Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ

Genetic diversity of Salmonella enterica during acute human infections

The ubiquitous bacterial pathogen Salmonella enterica is the causative agent of both enteric fever and gastroenteritis. Despite its significant global health burden, we lack an understanding of its genetic diversity during acute infection, with ramifications for treatment and prevention. Here, we investigated within-host infection diversity of acute salmonellosis using whole-genome sequencing of blood or stool isolates obtained from 23 different patients. We found that intestinal infections exhibited greater genetic variation than blood infections, including in their plasmid content. While same-patient isolates were separated by 10 single nucleotide polymorphisms or less, they often differed in the carriage of genes or alleles, including those associated with antibiotic resistance or virulence. Given the longstanding emphasis on single colony isolation in clinical and laboratory microbiology, these findings have implications for how we both study evolution and transmission and how we treat salmonellosis in an age of increasing antibiotic resistance.

Disinfectants and one health review: The role of reactive oxygen species in the bactericidal activity of chlorine against Salmonella

Salmonella are among the most common foodborne pathogens in humans, and they are associated with mild to severe diseases commonly referred to as salmonellosis. The genus resides in various animals' intestinal tracts, including humans. It is one of the most diverse genera of bacteria, including over 2500 serovars. Consumption of poultry products contaminated with Salmonella is a significant source of disease transmission in humans. Because of this food safety concern, the poultry industry and governments spend billions of dollars on Salmonella containment methods. However, a completely effective strategy is yet to be established. Chlorine has been commonly used as a disinfectant in the poultry industry. In humans, antibiotic therapy is the primary means for managing Salmonella infection. However, widespread use of both compounds at sub-inhibitory concentrations has allowed resistant strains to emerge and rapidly spread globally. Both antimicrobial compounds involve generating reactive oxygen species (ROS) as a bactericidal mechanism of action. However, ROS generation and its association with bacterial survival and growth inhibition have not been widely explored. Thus, a better understanding of ROS generation during antimicrobial treatments may help devise better Salmonella containment strategies.

Evasion of serum antibodies and complement by Salmonella Typhi and Paratyphi A

Nontyphoidal and enteric fever serovars of Salmonella enterica display distinctive interactions with serum antibodies and the complement system, which initiate the host immune response to invading microbes. This study examines the contributions of lipopolysaccharide O-antigen (O-ag) and the S. Typhi Vi polysaccharide capsule to serum resistance, complement activation and deposition, and immunoglobulin (Ig) binding in nontyphoidal S. enterica serovar Typhimurium and the enteric fever serovars S. Typhi and S. Paratyphi A. Although all three serovars are resistant to serum killing, S. Typhi and S. Paratyphi A exhibit lower levels of Ig binding, complement binding and complement activation compared to S. Typhimurium. In S. Typhimurium, WzzB-dependent long O-antigen (L O-ag) production with 16-to-35 repeating O-ag units, and FepE-dependent very long O-antigen (VL O-ag) production with over 100 repeating O-ag units, are required for serum resistance but do not prevent IgM binding or complement deposition. S. Typhi lacks VL O-ag, but its production of Vi capsule inhibits IgM binding and complement deposition, while acting in concert with L O-ag to resist serum killing. In S. Paratyphi A, L O-ag production is deficient due to a hypofunctional WzzB protein, but this is compensated by greater quantities of VL O-ag, which are required for serum resistance. Restoration of WzzB function by exchange with the S. Typhimurium or S. Typhi wzzB alleles can restore L O-ag production in S. Paratyphi A but decreases VL O-ag production, resulting in increased IgM binding. Replacement of the S. Paratyphi A O2-type polysaccharide with the S. Typhi O9 polysaccharide further increases IgM binding of S. Paratyphi A, which enhances complement activation but not complement deposition. Lastly, a gene duplication of rfbV in S. Paratyphi A is necessary for higher levels of VL O-ag and resistance to complement deposition and antibody binding. Collectively, these observations demonstrate fundamental differences between nontyphoidal and enteric fever Salmonella serovars in their interactions with innate immune effectors. Whereas nontyphoidal S. Typhimurium elicits, exploits and withstands the host acute inflammatory response, the enteric fever serovars S. Typhi and S. Paratyphi A evade it by limiting antibody recognition and complement activation and deposition.

Antibiotic-recalcitrant Salmonella during infection

Antibiotic-recalcitrant infections, defined as the prolonged carriage of pathogenic bacteria even in the presence of antibiotics, are often caused by bacteria that are genetically susceptible to the drug. These recalcitrant bacteria fail to proliferate in the presence of antibiotics but remain viable such that they may recolonize their niche following antibiotic withdrawal. Significant progress has been made in our understanding of antibiotic-recalcitrant Salmonella, which are thought to be the source of infection relapse. In recent years, it has been shown that recalcitrant bacteria manipulate host immune defences and could directly contribute to the spread of antimicrobial resistance. In this Review, we provide an overview of what is currently known about the antibiotic recalcitrance of Salmonella during infection and highlight knowledge gaps requiring additional research in the future.

Modulation of host Rab GTPases by Salmonella: mechanisms of immune evasion and intracellular replication

Salmonella is one of the major pathogens responsible for foodborne illnesses worldwide, characterized by diverse serotypes and a broad host range. As an intracellular bacterium, Salmonella invades host cells and establishes a protected niche known as the Salmonella-containing vacuoles (SCVs), which provide a suitable environment for intracellular survival. Rab GTPases, key regulators of intracellular membrane trafficking, play a crucial role in the biogenesis and dynamics of SCVs. Through its type III secretion systems (T3SSs), Salmonella delivers a repertoire of effector proteins into host cells, which modulate the activity of Rab GTPases and alter membrane trafficking to facilitate SCVs formation and maintenance. This review summarizes recent advances in understanding how Salmonella effectors manipulate Rab GTPases to promote intracellular survival and evade host innate immune responses.

Bacterial genome structural variation: prevalence, mechanisms, and consequences

A vast number of bacterial genome sequences are publicly available. However, the majority were generated using short-read sequencing, producing fragmented assemblies. Long-read sequencing can generate closed assemblies, and they reveal that bacterial genome structure, the order and orientation of genes on the chromosome, is highly variable for many species. Growing evidence suggests that genome structure is a determinant of genome-wide gene expression levels and thus phenotype. We review this developing picture of genome structure variation among bacteria, the challenges for the study of this phenomenon, and its impact on adaptation and evolution, including virulence and infection.

The genomic characteristics of dominant Salmonella enterica serovars from retail pork in Sichuan province, China

Foodborne Salmonella is the main cause of salmonellosis in China. Porcine animals are a reservoir for this bacterium consequently posing a threat to food safety and public health. In this study, 157 out of 240 pork samples (65.42 %) were identified as Salmonella-positive. From these, after isolation and deduplication, 376 Salmonella isolates were collected. Twenty four serovars were identified based on WGS, among which S. London/ST155 (24.47 %), S. Rissen/ST469 (23.40 %), S. Derby/ST40 (13.56 %), and S. 4,[5],12:i:- (monophasic S. Typhimurium)/ST34 (13.30 %) were dominant. In all, 69.68 % (262/376) of these isolates expressed multidrug resistance (MDR, defined as resistance to compounds in three or more antimicrobial classes) phenotypes with S. London (54.35 %, 50/92) accounting for the highest proportion of these. Notably, the resistance to front-line critically important antimicrobial agents (CIA), including cephalosporins, ciprofloxacin, and azithromycin was 0.80 %. Based on in silico analysis, antimicrobial resistant-encoding genes (ARG) identified in the MDR isolates included aac(3)-IId, aac(6')-Iaa, blaTEM-1B, mph(A), qnrB6, aac(6')-Ib-cr, sul1, sul2, and tet(A), which expressed resistance to aminoglycosides, β-lactams, macrolides, quinolones, sulfonamides, and tetracyclines. Furthermore, diverse biocide and heavy metal resistance-encoding genes were distributed across different serovars with triC encoding triclosan resistance being identified exclusively in S. London. Moreover, monophasic S. 4,[5],12:i:- carried the greatest number of virulence factors and heavy metal resistance genes among the dominant serovars. This study extended our understanding of the genomic epidemiology and multidrug resistance of Salmonella derived from pork and highlighted the potential risk to human health, posed by commonly encountered serovars.

