Combining Whole-Genome Sequencing and Multimodel Phenotyping To Identify Genetic Predictors of Salmonella Virulence

Abstract

Salmonella comprises more than 2,600 serovars. Very few environmental and uncommon serovars have been characterized for their potential role in virulence and human infections. A complementary in vitro and in vivo systematic high-throughput analysis of virulence was used to elucidate the association between genetic and phenotypic variations across Salmonella isolates. The goal was to develop a strategy for the classification of isolates as a benchmark and predict virulence levels of isolates. Thirty-five phylogenetically distant strains of unknown virulence were selected from the Salmonella Foodborne Syst-OMICS (SalFoS) collection, representing 34 different serovars isolated from various sources. Isolates were evaluated for virulence in 4 complementary models of infection to compare virulence traits with the genomics data, including interactions with human intestinal epithelial cells, human macrophages, and amoeba. In vivo testing was conducted using the mouse model of Salmonella systemic infection. Significant correlations were identified between the different models. We identified a collection of novel hypothetical and conserved proteins associated with isolates that generate a high burden. We also showed that blind prediction of virulence of 33 additional strains based on the pan-genome was high in the mouse model of systemic infection (82% agreement) and in the human epithelial cell model (74% agreement). These complementary approaches enabled us to define virulence potential in different isolates and present a novel strategy for risk assessment of specific strains and for better monitoring and source tracking during outbreaks. IMPORTANCE Salmonella species are bacteria that are a major source of foodborne disease through contamination of a diversity of foods, including meat, eggs, fruits, nuts, and vegetables. More than 2,600 different Salmonella enterica serovars have been identified, and only a few of them are associated with illness in humans. Despite the fact that they are genetically closely related, there is enormous variation in the virulence of different isolates of Salmonella enterica. Identification of foodborne pathogens is a lengthy process based on microbiological, biochemical, and immunological methods. Here, we worked toward new ways of integrating whole-genome sequencing (WGS) approaches into food safety practices. We used WGS to build associations between virulence and genetic diversity within 83 Salmonella isolates representing 77 different Salmonella serovars. Our work demonstrates the potential of combining a genomics approach and virulence tests to improve the diagnostics and assess risk of human illness associated with specific Salmonella isolates.

Genomic and phenotypic analysis of SspH1 identifies a new Salmonella effector, SspH3

“…NTS can infect a broad range of animals and has been associated with foods of nearly every type ranging from spices to poultry to leafy vegetables. Isolates of S. enterica display a remarkable genetic diversity, with regards to multiple virulence plasmids and no less than 23 pathogenicity islands have been described (Crouse et al., 2020). The diversity of virulence determinants makes assessing the threat of individual isolates of S. enterica challenging, moreover, most studies of S. enterica virulence have focused on only a few isolates.…”

“…While the contributions of some effectors to Salmonella internalization and intracellular replication are well defined, the role of other secreted proteins during infection remains unclear. Identifying the role of individual Salmonella effectors is confounded by the diversity within T3SS effector repertoires, it is becoming increasingly appreciated that myriad of pathogenicity islands within Salmonella results in isolates that cause a broad spectrum of disease severity (Crouse et al., 2020). One Salmonella T3SS effector whose role during infection remains unclear is SspH1.…”

Panomics to decode virulence and fitness in Gram-negative bacteria

“…Proteogenomics was employed recently ( Karash et al., 2017 ) to identify the potential genes and proteins that play a role in S. Typhimurium's resistance to H 2 O 2 , thus deepening the current understanding of S. Typhimurium's survival mechanisms in macrophages. Another research ( Crouse et al., 2020 ) focused on integrating WGS techniques into food safety practices could establish links between virulence and genetic diversity in Salmonella . They have also presented a novel approach for risk assessment of particular strains as well as for improved monitoring and source tracking during outbreaks.…”

Application of a High-Throughput Targeted Sequence AmpliSeq Procedure to Assess the Presence and Variants of Virulence Genes in Salmonella

“…For instance, the serovar Typhimurium causes a typhoid-like illness in mice, but in the overwhelming number of human cases, it results in gastroenteritis. Many other models including monocytic macrophage cells from humans (U937 and THP-1; [6]) and non-macrophage cell lines from mice (RAW264.7) and humans (Caco-2 and INT-407; [7,8]), amoeba [8] and in vitro gastrointenstinal systems [9] have provided further illumination of Salmonella virulence. Collectively, many VGs have been well-characterized and proven to affect Salmonella behaviour and by extension the epidemiology of the disease.…”