 years. (b–e) AMR features of each isolate in the tree. (b) SGI type (see the key, dash indicates no SGI detected). (c) AMR phenotypes, indicated as boxes coloured by antimicrobial class (see the key, I in the box denotes intermediate resistance). (d) AMR genes located within the SGI1 are indicated with boxes coloured by antimicrobial class (* in the box indicates gene is interrupted). (e) Plasmid incompatibility group(s) identified in each genome; AMR genes located within these plasmids are printed, coloured by antimicrobial class; genes in brackets are genes for which it was not possible to determine location.