Current Antimicrobial Susceptibility Trends and Clinical Outcomes of Typhoidal Salmonella in a Large Health Authority in British Columbia, Canada

BACKGROUND

From 2018 to 2021, travel-related extensively drug-resistant (XDR) Salmonella Typhi was identified in Ontario, Canada. Opportunities remain to characterize typhoidal Salmonella antimicrobial susceptibility trends (including multi-drug resistance phenotypes; MDR) within a large health authority in British Columbia, Canada.

METHODS

This retrospective study included patients with Salmonella Typhi or Paratyphi A, B or C bacteremia identified at Fraser Health regional microbiology laboratory from 2018 to 2024. The primary outcome was the proportion of cases with MDR and XDR typhoidal Salmonella. Secondary outcomes included annual antimicrobial susceptibility for ampicillin, ceftriaxone, ciprofloxacin, trimethoprim-sulfamethoxazole, ertapenem, meropenem and azithromycin. Clinical outcomes included hospitalization length, and 30-day mortality, clinical cure and infection relapse.

RESULTS

Among 271 patients, most were previously healthy and recently travelled. There were extended spectrum beta-lactamase (1.1%) and MDR (1.5%) typhoidal Salmonella, with no XDR cases observed. In 2024, ciprofloxacin resistance was 96% while susceptibility rates were high for other studied antimicrobials. Within 30 days, no deaths were reported; however, six patients (3%) had infection relapse.

CONCLUSIONS

Currently, in British Columbia, MDR typhoidal Salmonella remains rare. Empiric ciprofloxacin should be avoided due to persistently high resistance rates. With ongoing travel patterns, it is beneficial for institutions to continue typhoidal Salmonella antimicrobial susceptibility surveillance, and travelers should seek pre-travel health assessments.

The interplay between Salmonella and host: Mechanisms and strategies for bacterial survival

Salmonella, an intracellular pathogen, infects both humans and animals, causing diverse diseases such as gastroenteritis and enteric fever. The Salmonella type III secretion system (T3SS), encoded within its pathogenicity islands (SPIs), is critical for bacterial virulence by directly delivering multiple effectors into eukaryotic host cells. Salmonella utilizes these effectors to facilitate its survival and replication within the host through modulating cytoskeletal dynamics, inflammatory responses, the biogenesis of Salmonella-containing vacuole (SCV), and host cell survival. Moreover, these effectors also interfere with immune responses via inhibiting innate immunity or antigen presentation. In this review, we summarize the current progress in the survival strategies employed by Salmonella and the molecular mechanisms underlying its interactions with the host. Understanding the interplay between Salmonella and host can enhance our knowledge of the bacterium's pathogenic processes and provide new insights into how it manipulates host cellular physiological activities to ensure its survival.

Profiling Salmonella transcriptional dynamics during macrophage infection using a comprehensive reporter library

Salmonella enterica serovar Typhimurium must adapt to rapid environmental shifts, including those encountered upon entry and during replication to survive within macrophages during pathogenesis. Despite extensive RNA-seq-based investigations, questions remain regarding the range, timing and magnitude of response dynamics. Here we constructed a comprehensive GFP-reporter strain library representing 2,901 computationally identified Salmonella promoter regions to study time-resolved Salmonella transcriptional responses. Promoter activity was measured during in vitro growth and during intracellular infection of RAW 264.7 macrophages. Using bulk measurements and single-cell imaging, we uncovered condition-specific transcriptional regulation and population-level heterogeneity in SPI2-related promoter activity. We also discovered previously unidentified transcriptional activity from 234 promoters. These analyses revealed metabolic shifts including requirements for mntS expression to support manganese homeostasis and expression of Entner-Doudoroff pathway-associated genes to support growth within macrophages. Our library and datasets, made available through the online tool SalComKinetics, provide resources for systems-level interrogation of Salmonella transcriptional dynamics.

AI-2 Signaling: A Potential Driver of Bacteremia in Non-Typhoidal Salmonella Infections

Introduction

Non-typhoidal Salmonella (NTS) infections typically present as localized inflammation near the intestinal mucosal epithelium. However, some NTS strains can breach the intestinal barrier and enter the bloodstream, leading to bacteremia and severe systemic infections. The mechanisms by which NTS invades the bloodstream remain unclear.

Methods

In this study, we isolated 36 NTS strains from patients with diarrhea and bacteremia at First Affiliated Hospital of Huzhou University. Strains represented two distinct clinical manifestations, and were subjected to whole-genome sequencing, comparative genomics, and genetic differentiation analysis to identify genes potentially involved in bloodstream invasion. Additionally, we conducted inhibition assays using quercetin, a chemical inhibitor of the identified gene pathways, to validate our findings.

Results

Our analysis revealed that genes distinguishing the bloodstream Salmonella isolates from the fecal Salmonella isolates were primarily involved in the AI-2 quorum sensing pathway and biofilm-associated protein transport. Subsequent biofilm formation assays demonstrated that the bloodstream isolates exhibited significantly higher biofilm formation capacity compared to the fecal isolates. Upon the addition of quercetin, biofilm formation was equally inhibited in both groups. Collectively, these findings suggest that genes involved in the AI-2 pathway and biofilm-associated protein transport may be key factors contributing to the development of bacteremia in NTS infections.

A Mini-Review on Multi-Hurdle Control of Salmonella Along Poultry Production Continuum

This mini-review presents common strategies for controlling Salmonella in poultry, addressing combined pre-harvest and post-harvest interventions to create a multi-hurdle approach. The goal is to highlight integrated approaches that enhance overall food safety and sustainability within the poultry industry. Current pre-harvest and post-harvest strategies are discussed, including industry practices and regulatory frameworks. Emphasis is placed on the implementation of biosecurity measures, vaccination, feed management, and environmental control in pre-harvest settings, as well as processing plant interventions such as antimicrobials for carcass decontamination, sanitation, and quality control measures. Pre-harvest strategies that have shown promise include enhanced biosecurity protocols, selective vaccinations for pathogenic Salmonella strains, and advanced feeding regimens. Post-harvest interventions, such as antimicrobial application for decontamination, have improved sanitation practices, and pathogen reduction technologies are also critical in reducing Salmonella prevalence. An integrated approach that combines both pre-harvest and post-harvest measures is essential for an effective Salmonella control program. Implementing a continuum of control strategies for Salmonella in poultry production is vital for ensuring food safety and protecting public health. Collaborative efforts between researchers, industry stakeholders, and policymakers are necessary to address emerging issues and enhance overall effectiveness.

Virulence factors of Salmonella Typhi: interplay between the bacteria and host macrophages

Salmonella Typhi (S. Typhi) is a Gram-negative bacterium that exclusively infects humans and causes typhoid fever- a major global public health concern responsible for approximately 9 million infections and 110,000 deaths annually. Macrophages, a key component of the innate immune system, play essential roles in pathogen clearance, antigen presentation, immune regulation, and tissue repair. As one of the primary targets of S. Typhi infection, macrophages significantly influence disease onset and progression. S. Typhi expresses a range of virulence factors, including the virulence-associated (Vi) capsule, outer membrane proteins (OMPs), flagella, fimbriae, type III secretion systems (T3SSs) and other genes encoded on Salmonella pathogenicity islands (SPIs), as well as toxins, regulatory factors, and virulence plasmids. These virulence factors facilitate S. Typhi's intracellular survival within macrophages by mediating processes such as adhesion, invasion, nutrient acquisition and immune evasion, ultimately enabling systemic infection. This review explores the role and molecular mechanisms of S. Typhi virulence factors in counteracting macrophage antimicrobial functions, providing insights for future research on typhoid pathogenesis and the development of potential therapeutic interventions.

A Multicellular In Vitro Model of the Human Intestine with Immunocompetent Features Highlights Host-Pathogen Interactions During Early Salmonella Typhimurium Infection

Studying the molecular basis of intestinal infections caused by enteric pathogens at the tissue level is challenging, because most human intestinal infection models have limitations, and results obtained from animals may not reflect the human situation. Infections with Salmonella enterica serovar Typhimurium (STm) have different outcomes between organisms. 3D tissue modeling of primary human material provides alternatives to animal experimentation, but epithelial co-culture with immune cells remains difficult. Macrophages, for instance, contribute to the immunocompetence of native tissue, yet their incorporation into human epithelial tissue models is challenging. A 3D immunocompetent tissue model of the human small intestine based on decellularized submucosa enriched with monocyte-derived macrophages (MDM) is established. The multicellular model recapitulated in vivo-like cellular diversity, especially the induction of GP2 positive microfold (M) cells. Infection studies with STm reveal that the pathogen physically interacts with these M-like cells. MDMs show trans-epithelial migration and phagocytosed STm within the model and the levels of inflammatory cytokines are induced upon STm infection. Infected epithelial cells are shed into the supernatant, potentially reflecting an intracellular reservoir of invasion-primed STm. Together, the 3D model of the human intestinal epithelium bears potential as an alternative to animals to identify human-specific processes underlying enteric bacterial infections.

