Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa

Abstract

Since its emergence in the beginning of the 90’s, multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar Kentucky has become a significant public health problem, especially in East Africa. This study aimed to investigate the antimicrobial resistance profile and the genotypic relatedness of Salmonella Kentucky isolated from animal sources in Ethiopia and Kenya (n=19). We also investigated population evolutionary dynamics through phylogenetic and pangenome analyses with additional publicly available Salmonella Kentucky ST198 genomes (n=229). All the 19 sequenced Salmonella Kentucky isolates were identified as ST198. Among these isolates, the predominant genotypic antimicrobial resistance profile observed in ten (59.7%) isolates included the aac(3)-Id, aadA7, strA-strB, blaTEM-1B, sul1, and tet(A) genes, which mediated resistance to gentamicin, streptomycin/spectinomycin, streptomycin, ampicillin, sulfamethoxazole and tetracycline, respectively; and gyrA and parC mutations associated to ciprofloxacin resistance. Four isolates harbored plasmid types Incl1 and/or Col8282; two of them carried both plasmids. Salmonella Pathogenicity islands (SPI-1 to SPI-5) were highly conserved in the 19 sequenced Salmonella Kentucky isolates. Moreover, at least one Pathogenicity Island (SPI 1–4, SPI 9 or C63PI) was identified among the 229 public Salmonella Kentucky genomes. The phylogenetic analysis revealed that almost all Salmonella Kentucky ST198 isolates (17/19) stemmed from a single strain that has accumulated ciprofloxacin resistance-mediating mutations. A total of 8,104 different genes were identified in a heterogenic and still open Salmonella Kentucky ST198 pangenome. Considering the virulence factors and antimicrobial resistance genes detected in Salmonella Kentucky, the implications of this pathogen to public health and the epidemiological drivers for its dissemination must be investigated.

Characterization of Extensively Drug-Resistant Salmonella enterica Serovar Kentucky Sequence Type 198 Isolates from Chicken Meat Products in Xuancheng, China

“…Kentucky ST198 became the second most prevalent serotype (3.10% [13/420 strains]) in the production chain of broiler chickens in Sichuan Province, China ( 13 ). It has also been increasingly detected in animals and clinics in countries outside China, e.g., India (3.49% in animals and 0.31% in patients), East Africa, Spain, and Switzerland ( 16 – 19 ).…”

Genomic Features and Phylogenetic Analysis of Antimicrobial-Resistant Salmonella Mbandaka ST413 Strains

“…The presence of C63PI (six/six) and SPI 9 (six/six) was noticed herein in all S. Mbandaka genomes. Although SPIs 1-5 are common in Salmonella serovars [ 46 ], there are divergences regarding the presence and absence of genes in these islands [ 45 , 47 ]. Many of those mainly found in SPI 2 encode structural and effector proteins of a type III secretion system (T3SS) that transfer essential virulence effectors with important functions during cell infection [ 45 ].…”

“…SPI 3 harbours the mgtCB virulence genes that are related to Mg 2+ uptake when under restricted availability of this cation, such as within the macrophage environment [ 45 , 51 ]. While the mgtCB genes were predicted in S. Mbandaka isolates, other regions of SPI 3 were absent in all the genomes [ 47 ], possibly implying that these genes are not essential for Salmonella serovar infection. Although the expressions of virulence genes are not the focus of this work, we acknowledge that additional research into the variation in the virulence factors and the interaction of those genes will further our understanding of the role of the virulence mechanism in this serovar and contribute valuable insights into the broader landscape of Salmonella pathogenesis.…”

Genomic and phenotypic characterization of Salmonella enterica serovar Kentucky

“…In Europe, human Kentucky-II cases (ST198) are often linked to international travel [62]; however, studies have shown that this lineage is expanding significantly in poultry flocks in Europe [33, 63, 64]. More recently, ST198 isolates (Kentucky-II) have been found in cattle and also swine in Africa [65]. Furthermore, of the ten SNP clusters with multiple source types that belong to the Kentucky-II lineage, isolates from seven of them were only found in cattle and humans.…”