Embracing Diversity: Differences in Virulence Mechanisms, Disease Severity, and Host Adaptations Contribute to the Success of Nontyphoidal Salmonella as a Foodborne Pathogen

Refinement of a Live Attenuated Salmonella enterica Serovar Newport Vaccine with Improved Safety

Non-typhoidal Salmonella (NTS) is a major cause of gastroenteritis and is responsible for approximately 93 million cases annually. In healthy individuals, gastroenteritis caused by NTS is usually self-limiting, however, NTS can cause severe invasive disease in immunocompromised patients. Very little research has been directed towards development of vaccines against Salmonella serogroups O:6,7 or O:8. We have constructed a live attenuated serogroup O:8 vaccine, CVD 1979, by deleting guaBA, htrA, and aroA from the genome of S. Newport. We have shown that the candidate vaccine is well tolerated in mice and elicits serum immunoglobulin G (IgG) antibodies against core O-polysaccharide (COPS) when administered orally. Immunized mice were challenged intraperitoneally with wild-type S. Newport and bacterial burden in the liver and spleen was found to be significantly reduced in the livers of immunized mice compared to control mice. We also observed moderate vaccine efficacy (45%) against lethal challenge with the serogroup O:8 serovar, S. Muenchen, but low vaccine efficacy (28%) following lethal challenge with a serogroup O:6,7 serovar, S. Virchow. In vitro, we have shown that antibodies generated by CVD 1979 only recognize lipopolysaccharide (LPS) from serogroup O:8 but not serogroup O:6,7 serovars, and that they mediate opsonophagocytic antibody (OPA) activity against serogroup O:8 but not serogroup O:6,7 serovars. We also showed that OPA activity can be blocked by pre-incubating the antisera with serogroup O:8 lipopolysaccharide. Taken together, our data demonstrate that we have constructed a well-tolerated, effective live attenuated S. Newport vaccine which elicits functional antibodies against serogroup O:8 but not O:6,7 serovars.

Vaccination and Infection of Swine With Salmonella Typhimurium Induces a Systemic and Local Multifunctional CD4+ T-Cell Response

The gram-negative facultative intracellular bacteria Salmonella Typhimurium (STM) often leads to subclinical infections in pigs, but can also cause severe enterocolitis in this species. Due to its high zoonotic potential, the pathogen is likewise dangerous for humans. Vaccination with a live attenuated STM strain (Salmoporc) is regarded as an effective method to control STM infections in affected pig herds. However, information on the cellular immune response of swine against STM is still scarce. In this study, we investigated the T-cell immune response in pigs that were vaccinated twice with Salmoporc followed by a challenge infection with a virulent STM strain. Blood- and organ-derived lymphocytes (spleen, tonsils, jejunal and ileocolic lymph nodes, jejunum, ileum) were stimulated in vitro with heat-inactivated STM. Subsequently, CD4⁺ T cells present in these cell preparations were analyzed for the production of IFN-γ, TNF-α, and IL-17A by flow cytometry and Boolean gating. Highest frequencies of STM-specific cytokine-producing CD4⁺ T cells were found in lamina propria lymphocytes of jejunum and ileum. Significant differences of the relative abundance of cytokine-producing phenotypes between control group and vaccinated + infected animals were detected in most organs, but dominated in gut and lymph node-residing CD4⁺ T cells. IL-17A producing CD4⁺ T cells dominated in gut and gut-draining lymph nodes, whereas IFN-γ/TNF-α co-producing CD4⁺ T cells were present in all locations. Additionally, the majority of cytokine-producing CD4⁺ T cells had a CD8α⁺CD27^- phenotype, indicative of a late effector or effector memory stage of differentiation. In summary, we show that Salmonella-specific multifunctional CD4⁺ T cells exist in vaccinated and infected pigs, dominate in the gut and most likely contribute to protective immunity against STM in the pig.

Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana

Salmonella enterica serovar Javiana is the fourth most reported serovar of laboratory-confirmed human Salmonella infections in the U.S. and in Tennessee (TN). Although Salmonella ser. Javiana is a common cause of human infection, the majority of cases are sporadic in nature rather than outbreak-associated. To better understand Salmonella ser. Javiana microbial population structure in TN, we completed a phylogenetic analysis of 111 Salmonella ser. Javiana clinical isolates from TN collected from Jan. 2017 to Oct. 2018. We identified mobile genetic elements and genes known to confer antibiotic resistance present in the isolates, and performed a pan-genome-wide association study (pan-GWAS) to compare gene content between clades identified in this study. The population structure of TN Salmonella ser. Javiana clinical isolates consisted of three genetic clades: TN clade I (n = 54), TN clade II (n = 4), and TN clade III (n = 48). Using a 5, 10, and 25 hqSNP distance threshold for cluster identification, nine, 12, and 10 potential epidemiologically-relevant clusters were identified, respectively. The majority of genes that were found to be over-represented in specific clades were located in mobile genetic element (MGE) regions, including genes encoding integrases and phage structures (91.5%). Additionally, a large portion of the over-represented genes from TN clade II (44.9%) were located on an 87.5 kb plasmid containing genes encoding a toxin/antitoxin system (ccdAB). Additionally, we completed phylogenetic analyses of global Salmonella ser. Javiana datasets to gain a broader insight into the population structure of this serovar. We found that the global phylogeny consisted of three major clades (one of which all of the TN isolates belonged to) and two cgMLST eBurstGroups (ceBGs) and that the branch length between the two Salmonella ser. Javiana ceBGs (1,423 allelic differences) was comparable to those from other serovars that have been reported as polyphyletic (929–2,850 allelic differences). This study demonstrates the population structure of TN and global Salmonella ser. Javiana isolates, a clinically important Salmonella serovar and can provide guidance for phylogenetic cluster analyses for public health surveillance and response.

Immunogenicity and duration of immunity of the polyvalent vaccine against chicken salmonellosis

Poultry salmonellosis causes serious economic damage and must be prevented by disinfection, zoohygienic measures or by vaccination. To develop a new polyvalent vaccine against poultry salmonellosis, we used bacterial strains of Salmonella enteritidis, S. typhimurium and S. gallinarum. Antigenic and immunogenic efficacy of the vaccine was tested on specific-pathogen free chickens, which were divided into five groups of 10 birds in each group and were vaccinated intramuscularly at 8 and 12 weeks: group A (non-immunized control), group B (S. enteritidis mono-vaccine), group C (S. typhimurium mono-vaccine), group D (S. gallinarum mono-vaccine) and group E (trivalent vaccine Polimun Salmo). None of the immunized birds showed such adverse reactions as abnormal behaviour, mortality or signs of anorexia, depression or diarrhea. Two weeks after the revaccination, 5 birds in each group were challenged by watering 3 cm3 of working suspensions of S. gallinarum, S. typhimurium and S. enteritidis control strains at a concentration of 1 × 109 CFU. 72 h after the challenge, faeces were collected from all chickens in each group to identify Salmonella excretion with faeces, and the chickens were euthanized. Significant protection against the virulent challenge was observed in all immunized groups based on mortality and post-mortem lesions compared with the non-immunized control group. Blood samples were selected weekly from 5 chickens of each group for 184 days. The antigenic efficacy of the vaccines was studied by reaction of haemagglutination in the obtained serum. The potent antigen-specific response to lymphocyte activation found in all immunized groups indicated the induction of immune responses. Overall, the results showed that persistent immunity is formed in 4 weeks after the revaccination and lasts for a productive period. Immune response of chickens on day 184 after vaccination with Polimun Salmo was 1: 647, indicating that the developed polyvalent vaccine against common serovars of S. enterica in poultry is effective and immunogenic and can be further used in field studies.

Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project

Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing. Results: The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees. Conclusions: The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.

Structural Analysis of Binding Determinants of Salmonella typhimurium Trehalose-6-phosphate Phosphatase Using Ground-State Complexes

Trehalose-6-phosphate phosphatase (T6PP) catalyzes the dephosphorylation of trehalose 6-phosphate (T6P) to the disaccharide trehalose. The enzyme is not present in mammals but is essential to the viability of multiple lower organisms as trehalose is a critical metabolite, and T6P accumulation is toxic. Hence, T6PP is a target for therapeutics of human pathologies caused by bacteria, fungi, and parasitic nematodes. Here, we report the X-ray crystal structures of Salmonella typhimurium T6PP (StT6PP) in its apo form and in complex with the cofactor Mg²⁺ and the substrate analogue trehalose 6-sulfate (T6S), the product trehalose, or the competitive inhibitor 4-n-octylphenyl α-d-glucopyranoside 6-sulfate (OGS). OGS replaces the substrate phosphoryl group with a sulfate group and the glucosyl ring distal to the sulfate group with an octylphenyl moiety. The structures of these substrate-analogue and product complexes with T6PP show that specificity is conferred via hydrogen bonds to the glucosyl group proximal to the phosphoryl moiety through Glu123, Lys125, and Glu167, conserved in T6PPs from multiple species. The structure of the first-generation inhibitor OGS shows that it retains the substrate-binding interactions observed for the sulfate group and the proximal glucosyl ring. The OGS octylphenyl moiety binds in a unique manner, indicating that this subsite can tolerate various chemotypes. Together, these findings show that these conserved interactions at the proximal glucosyl ring binding site could provide the basis for the development of broad-spectrum therapeutics, whereas variable interactions at the divergent distal subsite could present an opportunity for the design of potent organism-specific therapeutics.