Exosomal miR-27a-5p attenuates inflammation through Toll-like receptor 7 in foodborne Salmonella infections

Salmonella is a common food-borne pathogen that is highly pathogenic and infectious, causing serious harm to livestock breeding and food safety. Uncovering the mechanisms of Salmonella infection and immune evasion can effectively prevent Salmonella contamination of livestock and poultry food. Here, small RNA sequencing results showed that exosomes produced by naïve murine macrophages RAW 264.7 cells contained a unique enrichment of a set of microRNAs (miRNAs) after Salmonella infection. Quantitative real-time polymerase chain reaction (qPCR) analysis verified that the tested miRNA (i.e. miR-27a-5p, miR-92a-1-5p and miR-1249-5p) showed similar expression patterns, consistent with small RNA sequencing data. TargetScan database predicted that the most promising targets for the differentially expressed miRNAs were abundant in the immune system, infectious diseases, and signal transduction pathways. Dual-luciferase reporter assays confirmed that Toll-like receptor 7 (TLR7) was the target of miR-27a-5p. Western blotting and enzyme-linked immunosorbent assay (ELISA) results revealed that overexpression of miR-27a-5p suppressed inflammation by targeting TLR7/nuclear factor kappa-B (NF-κB) signaling pathway and leading interleukin-6 (IL-6) and IL-1β cytokines slightly reduction in recipient macrophages, suggesting that exosomal miR-27a-5p uptake by naïve macrophages may inhibit pro-inflammatory macrophage differentiation. Therefore, these results contribute to our systematic understanding of the mechanism of exosomal miRNA in Salmonella infection, providing a potential target for preventing immune escape from Salmonella.

Ecotin protects Salmonella Typhimurium against the microbicidal activity of host proteases

Salmonella enterica serovar Typhimurium causes acute diarrhea upon oral infection in humans. The harsh and proteolytic environment found in the gastrointestinal tract is the first obstacle that these bacteria face after infection. However, the mechanisms that allow Salmonella to survive the hostile conditions of the gut are poorly understood. The ecotin gene is found in an extensive range of known phyla of bacteria and it encodes a protein that has been shown to inhibit serine proteases. Thus, in the present work we studied the role of ecotin of Salmonella Typhimurium in host-pathogen interactions. We found that the Salmonella Typhimurium ∆ecotin strain exhibited lower inflammation in a murine model of Salmonella induced colitis. The ∆ecotin mutant was more susceptible to the action of pancreatin and purified pancreatic elastase. In addition, the lack of ecotin led to impaired adhesion to Caco-2 and HT-29 cell lines, related to the proteolytic activity of brush border enzymes. Besides, ∆ecotin showed higher susceptibility to lysosomal proteolytic content and intracellular replication defects in macrophages. In addition, we found Ecotin to have a crucial role in Salmonella against the microbicidal action of granule contents and neutrophil extracellular traps released from human polymorphonuclear leukocytes. Thus, the work presented here highlights the importance of ecotin in Salmonella as countermeasures against the host proteolytic defense system.

Genomic identification of a pair of multidrug-resistant but non-pathogenic Salmonella enterica serovar Goldcoast isolates in southeast China

Introduction

Salmonella is an important foodborne pathogen that can induce severe diseases such as gastrointestinal disease and typhoid fever. Accumulating evidence revealed that Salmonella's resistance to antibiotics also seriously affects human health. Pathogenic Salmonella enterica serovar Goldcoast (S. Goldcoast) was first detected in 2010 in China and was predicted to have an increasing tendency.

Methods

The MacConkey agar, Salmonella Shigella agar, three-sugar iron agar slant, and Gram-stained microscopic examination were used for strain identification. Gram-negative bacteria identification cards explored more properties of the isolates, while antimicrobial susceptibility testing was used to examine the multidrug resistance. The 2nd and 3rd generation sequencing revealed the genetic information of the isolates.

Results

Two non-pathogenic isolates with multidrug resistance, JS33 and JS34, harbored 42 antibiotic-resistant genes (ARGs) in contig1 and 13 ARGs in contig2, were isolated from a healthy donor living in southeast China and identified as S. Goldcoast (6,8:r:l,w). Interestingly, JS33 and JS34 showed identical responses to more than 20 antimicrobial agents and were resistant to ampicillin, selectrin, chloramphenicol, tetracycline, and streptomycin. However, JS33 differed from JS34 in hydrogen sulfide (H2S) generation. The genomic sequencing identified a deletion in thiosulfate reductase (K08352) in JS34.

Discussion

H2S is an essential physiological regulator linked to inflammation and cancer. Therefore, genomic identification of JS33 and JS34 provided us with a better understanding of drug resistance and could be used as model strains to study the effects of microbial H2S production on the host. Since JS33 and JS34 did not induce gastrointestinal infection or other clinical symptoms as previously reported, the appearance of non-pathogenic S. Goldcoast in southeast China warned us to prepare for the prevalence of antimicrobial-resistant S. Goldcoast in China.

Construction and characterization of bioluminescent Salmonella Reading outbreak and non-outbreak strains

Salmonella enterica serotype Reading has recently been identified as a significant foodborne pathogen from contaminated poultry products. There is a critical need for close monitoring of this newly emerged pathogen. This study developed bioluminescent strains of S. Reading for real-time pathogen tracking using bioluminescence imaging. Two strains of S. Reading were used: an outbreak strain and a non-outbreak strain. The chloramphenicol acetyltransferase gene was cloned into the plasmid pBS-slpGFPluxABCDE, which carries luxABCDE operon and an ampicillin resistance gene. The newly constructed plasmid was then transformed into the outbreak and non-outbreak strains of S. Reading by electroporation. The resulting colonies were confirmed by visualizing bioluminescence using an in vivo imaging system and by testing their resistance to chloramphenicol. These strains demonstrated a high bioluminescence level (108-109 Photons/s/cm2/sr) and were tested for growth and plasmid stability by daily subculturing in Luria-Bertani medium with and without antibiotics. The plasmid remained stable for 8 days under non-selective conditions, and growth rates were comparable to non-bioluminescent parent strains in antibiotic-free conditions. However, growth was notably different in the presence of chloramphenicol, indicating successful plasmid retention and function. This study successfully created stable bioluminescent S. Reading strains, marking a significant step forward in monitoring and potentially reducing the spread of this emergent foodborne pathogen in the poultry industry.

IMPORTANCE

Salmonella enterica serotype Reading has recently become a significant foodborne pathogen linked to poultry products. To enhance pathogen monitoring, this study developed bioluminescent strains of S. Reading by inserting the chloramphenicol acetyltransferase gene into a plasmid containing a bioluminescence gene cluster. These modified strains were transformed into outbreak and non-outbreak bacterial strains via electroporation. The bioluminescent strains demonstrated stable plasmid retention and high bioluminescence levels. They also showed growth comparable to their parent strains, even in the absence of antibiotics. These bioluminescent strains could potentially facilitate real-time monitoring and control of S. Reading in poultry industries.

