Evaluation of WGS-subtyping methods for epidemiological surveillance of foodborne salmonellosis

Abstract

Background: Salmonellosis is one of the most common foodborne diseases worldwide. Although human infection by non-typhoidal Salmonella (NTS) enterica subspecies enterica is associated primarily with a self-limiting diarrhoeal illness, invasive bacterial infections (such as septicaemia, bacteraemia and meningitis) were also reported. Human outbreaks of NTS were reported in several countries all over the world including developing as well as high-income countries. Conventional laboratory methods such as pulsed field gel electrophoresis (PFGE) do not display adequate discrimination and have their limitations in epidemiological surveillance. It is therefore very crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological characterisation and outbreak investigation. Methods: Here, we used different whole genome sequence (WGS)-based subtyping methods for retrospective investigation of two different outbreaks of Salmonella Typhimurium and Salmonella Dublin that occurred in 2013 in UK and Ireland respectively. Results: Single nucleotide polymorphism (SNP)-based cluster analysis of Salmonella Typhimurium genomes revealed well supported clades, that were concordant with epidemiologically defined outbreak and confirmed the source of outbreak is due to consumption of contaminated mayonnaise. SNP-analyses of Salmonella Dublin genomes confirmed the outbreak however the source of infection could not be determined. The core genome multilocus sequence typing (cgMLST) was discriminatory and separated the outbreak strains of Salmonella Dublin from the non-outbreak strains that were concordant with the epidemiological data however cgMLST could neither discriminate between the outbreak and non-outbreak strains of Salmonella Typhimurium nor confirm that contaminated mayonnaise is the source of infection, On the other hand, other WGS-based subtyping methods including multilocus sequence typing (MLST), ribosomal MLST (rMLST), whole genome MLST (wgMLST), clustered regularly interspaced short palindromic repeats (CRISPRs), prophage sequence profiling, antibiotic resistance profile and plasmid typing methods were less discriminatory and could not confirm the source of the outbreak. Conclusions: Foodborne salmonellosis is an important concern for public health therefore, it is crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological surveillance and outbreak investigation. In this study, we showed that SNP-based analyses do not only have the ability to confirm the occurrence of the outbreak but also to provide definitive evidence of the source of the outbreak in real-time.

Discerning the Antimicrobial Resistance, Virulence, and Phylogenetic Relatedness of Salmonella Isolates Across the Human, Poultry, and Food Materials Sources in Malaysia

“…In the same vein, the phylogenetic tree obtained from SNPs exhibited diverse clustering of the isolates with an initial one singleton and two clades that subsequently bifurcated. Phylogenetic analysis based on WGS-derived has proven to be a superior cluster resolution method compared to many of the standard subtyping methods (Mohammed and Thapa, 2020;Ford et al, 2021). In order to determine the genetic relatedness among the isolates and infer their evolutionary history based on a genome-wide scale, across the genomes of all S. Enteritidis and closely related serovars were identified.…”

Characterisation of Phage Susceptibility Variation in Salmonellaenterica Serovar Typhimurium DT104 and DT104b

“…Zoonotic S. Typhimurium DT104, as well as DT104b, has a broad-host-range, and it is primarily transmitted through food sources and the faecal-oral route. The infection ranges from self-limiting gastroenteritis to invasive disease that requires prompt antibiotic therapy [1,2].…”

“…Non-typhoidal Salmonella (NTS) serovars predominantly cause a self-limiting diarrhoeal illness; however, they have recently observed to cause invasive extra-intestinal disease, including bacteraemia and focal systemic infections [1,2].…”

Comparison of Conventional Molecular and Whole-Genome Sequencing Methods for Differentiating Salmonella enterica Serovar Schwarzengrund Isolates Obtained from Food and Animal Sources

“…Studies have shown that SNP and genomic MLST results are congruent and both approaches can analyze the outbreaks of foodborne illnesses [49]. However, a recent study that investigated two outbreaks using different WGS subtyping methods revealed that SNP-based analyses have the ability to confirm the occurrence of the outbreak while both cgMLST and wgMLST could neither differentiate outbreak-related Salmonella Typhimurium isolates from outbreak-unrelated isolates nor confirm the source of infection [50]. Consequently, WGS based on SNP was selected for further investigation.…”