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

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.

Spatial and space-time clustering and demographic characteristics of human nontyphoidal Salmonella infections with major serotypes in Toronto, Canada

Nontyphoidal Salmonella enterica (NTS) causes a substantial health burden to human populations in Canada and worldwide. Exposure sources and demographic factors vary by location and can therefore have a major impact on salmonellosis clustering. We evaluated major NTS serotypes: S. Enteritidis (n = 620), S. Typhimurium (n = 150), S. Thompson (n = 138), and S. Heidelberg (n = 136) reported in the city of Toronto, Canada, between January 1, 2015, and December 31, 2017. Cases were analyzed at the forward sortation area (FSA)—level (an area indicated by the first three characters of the postal code). Serotype-specific global and local clustering of infections were evaluated using the Moran's I method. Spatial and space-time clusters were investigated using Poisson and multinomial scan statistic models. Case-case analyses using a multinomial logistic regression model was conducted to compare seasonal and demographic factors among the different serotypes. High infection rate FSAs clustered in the central region of Toronto for S. Enteritidis, in the south-central region for S. Typhimurium, in north-west region for S. Thompson, and in the south-east region for S. Heidelberg. The relative risk ratio of S. Enteritidis infections was significantly higher in cases who reported travel outside of Ontario. The relative risk ratio of infections was significantly higher in summer for S. Typhimurium, and in fall for S. Thompson. The relative risk ratio of infection was highest for the 0–9 age group for S. Typhimurium, and the 20–39 age group for S. Heidelberg. Our study will aid public health stakeholders in designing serotype-specific geographically targeted disease prevention programs.

Sources of human infection by Salmonella enterica serotype Javiana: A systematic review

Non-typhoidal Salmonella (NTS) infection is one of the major causes of diarrheal disease throughout the world. In recent years, an increase in human S. Javiana infection has been reported from the southern part of the United States. However, the sources and routes of transmission of this Salmonella serotype are not well understood. The objective of this study was to perform a systematic review of the literature to identify risk factors for human S. Javiana infection. Using PRISMA guidelines, we conducted a systematic search in Web of Science, PubMed, and the Morbidity and Mortality Weekly Report (MMWR). Searches returned 63 potential articles, of which 12 articles met all eligibility criteria and were included in this review. A review of the literature indicated that both food and non-food (such as animal contact) exposures are responsible for the transmission of S. Javiana infection to humans. Consumption of fresh produce (tomatoes and watermelons), herbs (paprika-spice), dairy products (cheese), drinking contaminated well water and animal contact were associated with human S. Javiana infections. Based on the findings of this study, control of human S. Javiana infection should include three factors, (a) consumption of drinking water after treatment, (b) safe animal contact, and (c) safe food processing and handling procedures. The risk factors of S. Javiana infections identified in the current study provide helpful insight into the major vehicles of transmission of S. Javiana. Eventually, this will help to improve the risk management of this Salmonella serotype to reduce the overall burden of NTS infection in humans.

Invasive Salmonella Enteritidis infection complicated by bacterial meningitis and vertebral osteomyelitis shortly after influenza A infection in an immunocompetent young adult

Non-typhoidal Salmonella usually manifests as a self-limited acute gastroenteritis but may also cause severe invasive infections almost exclusively among children or immunosuppressed patients. A previously healthy 22-year-old man developed high fever with coma, multiple organ failure and shock. He had visited another hospital complaining of fever 2 days previously and was diagnosed with a common cold. No obvious site of infection was identified by radiology and a rapid test for influenza A virus was positive, indicating possible influenza-associated encephalopathy. However, blood as well as CSF culture yielded Salmonella enterica serotype Enteritidis. Therefore, the patient was considered to be suffering from bacterial meningitis with septic shock concomitant with influenza infection. Antiviral drugs and therapy for septic shock were initiated. He stabilized relatively quickly and his mental status dramatically improved. The patient denied preceding gastrointestinal symptoms, but mentioned that he received positive fecal Salmonella species culture results without medical intervention about 3 months previously. His laboratory values showed marked improvement but his elevated inflammatory markers and fever were sustained. On the 17th day of hospitalization, he complained of back pain and MRI showed lumbar vertebral osteomyelitis. This case indicates that (i) invasive Salmonella infection can be developed even in previously healthy adults; (ii) chronic carriage of Salmonella is a predisposing factor to development of invasive infections, and influenza infection may contribute to such "breakthrough infections"; (iii) attention to manifestation of metastatic extra-intestinal foci even after resolution of sepsis is necessary.