Comparative Patho-Genomics of Salmonella enterica Serovar Enteritidis Reveal Potential Host-Specific Virulence Factors

Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of the most common causes of bacterial foodborne infections worldwide. It has an extensive host range, including birds and humans, making it one of the most adaptable Salmonella serovars. This study aims to define the virulence gene profile of S. Enteritidis and identify genes critical to its host specificity. Currently, there is limited understanding of the molecular mechanisms that allow S. Enteritidis to continue as an important foodborne pathogen. To better understand the genes that may play a role in the host-specific virulence and/or fitness of S. Enteritidis, we first compiled a virulence gene profile-based genome analysis of sequenced S. Enteritidis strains isolated from shell eggs in our laboratory. This analysis was subsequently used to compare the representative genomes of Salmonella serovars with varying host ranges and S. Enteritidis genomes. The study involved a comprehensive and direct examination of the conservation of virulence and/or fitness factors, especially in a host-specific manner-an area that has not been previously explored. Key findings include the identification of 10 virulence-associated clusters of orthologous genes (COGs) specific to poultry-colonizing serovars and 12 virulence-associated COGs unique to human-colonizing serovars. Virulence/fitness-associated gene analysis identified more than 600 genes. The genome sequences of the two S. Enteritidis isolates were compared to those of the other serovars. Genome analysis revealed a core of 2817 COGs that were common to all the Salmonella serovars examined. Comparative genome analysis revealed that 10 virulence-associated COGs were specific to poultry-colonizing serovars, whereas 12 virulence-associated COGs were present in all human-colonizing serovars. Phylogenetic analyses further highlight the evolution of host specificity in S. Enteritidis. This study offers the first comprehensive analysis of genes that may be unique to and possibly essential for the colonization and/or pathogenesis of S. Enteritidis in various and specific hosts.

Phage-ELISA for ultrasensitive detection of Salmonella enteritidis

The M13 phage carries approximately 5 copies of the pIII protein, each of which is capable of displaying a single-chain variable fragment (scFv) that targets a specific antigen. This feature enables the M13 phage to be widely employed in the construction of scFv libraries, thereby facilitating the identification of antibodies with high specificity and affinity for target antigens. In this study, mice were immunized three times with Salmonella enteritidis (strain C50041) to induce diverse antibodies. The variable region sequences were subsequently amplified by PCR using genome extracted from the mice's splenic cells and fused to the pIII protein to construct the scFv phage display library (C50041-M13-scFv). Through biopanning with the C50041-M13-scFv library, a phage clone (C50041-scFv-4) exhibiting high affinity for the target bacteria was successfully obtained. Moreover, the scFv antibody (scFv-4) derived from C50041-scFv-4 was expressed in a prokaryotic expression system and validated to possess high specificity and affinity for C50041 through in vitro adsorption assays. Additionally, a phage-ELISA method was established: initially, bacteria were immobilized on the bottom surface of a 96-well plate. Next, the positive clone C50041-scFv-4 was introduced to specifically bind to the host cells. Finally, horseradish peroxidase (HRP)-conjugated anti-pVIII antibodies were used to detect the pVIII proteins of the bound phage clones. Owing to the capacity of multiple C50041-scFv-4 probes to simultaneously bind to a single target Salmonella and each phage clone's ability to accommodate hundreds of HRP-labeled antibodies, the proposed phage-ELISA demonstrated remarkable sensitivity (104 CFU mL-1) for detecting Salmonella enteritidis samples. This sensitivity surpasses that of traditional ELISA by one order of magnitude in this study. Our phage-ELISA technology exhibits broad applicability across various biological species and provides an improved and robust platform for pathogen detection including bacteria and viruses.

Isolation, characterization and liposome-loaded encapsulation of a novel virulent Salmonella phage vB-SeS-01

Introduction

Salmonella is a common foodborne pathogenic bacterium, displaying facultative intracellular parasitic behavior, which can help the escape against antibiotics treatment. Bacteriophages have the potential to control both intracellular and facultative intracellular bacteria and can be developed as antibiotic alternatives.

Methods

This study isolated and characterized vB-SeS-01, a novel Guernseyvirinae phage preying on Salmonella enterica, whose genome is closely related to those of phages SHWT1 and vB-SenS-EnJE1. Furthermore, nine phage-carrying liposome formulations were developed by film hydration method and via liposome extruder.

Results and Discussion

Phage vB-SeS-01 displays strong lysis ability against 9 out of 24 tested S. enterica strains (including the pathogenic "Sendai" and "Enteritidis" serovars), high replicability with a burst size of 111 ± 15 PFU/ cell and a titre up to 2.1 × 1011 PFU/mL, and broad pH (4.0 ~ 13.0) and temperature (4 ~ 80°C) stabilities. Among the nine vB-SeS-01 liposome-carrying formulations, the one encapsulated with PC:Chol:T80:SA = 9:1:2:0.5 without sonication displayed the optimal features. This formulation carried up to 1011 PFU/mL, with an encapsulation rate of 80%, an average size of 172.8 nm, and a polydispersity index (PDI) of 0.087. It remained stable at 4°C and 23°C for at least 21 days and at 37°C for 7 days. Both vB-SeS-01 and vB-SeS-01-loaded liposomes displayed intracellular antimicrobial effects and could reduce the transcription level of some tested intracellular inflammatory factors caused by the infected S. enterica sv. Sendai 16,226 and Enteritidis 50041CMCC.

Whole-genome sequencing-based characterization of Salmonella enterica Serovar Enteritidis and Kentucky isolated from laying hens in northwest of Iran, 2022-2023

BACKGROUND

The transmission of Salmonella spp. to human through the consumption of contaminated food products of animal origin, mainly poultry is a significant global public health concern. The emerging multidrug resistant (MDR) clones of non-typhoidal Salmonella (NTS) serovars, have spread rapidly worldwide both in humans and in the food chain. In this study NTS strains were isolated from diseased laying hens in Iran and were further studied by whole-genome sequencing (WGS) to investigate the prevalent serovars, multilocus sequence types, antimicrobial resistance and virulence genes.

RESULTS

Out of eight isolated Salmonella spp. six were identified as S. Enteritidis serovar ST11 (n = 5) or ST5824 (n = 1), and two isolates were recognized as S. Kentucky serotype ST198 lineages. The aminoglycoside resistance gene aac(6')-Iaa was the most frequently detected gene being present in all serovars, but it did not confer phenotypic resistance to corresponding agents (tobramycin and amikacin). All S. Enteritidis isolates carried a single GyrA D87N/Y substitution. Other identified antimicrobial resistance genes (ARGs) including tetA, floR, sul1, dfrA1, aph(3')-Ia and double gyrA and parC mutations conferring high-level ciprofloxacin resistance (CIPR) (MIC ≥ 16mg/L) were only found in S. Kentucky isolates. The comparison of phenotypic and genotypic antimicrobial resistance (AMR) profiles revealed inconsistent results for some antibiotics. A total of 11 different Salmonella Pathogenicity Islands (SPIs) including SPIs-1, to 5, 9, 10, 13, 14, C63PI, CS54 and several virulence genes related to type III secretion system, adhesins, iron and magnesium uptake, serum and antimicrobial peptide resistance were detected among the isolates.

CONCLUSIONS

Our study reports emergence of a highly MDR- CIPR S. Kentucky ST198 clone form poultry associated sources in Iran. The presence of numerous virulence determinants, SPIs and ARGs in the examined NTS isolates poses a significant risk for food safety. The inconsistencies between the genotypic and phenotypic AMR profiles indicate that WGS data alone may not be always sufficient for guiding therapeutic strategies.

Biomolecule screen identifies several inhibitors of Salmonella enterica surface colonization

Salmonella enterica is a foodborne pathogen commonly found in agricultural facilities; its prevalence, as well as increasing levels of disinfectant- and antibiotic-resistance, has significant costs for agriculture as well as human health. In an effort to identify potential new inhibitors of S. enterica on abiotic surfaces, we developed a biomolecule screen of nutrient-type compounds because nutrients would have lower toxicity in animal facilities and bacterial nutrient utilization pathways might prove less susceptible to the development of bacterial resistance. After screening 285 nutrient-type compounds, we identified ten that significantly inhibited the ability of S. enterica to colonize a plastic surface. After conducting a dose-response curve, salicylic acid was selected for further testing due to its low minimal inhibitory concentration (62.5 μM) as well as a low total inhibitory concentration (250 μM). Salicylic acid was also able to inhibit surface colonization of a wide range of bacterial pathogens, suggesting that our biomolecule screen might have broader application beyond S. enterica. Finally, we determined that salicylic acid was also able to inhibit S. enterica colonization of an organic surface on eggshells. Together, these results suggest that nutrient-type biomolecules may provide an avenue for preventing resistant bacteria from contaminating surfaces.

