Comparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica: a large-scale analysis of 37 serotypes with a public health impact in the USA

Abstract

Serotyping has traditionally been used for subtyping of non-typhoidal Salmonella (NTS) isolates. However, its discriminatory power is limited, which impairs its use for epidemiological investigations of source attribution. Whole-genome sequencing (WGS) analysis allows more accurate subtyping of strains. However, because of the relative newness and cost of routine WGS, large-scale studies involving NTS WGS are still rare. We aimed to revisit the big picture of subtyping NTS with a public health impact by using traditional serotyping (i.e. reaction between antisera and surface antigens) and comparing the results with those obtained using WGS. For this purpose, we analysed 18 282 sequences of isolates belonging to 37 serotypes with a public health impact that were recovered in the USA between 2006 and 2017 from multiple sources, and were available at the National Center for Biotechnology Information (NCBI). Phylogenetic trees were reconstructed for each serotype using the core genome for the identification of genetic subpopulations. We demonstrated that WGS-based subtyping allows better identification of sources potentially linked with human infection and emerging subpopulations, along with providing information on the risk of dissemination of plasmids and acquired antimicrobial resistance genes (AARGs). In addition, by reconstructing a phylogenetic tree with representative isolates from all serotypes (n=370), we demonstrated genetic variability within and between serotypes, which formed monophyletic, polyphyletic and paraphyletic clades. Moreover, we found (in the entire data set) an increased detection rate for AARGs linked to key antimicrobials (such as quinolones and extended-spectrum cephalosporins) over time. The outputs of this large-scale analysis reveal new insights into the genetic diversity within and between serotypes; the polyphyly and paraphyly of certain serotypes may suggest that the subtyping of NTS to serotypes may not be sufficient. Moreover, the results and the methods presented here, leading to differentiation between genetic subpopulations based on their potential risk to public health, as well as narrowing down the possible sources of these infections, may be used as a baseline for subtyping of future NTS infections and help efforts to mitigate and prevent infections in the USA and globally.

Characterization of Basal Transcriptomes Identifies Potential Metabolic and Virulence-Associated Adaptations Among Diverse Nontyphoidal Salmonella enterica Serovars

“…Preliminary analysis of WGS data downloaded from the NCBI Pathogen Detection Isolate Browser for an initial set of isolates revealed a polyphyletic structure in S. Cerro, with a smaller clade of five isolates clustering separately from the main S. Cerro clade within section Typhi (Supplementary Figure S1), which was consistent with previous findings that suggested that S. Cerro is a polyphyletic serovar (Worley et al, 2018). Therefore, only isolates belonging to the larger S. Cerro clade were included, as the smaller clade of S. Cerro is considerably more rare (Elnekave et al, 2020) and is not considered to be the predominant clade prevalent among cattle (Rodriguez-Rivera et al, 2014;Kovac et al, 2017). Additionally, WGS data for the three strains characterized with RNA-seq were included: S. Cerro FSL R8-2349 was sequenced at Cornell University Biotechnology Resource Center (Ithaca, NY), S. Javiana FSL S5-0395 was sequenced at Université Laval (Québec City, QC), and a closed genome of S. Typhimurium ATCC 14028S was downloaded from NCBI (Supplementary File S1).…”

“…Cerro clade were included, as the smaller clade of S . Cerro is considerably more rare ( Elnekave et al, 2020 ) and is not considered to be the predominant clade prevalent among cattle ( Rodriguez-Rivera et al, 2014 ; Kovac et al, 2017 ). Additionally, WGS data for the three strains characterized with RNA-seq were included: S .…”

Prevalence, Serotype Distribution and Antimicrobial Resistance of Non-Typhoidal Salmonella in Hospitalized Patients in Conghua District of Guangzhou, China

“…According to the White-Kauffmann-Le Minor scheme, Salmonella composed of over 2600 serotypes, where most (approximately 1600 serotypes) of the them belong to the subspecies enterica (Elnekave et al, 2020). Though many serotypes (more than 200) have been identified as capable agents of producing pathology in humans, Salmonella Enteritidis (S. Enteritidis) and Salmonella Typhimurium (S. Typhimurium) are the two most common serotypes causing human salmonellosis (Xue et al, 2021;Xu et al, 2021).…”

Genomic characterization of multidrug-resistant Salmonella serovar Kentucky ST198 isolated in poultry flocks in Spain (2011–2017)

“…The recent reports describing MDR S. Kentucky isolates circulating in livestock in several EU MSs [1] suggest the possible establishment of this clone in the European food animal production systems. However, the usefulness of serotype-based identification for epidemiological purposes is limited because it may lead to the clustering of highly unrelated strains [62]. For this reason, we performed the present study based on whole genome sequencing (WGS) analysis in an attempt to assess the genetic relatedness between S. Kentucky strains circulating in poultry species in Spain, given the recent reports of the presence of MDR isolates belonging to this serotype [24].…”