Foodborne Infections and Salmonella: Current Primary Prevention Tools and Future Perspectives

Salmonella is considered the major zoonotic and foodborne pathogen responsible for human infections. It includes the serovars causing typhoid fever (S. typhi and S. paratyphi) and the non-typhoidal salmonella (NTS) serovars (S. enteritidis and S. typhimurium), causing enteric infections known as "Salmonellosis". NTS represents a major public health burden worldwide. The consumption of S. enteritidis-contaminated animal foods is the main source of this disease in humans, and eradicating bacteria from animals remains a challenge. NTS causes various clinical manifestations, depending on the quantity of bacteria present in the food and the immune status of the infected individual, ranging from localized, self-limiting gastroenteritis to more serious systemic infections. Salmonellosis prevention is based on hygienic and behavioral rules related to food handling that aim to reduce the risk of infection. However, no vaccine against NTS is available for human use. This aspect, in addition to the increase in multidrug-resistant strains and the high morbidity, mortality, and socioeconomic costs of NTS-related diseases, makes the development of new prevention and control strategies urgently needed. The success of the vaccines used to protect against S. typhi encouraged the development of NTS vaccine candidates, including live attenuated, subunit-based, and recombinant-protein-based vaccines. In this review, we discuss the epidemiological burden of Salmonellosis and its primary prevention, focusing on the current status and future perspectives of the vaccines against NTS.

Integrons in the Age of Antibiotic Resistance: Evolution, Mechanisms, and Environmental Implications: A Review

Integrons, which are genetic components commonly found in bacteria, possess the remarkable capacity to capture gene cassettes, incorporate them into their structure, and thereby contribute to an increase in genomic complexity and phenotypic diversity. This adaptive mechanism allows integrons to play a significant role in acquiring, expressing, and spreading antibiotic resistance genes in the modern age. To assess the current challenges posed by integrons, it is necessary to have a thorough understanding of their characteristics. This review aims to elucidate the structure and evolutionary history of integrons, highlighting how the use of antibiotics has led to the preferential selection of integrons in various environments. Additionally, it explores their current involvement in antibiotic resistance and their dissemination across diverse settings, while considering potential transmission factors and routes. This review delves into the arrangement of gene cassettes within integrons, their ability to rearrange, the mechanisms governing their expression, and the process of excision. Furthermore, this study examines the presence of clinically relevant integrons in a wide range of environmental sources, shedding light on how anthropogenic influences contribute to their propagation into the environment.

Genetic engineering of Salmonella spp. for novel vaccine strategies and therapeutics

Salmonella enterica is a diverse species that infects both humans and animals. S. enterica subspecies enterica consists of more than 1,500 serovars. Unlike typhoidal Salmonella serovars which are human host-restricted, non-typhoidal Salmonella (NTS) serovars are associated with foodborne illnesses worldwide and are transmitted via the food chain. Additionally, NTS serovars can cause disease in livestock animals causing significant economic losses. Salmonella is a well-studied model organism that is easy to manipulate and evaluate in animal models of infection. Advances in genetic engineering approaches in recent years have led to the development of Salmonella vaccines for both humans and animals. In this review, we focus on current progress of recombinant live-attenuated Salmonella vaccines, their use as a source of antigens for parenteral vaccines, their use as live-vector vaccines to deliver foreign antigens, and their use as therapeutic cancer vaccines in humans. We also describe development of live-attenuated Salmonella vaccines and live-vector vaccines for use in animals.

Geography, Antimicrobial Resistance, and Genomics of Salmonella enterica (Serotypes Newport and Anatum) from Meat in Mexico (2021-2023)

Salmonella enterica non-typhoidal is a major contributor to diarrheal diseases, with over 2600 serovars identified across diverse environments. In Mexico, serovars Newport and Anatum have shown a marked increase, especially in foodborne disease, posing a public health problem. We conducted a cross-sectional study from 2021 to 2023 using active epidemiological surveillance to assess contamination in ground beef and pork at butcher shops nationwide. It involved isolation, phenotypic antimicrobial resistance, comparative genomics, spatial distribution, antimicrobial-resistance genes, and pangenome analysis. A total of 402 non-typhoidal S. enterica strains were isolated, including 59 Newport and 50 Anatum. After curating for redundancy, 45 Newport and 32 Anatum strains remained. We found that 75% of Newport strains exhibited multidrug resistance (MDR), compared to 25% of Anatum strains. Salmonella Newport also showed a broader distribution and stronger antibiotic-resistance capacity, particularly due to genes such as mphA and ramA. Our pangenome analysis showed a predominance of cell maintenance and survival-process genes in the accessory genome of both serotypes. Considering unique genes, Salmonella Anatum and Newport showed a notorious abundance of genes with functions related to replication, recombination, and repair. The substantial rise of Anatum and Newport strains in meat samples for human consumption presents an epidemiological alert, highlighting the critical need for stringent surveillance programs to mitigate human and ecosystem health risks.

Advancing vaccine technology through the manipulation of pathogenic and commensal bacteria

Advancements in vaccine technology are increasingly focused on leveraging the unique properties of both pathogenic and commensal bacteria. This revolutionary approach harnesses the diverse immune modulatory mechanisms and bacterial biology inherent in different bacterial species enhancing vaccine efficacy and safety. Pathogenic bacteria, known for their ability to induce robust immune responses, are being studied for their potential to be engineered into safe, attenuated vectors that can target specific diseases with high precision. Concurrently, commensal bacteria, which coexist harmlessly with their hosts and contribute to immune system regulation, are also being explored as novel delivery systems and in microbiome-based therapy. These bacteria can modulate immune responses, offering a promising avenue for developing effective and personalized vaccines. Integrating the distinctive characteristics of pathogenic and commensal bacteria with advanced bacterial engineering techniques paves the way for innovative vaccine and therapeutic platforms that could address a wide range of infectious diseases and potentially non-infectious conditions. This holistic approach signifies a paradigm shift in vaccine development and immunotherapy, emphasizing the intricate interplay between the bacteria and the immune systems to achieve optimal immunological outcomes.

Non-typhoidal Salmonella in humans in India, Vietnam, Bangladesh and Sri Lanka: a systematic review

Objectives

Non-typhoidal Salmonella (NTS) commonly causes a self-limiting illness but invasive disease (iNTS) can be life-threatening. Antimicrobial resistance (AMR) increases the risk of mortality. This systematic review aimed to estimate the proportion of NTS isolated in those attending healthcare services, serovar burden, AMR, serovar-specific AMR, and case fatality rate (CFR) in India, Bangladesh, Sri Lanka and Vietnam.

Methods

The review included quantitative studies on NTS and AMR from 1980 to 2020 but excluded studies unrelated to humans or selected countries. Data were extracted from articles identified from Ovid SP, Web of Science, Wiley Cochrane Library, Elsevier Scopus and WHO Global Index Medicus. The Joanna Briggs Institute Critical Appraisal Tools Checklist for Prevalence Studies was used for risk-of-bias assessment. Meta-analyses were performed for the proportion of NTS isolated, the proportion of specific serovars isolated, percentage of AMR and CFR.

Results

Six thousand and twenty-six isolates (79 serovars) were identified from 73 studies, with Salmonella enterica serovar Typhimurium being the most common. Of the 73 selected studies, 46% were hospital/laboratory surveillance studies, examining the aetiology of invasive or non-invasive infections. The pooled proportion estimate for non-iNTS was 2.1% (95% CI: 1.2%-3.2%) and for iNTS was 0.3% (95% CI: 0.1%-0.5%). The pooled CFR was 14.9% (95% CI: 4.0%-29.6%). Pooled resistance estimates for ampicillin, ceftriaxone, chloramphenicol, ciprofloxacin, co-trimoxazole, nalidixic acid and azithromycin were calculated. MDR iNTS was less prevalent in India [22.3% (95% CI: 0.0%-66.8%)] than in Vietnam [41.2% (95% CI: 33.6%-49.3%)]. Heterogeneity of studies was high as the majority were observational surveillance studies.

Conclusions

Despite data scarcity in some countries, this review highlights the continued contribution of NTS infection to disease burden, compounded by high AMR rates.

TolC facilitates the intracellular survival and immunomodulation of Salmonella Typhi in human host cells

Salmonella enterica serovar Typhi (S. Typhi) causes typhoid fever, a systemic infection that affects millions of people worldwide. S. Typhi can invade and survive within host cells, such as intestinal epithelial cells and macrophages, by modulating their immune responses. However, the immunomodulatory capability of S. Typhi in relation to TolC-facilitated efflux pump function remains unclear. The role of TolC, an outer membrane protein that facilitates efflux pump function, in the invasion and immunomodulation of S. Typhi, was studied in human intestinal epithelial cells and macrophages. The tolC deletion mutant of S. Typhi was compared with the wild-type and its complemented strain in terms of their ability to invade epithelial cells, survive and induce cytotoxicity in macrophages, and elicit proinflammatory cytokine production in macrophages. The tolC mutant, which has a defective outer membrane, was impaired in invading epithelial cells compared to the wild-type strain, but the intracellular presence of the tolC mutant exhibited greater cytotoxicity and induced higher levels of proinflammatory cytokines (IL-1β and IL-8) in macrophages compared to the wild-type strain. These effects were reversed by complementing the tolC mutant with a functional tolC gene. Our results suggest that TolC plays a role in S. Typhi to efficiently invade epithelial cells and suppress host immune responses during infection. TolC may be a potential target for the development of novel therapeutics against typhoid fever.

LGG promotes activation of intestinal ILC3 through TLR2 receptor and inhibits salmonella typhimurium infection in mice

Salmonella is a foodborne pathogen that causes disruption of intestinal mucosal immunity, leading to acute gastroenteritis in the host. In this study, we found that Salmonella Typhimurium (STM) infection of the intestinal tract of mice led to a significant increase in the proportion of Lacticaseibacillus, while the secretion of IL-22 from type 3 innate lymphoid cells (ILC3) increased significantly. Feeding Lacticaseibacillus rhamnosus GG (LGG) effectively alleviated the infection of STM in the mouse intestines. TLR2-/- mice experiments found that TLR2-expressing dendritic cells (DCs) are crucial for LGG's activation of ILC3. Subsequent in vitro experiments showed that heat-killed LGG (HK-LGG) could promote DCs to secrete IL-23, which in turn further promotes the activation of ILC3 and the secretion of IL-22. Finally, organoid experiments further verified that IL-22 secreted by ILC3 can enhance the intestinal mucosal immune barrier and inhibit STM infection. This study demonstrates that oral administration of LGG is a potential method for inhibiting STM infection.

Antimicrobial Susceptibility Profiles of Salmonella spp. Isolates from Clinical Cases of Waterfowl in Hungary Between 2022 and 2023

The global spread of antimicrobial resistance is one of the most significant challenges of the 21st century. The waterfowl sector is an economically decisive part of the poultry industry, yet it remains under-researched, and its antibiotic usage is less monitored. Our study aimed to determine the antimicrobial susceptibility of avian pathogenic Salmonella strains, which are still prevalent in ducks and geese, against antibiotics critical for both animal and human health, and to compare these findings with human resistance data. We analyzed 71 Salmonella strains, collected by the National Reference Laboratory from samples originating from 29 settlements across Hungary between 2022 and 2023, using the minimum inhibitory concentration (MIC) method. Notably, the duck strains (n = 52) exhibited 57.7% resistance to potentiated sulfonamides, 28.8% resistance to doxycycline, and 25% resistance to cefotaxime. Among the geese strains (n = 19), 52.6% showed resistance to potentiated sulfonamides, followed by 26.3% resistance to doxycycline and amoxicillin-clavulanic acid, and 15.8% resistance to cefotaxime, ceftiofur, and ceftriaxone. When compared to human resistance data, we found significantly lower resistance levels for amoxicillin in ducks (20.0%) and geese (8.3%) in the Dél-Alföld region, compared to ampicillin resistance in human samples (45.4%), in which amoxicillin analog is an antibiotic in human medicine. Resistance to ciprofloxacin was only observed in ducks (2.0%), whereas pefloxacin resistance in human medicine was notably higher (22.3%). Overall, the results for the waterfowl sector in the Dél-Alföld region of Hungary align with the international literature in several aspects. Further investigation using next-generation sequencing to identify the genetic basis of multi-resistant strains is warranted.

Bridging Classical Methodologies in Salmonella Investigation with Modern Technologies: A Comprehensive Review

Advancements in genomics and machine learning have significantly enhanced the study of Salmonella epidemiology. Whole-genome sequencing has revolutionized bacterial genomics, allowing for detailed analysis of genetic variation and aiding in outbreak investigations and source tracking. Short-read sequencing technologies, such as those provided by Illumina, have been instrumental in generating draft genomes that facilitate serotyping and the detection of antimicrobial resistance. Long-read sequencing technologies, including those from Pacific Biosciences and Oxford Nanopore Technologies, offer the potential for more complete genome assemblies and better insights into genetic diversity. In addition to these sequencing approaches, machine learning techniques like decision trees and random forests provide powerful tools for pattern recognition and predictive modeling. Importantly, the study of bacteriophages, which interact with Salmonella, offers additional layers of understanding. Phages can impact Salmonella population dynamics and evolution, and their integration into Salmonella genomics research holds promise for novel insights into pathogen control and epidemiology. This review revisits the history of Salmonella and its pathogenesis and highlights the integration of these modern methodologies in advancing our understanding of Salmonella.

First report of salmonella Dublin subdural empyema: A rare presentation of CNS infection

Subdural empyema can be precipitated by a range of pathogens. Common clinical symptoms include fever, headache, seizures, and changed mental status. Yet, cerebral infections caused by Salmonella are relatively uncommon as it is rare for Salmonella to invade the central nervous system. We present the first reported case of Salmonella enterica serovar Dublin causing subdural empyema in an 83-year-old female, which was successfully managed with surgical burr hole and drainage in addition to prolonged targeted antimicrobial therapy consisting of 2 g of intravenous Ceftriaxone twice daily for a total of 56 days. This report demonstrates the course of her illness and the corresponding treatment plan; which may help guide medical providers when encountering similar cases.

Genomic epidemiology and phenotypic characterisation of Salmonella enterica serovar Panama in Victoria, Australia

Salmonella enterica serovar Panama, a causative agent of non-typhoidal salmonellosis (NTS), is one of several serovars that causes invasive NTS disease (iNTS) in humans. S. Panama is an understudied pathogen, with its pathobiology poorly understood. It is a predominant iNTS serovar in Australia, a high-income country with high rates of salmonellosis, where S. Panama has been documented to have a high odds ratio (13.9-15.26) for causing iNTS. This study investigates the genomic epidemiology and antimicrobial resistance profiles of all S. Panama isolates recovered in Victoria, Australia, between 2000 and 2021. We examined the infection dynamics of S. Panama in seven isolates, representing the genetic diversity of the study population. Two sub-lineages, encompassed within a previously described Asian lineage, were identified. Multi-drug resistance (resistance to ≥3 drug classes) was detected in 46 (51.7%) Australian isolates. The plasmid-mediated colistin resistance gene, mcr1.1, was detected in one Australian S. Panama isolate, carried by an IncI plasmid previously reported in Salmonella and Escherichia coli isolates collected from poultry in South-East Asia. Examination of the intracellular replication dynamics of S. Panama isolates demonstrated diverse phenotypes. In THP-1 derived macrophages, despite low host cell uptake, S. Panama showed higher replication rates over time compared to S. enterica serovar Typhimurium. However, a causative genotype could not be identified to explain this observed phenotype. This study provides insights into the S. Panama isolates circulating in Australia over two-decades, finding that 78% were linked to international travel suggesting importation in Australia. It shows MDR was common in this iNTS serovar, and colistin resistance reported for the first time. It provides the first data on the host-pathogen interactions of S. Panama in Australia, which will aid our collective understanding of the pathobiology of S. Panama and iNTS serovars more broadly.

Serovars, virulence factors, and antimicrobial resistance profile of non-typhoidal Salmonella in the human-dairy interface in Northwest Ethiopia: A one health approach

Non-typhoidal Salmonella (NTS) is a zoonotic pathogen that exerts huge public health and economic impacts in the world. The severity of illness is mainly related to the serovars involved, the presence of virulence genes, and antimicrobial resistance (AMR) patterns. However, data are scarce on serovars, virulence genes, and AMR among NTS identified from the human-dairy interface in Northwest Ethiopia. Thus, this study investigated the serovars, common virulence genes, and AMR patterns of NTS isolates in the area. The study was conducted from June 2022 to August 2023 among randomly selected 58 dairy farms. A total of 362 samples were processed to detect NTS using standard bacteriological methods. The presumptive positive colonies were confirmed by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight (MALDi-ToF). Polymerase chain reaction (PCR) was used to detect virulence genes, including invA and spvC. A slide agglutination test according to the White-Kauffmann-Le Minor scheme was employed to identify the serovars of the NTS isolates. The Kirby-Bauer disk diffusion method was used to assess the antimicrobial susceptibility patterns. Of the processed samples (362), 28 (7.7%) NTS isolates were detected. When distributed among samples, the proportions were 11.9%, 10.5%, 10.3%, 5.2%, 4.3%, and 1.7% among cows' feces, dairy farm sewage, pooled raw milk, milk container swabs, milkers' stool, and milkers' hand swab samples, respectively. Six serovars were detected with the dominancy of S. Uganda (39.3%), followed by S. enterica subsp. diarizonae (25.0%) and S. Typhimurium (21.4%). Among the 28 NTS isolates, 100% and 21.4% had the virulence genes invA and spvC, respectively. The susceptibility profile showed that 89.3% of the NTS isolates were resistant to at least one antimicrobial agent and 46.4% were resistant to three or more classes of antimicrobials (multidrug-resistant). Among antimicrobials, isolates were highly resistant to ampicillin (57.1%), followed by tetracycline (42.9%) and chloramphenicol (35.7%). On the other hand, the NTS isolates were 100%, 96.4%, and 96.4% susceptible to ceftriaxone, azithromycin, and norfloxacin, respectively. In conclusion, we detected NTS from humans, dairy cows, raw milk, dairy utensils, and the environment (sewage), showing the potential of the human-dairy farm-environment nexus in the NTS circulation. These further highlight that the interface is a good point of intervention in the control and prevention of NTS infection. The susceptibility profiles of the isolate necessitate interventions including the prudent use of the antimicrobials.

One-tube detection of Salmonella Typhimurium using LAMP and CRISPR-Cas12b

Salmonella enterica serovar Typhimurium (ST) is a predominant serovar causing foodborne illnesses worldwide. Traditional detection methods often face challenges, including the need for specialized equipment, skilled operators, and lengthy procedures. To address these limitations, we developed a rapid, sensitive, and specific ST detection method by integrating loop-mediated isothermal amplification (LAMP) with the clustered regularly interspaced short palindromic repeats and associated protein 12b (CRISPR/Cas12b) system, all within a single tube. Our results indicate that the LAMP-CRISPR/Cas12b reaction can be completed isothermally in under 1 h without requiring specialized instruments. The platform's limit of detection (LoD) is 12.5 copies per reaction. Additionally, the system demonstrated 100% inclusivity and exclusivity when tested against 30 reference strains, highlighting its specificity. In practical applications, the LoDs for ST in pure nucleic acid and contaminated fecal samples were 2.32 and 23.2 CFU/mL, respectively, with higher sensitivity observed in pure nucleic acid samples. Overall, our findings underscore the potential of the one-tube LAMP-CRISPR/Cas12b platform as a rapid, sensitive, and specific tool for ST detection, particularly in resource-limited settings.

IMPORTANCE

Here, we have provided a novel one-step method for Salmonella Typhimurium detection in one pot by integrating the LAMP assay with the CRISPR/Cas12b system, offering significant advantages in terms of simplicity, speed, and accuracy.

D-galactonate metabolism in enteric bacteria: a molecular and physiological perspective

D-galactonate, a widely prevalent sugar acid, was first reported as a nutrient source for enteric bacteria in the 1970s. Since then, decades of research enabled a description of the modified Entner-Doudoroff pathway involved in its degradation and reported the structural and biochemical features of its metabolic enzymes, primarily in Escherichia coli K-12. However, only in the last few years, the D-galactonate transporter has been characterized, and the regulation of the dgo operon, encoding the structural genes for the transporter and enzymes of D-galactonate metabolism, has been detailed. Notably, in recent years, multiple evolutionary studies have identified the dgo operon as a dominant target for adaptation of E. coli in the mammalian gut. Despite considerable research on dgo operon, numerous fundamental questions remain to be addressed. The emerging relevance of the dgo operon in host-bacterial interactions further necessitates the study of D-galactonate metabolism in other enterobacterial strains.

Whole-Genome Sequencing Reveals the Population Structure and Genetic Diversity of Salmonella Typhimurium ST34 and ST19 Lineages

Salmonella Typhimurium is an invasive gastrointestinal pathogen for both humans and animals. To investigate the genetic framework and diversity of S. Typhimurium, a total of 194 S. Typhimurium isolates were collected from patients in a tertiary hospital between 2020 and 2021. Antimicrobial susceptibility testing was used to confirm the resistance phenotype. Whole-genome sequencing and bioinformatics analysis were performed to determine the sequence type, phylogenetic relationships, resistance gene profiles, Salmonella pathogenicity island (SPI) and the diversity of the core and pan genome. The result showed that 57.22% of S. Typhimurium isolates were multidrug resistant and resistance of total isolates to the first-line drug ciprofloxacin was identified in 60.82%. The population structure of S. Typhimurium was categorized into three lineages: ST19 (20.10%, 39/194), ST34-1 (47.42%, 92/194) and ST34-2 (40.65%, 63/194), with the population size exhibiting increasing trends. All lineages harbored variety of fimbrial operons, prophages, SPIs and effectors that contributed to the virulence and long-term infections of S. Typhimurium. Importantly, ST34-1 lineage might potentially be more invasive due to the possession of SPI1-effector gene sopE which was essential for the proliferation, internalization and intracellular presence of S. Typhimurium in hosts. Multiple antimicrobial resistance genes were characteristically distributed across three lineages, especially carbapenem genes only detected in ST34-1&2 lineages. The distinct functional categories of pan genome among three lineages were observed in metabolism, signaling and gene information processing. This study provides a theoretical foundation for the evolved adaptation and genetic diversity of S. Typhimurium ST19 and ST34, among which ST34 lineages with multidrug resistance and potential hypervirulence need to pay more attention to epidemiological surveillance.

A novel phospholipase A2 is a core component of the typhoid toxin genetic islet

Salmonella Typhi, the cause of typhoid fever, is a bacterial pathogen of substantial global importance. Typhoid toxin is a secreted AB-type toxin that is a key S. Typhi virulence factor encoded within a 5-gene genetic islet. Four genes in this islet have well-defined roles in typhoid toxin biology; however, the function of the fifth gene is unknown. Here, we investigate the function of this gene, which we name ttaP. We show that ttaP is cotranscribed with the typhoid toxin subunit cdtB, and we perform genomic analyses that indicate that TtaP is very highly conserved in typhoid toxin islets found in diverse salmonellae. We show that TtaP is a distant homolog of group XIV secreted phospholipase A2 (PLA2) enzymes, and experimentally demonstrate that TtaP is a bona fide PLA2. Sequence and structural analyses indicate that TtaP differs substantially from characterized PLA2s, and thus represents a novel class of PLA2. Secretion assays revealed that TtaP is neither cosecreted with typhoid toxin, nor is it required for toxin secretion. Although TtaP is a phospholipase that remains associated with the S. Typhi cell, assays that probed for altered cell envelope integrity failed to identify any differences between WT S. Typhi and a ttaP deletion strain. Collectively, this study identifies a biochemical activity for the lone uncharacterized typhoid toxin islet gene and lays the groundwork for exploring how this gene factors into S. Typhi pathogenesis. This study further identifies a novel class of PLA2, enzymes that have a wide range of industrial applications.

Defense mechanisms of Salmonella against antibiotics: a review

Salmonella is a foodborne pathogenic bacterium that causes salmonellosis worldwide. Also, Salmonella is considered a serious problem for food safety and public health. Several antimicrobial classes including aminoglycosides, tetracyclines, phenols, and β-Lactams are used to treat Salmonella infections. Antibiotics have been prescribed for decades to treat infections caused by bacteria in human and animal healthcare. However, intensive use of antibiotics resulted in antibiotic resistance (AR) among several foodborne bacteria including Salmonella. Furthermore, multi-drug resistance (MDR) of Salmonella has increased dramatically. In addition to MDR Salmonella, extensively drug resistant (XDR) as well as pan drug resistant (PDR) Salmonella were reported globally. Therefore, increasing AR is becoming a serious universal public health crisis. Salmonella developed many mechanisms to ensure its survival against antimicrobials. The most prominent defense mechanisms against these antibiotics include enzymatic inactivation, expelling drugs from the cell through efflux pumps, altering the structure of drugs, and changing or protecting the targets of drugs. Additionally, the formation of biofilms and plasmid-mediated AR by Salmonella, enhancing its resistance to various antibiotics, making it a challenging pathogen in both healthcare and food industry settings. This review focuses exclusively on providing a detailed overview of the mechanisms of AR in Salmonella.

The prevalence of antimicrobial drug resistance of non-typhoidal Salmonella in human infections in sub-Saharan Africa: a systematic review and meta-analysis

INTRODUCTION

Non-typhoidal Salmonella (NTS) bacteremia is common in sub-Saharan Africa. We examined the prevalence of antibiotic resistance to fluoroquinolones, third-generation cephalosporins, and multi-drug resistance (MDR) in NTS human isolates from sub-Saharan Africa.

METHODS

A systematic review was conducted using a search in Ovid Medline, Embase, and African Index Medicus of publications between 2000 and 2021. A random-effects model meta-analysis was performed using data from 66 studies that included 29,039 NTS blood and 1,065 stool isolates.

RESULTS

The pooled prevalence proportions of MDR were 0.685 (95% CI 0.574-0.778) and 0.214 (0.020-0.785) in blood vs. stool isolates. The corresponding estimates of fluoroquinolones resistance were 0.014 (0.008-0.025) vs. 0.021 (0.012-0.036) and third-generation cephalosporins resistance 0.019 (0.012-0.031) vs. 0.035 (0.006-0.185). Similar results were found for children and adults. Resistance prevalence to these antibiotics in blood isolates increased between 2000-2010 and 2011-2021. The guidelines employed to determine antimicrobial resistance and epidemiological characteristics (e.g. sample size, study duration) correlated with the resistance prevalence.

CONCLUSIONS

The prevalence of MDR and resistance to fluoroquinolones and third-generation cephalosporins in NTS in sub-Saharan Africa is alarming.

EXPERT OPINION

Standardized surveillance of antimicrobial drug resistance in NTS in sub-Saharan Africa is warranted to guide healthcare policymaking and antibiotic stewardship programs.

Unveiling a Comprehensive Multi-epitope Subunit Vaccine Strategy Against Salmonella subsp. enterica: Bridging Core, Subtractive Proteomics, and Immunoinformatics

Salmonella subsp. enterica (SE) presents a significant global health challenge in both developed and developing countries. Current SE vaccines have limitations, targeting specific strains and demonstrating moderate efficacy in adults, while also being unsuitable for young children and often unaffordable in regions with lower income levels where the disease is prevalent. To address these challenges, this study employed a computational approach integrating core proteomics, subtractive proteomics, and immunoinformatics to develop a universal SE vaccine and identify potential drug targets. Analysis of the core proteome of 185 SE strains revealed 1964 conserved proteins. Subtractive proteomics identified 9 proteins as potential vaccine candidates and 41 as novel drug targets. Using reverse vaccinology-based immunoinformatics, four multi-epitope-based subunit vaccine constructs (MESVCs) were designed, aiming to stimulate cytotoxic T lymphocyte, helper T lymphocyte, and linear B lymphocyte responses. These constructs underwent comprehensive evaluations for antigenicity, immunogenicity, toxicity, hydropathicity, and physicochemical properties. Predictive modeling, refinement, and validation were conducted to determine the secondary and tertiary structures of the SE-MESVCs, followed by docking studies with MHC-I, MHC-II, and TLR4 receptors. Molecular docking assessments showed favorable binding with all three receptors, with SE-MESVC-4 exhibiting the most promising binding energy. Molecular dynamics simulations confirmed the binding affinity and stability of SE-MESVC-4 with the TLR4/MD2 complex. Additionally, codon optimization and in silico cloning verified the efficient translation and successful expression of SE-MESVC-4 in Escherichia coli (E. coli) str. K12. Subsequent in silico immune simulation evaluated the efficacy of SE-MESVC-4 in triggering an effective immune response. These results suggest that SE-MESVC-4 may induce both humoral and cellular immune responses, making it a potential candidate for an effective SE vaccine. However, further experimental investigations are necessary to validate the immunogenicity and efficacy of SE-MESVC-4, bringing us closer to effectively combating SE infections.

Ceftriaxone-resistant Salmonella enterica serovar Newport: a case report from South India

Salmonella enterica serovar Newport is a human pathogen underreported in most developing countries. It is known for causing gastroenteritis and extraintestinal infections. In this case report, we report the case of ceftriaxone-resistant Salmonella enterica serovar Newport from South India, causing acute gastroenteritis in a sixty-year-old female patient having a history of antimicrobial therapy and recent hospital admission. Serovar Newport, especially among antibiotic-exposed patients, poses a significant public health threat due to its ability to acquire multidrug resistance. This emphasizes the necessity for robust surveillance and monitoring of nontyphoidal Salmonella infections, particularly given the limited data on serovar Newport in India. Vigilance in clinical practice and public health initiatives is crucial to effectively address the emergence and spread of multidrug-resistant strains.

Class 1 and 2 integrons and antibiotic resistance profile in Salmonella spp. from San Cristobal River, Laguna, Philippines

Infection with multidrug resistant bacteria is a significant public health concern. Bacteria culture of water samples (n=120) collected in San Cristobal River, Philippines, showed that half (n=60) were positive for Salmonella spp. Screening of all isolates (n=179) for susceptibility to antibiotics showed that most (76.4%; n=113) were positive for class 1 integrons, of which one isolate was also positive for the class 2 integron. The presence of class 1 integrons was associated with resistance to antibiotics (p<0.05). Sequencing of class 1 integron variable regions (VRs) differeciated 11 gene cassettes: dfrA1 or dfrA17; aadA1 or aadA2; blaCTX-M-2 or bla-OXA-1; SmdAB; CmlA1 and aaC 3-Id. However, sequencing of class 2 integron VR differenciated estX, sat2, and aadA1. These results provide insights into evolutionary changes within bacterial multidrug resistant cassettes, more accurately to estimate heath risk associated with the river water.            .

Non-typhoidal Salmonella in Nigeria: do outcomes of 'multisectoral' surveillance, treatment and control justify the intervention costs?

Non-typhoidal salmonellosis (NTS) is significant and an economic burden in Nigeria. To determine whether investment in NTS control is economically justifiable, Outbreak Costing Tool (OCT) was used to estimate the robust funding of public and animal health systems for epidemio-surveillance and control of multisectoral NTS outbreaks in Nigeria. Health, production, and economic data were collected and used to populate the tool for evaluation. The multisectoral NTS burden for the year 2020 in Nigeria was US$ 930,887,379.00. Approximately 4,835 technical officers, and 3,700 non-technical staff (n = 8,535) were needed with an investment of >2.2 million work hours. The investment cost for NTS control was US$ 53,854,660.87. The non-labour-related cost was 89.21% of the total intervention costs. The overall intervention's investment was 374.15% of the estimated national and subnational systems' annual budget for diarrhoeal diseases, and the outbreak response period attracted the highest costs (53%) of the total intervention. In conclusion, intervention against NTS was beneficial (benefit - cost ratio: 17.29), hence justifying the need for multisectoral surveillance-response against NTS in Nigeria. Complex sectoral silos must give way to coordinated collaborations to optimize benefits; and over-centralization of health interventions' associated delays must be removed through decentralized sub-national-focused framework that empowers rapid investigation, response, control, data collection, and analyses. It should assist anticipatory planning, and outbreak investigation and reduce critical response time. Anticipatory planning tools, when applied pre-emptively, can benefit budgeting, identify gaps, and assist in the delivery of cost-saving and effective measures against infectious disease.

Retrospective study on the occurrence of Salmonella serotypes in veterinary specimens of Atlantic Canada (2012-2021)

AIM

This study aimed to summarize the frequency and the antimicrobial susceptibility profiles of the Salmonella serotypes identified from the specimens of companion animals, livestock, avian, wildlife and exotic species within Atlantic Canada.

MATERIALS AND METHODS

The retrospective electronic laboratory data of microbiological analyses of a selected subset of samples from 03 January 2012 to 29 December 2021 submitted from various animal species were retrieved. The frequency of Salmonella serotypes identified, and their antimicrobial susceptibility results obtained using the disk diffusion or broth method were analysed. The test results were interpreted according to the Clinical and Laboratory Standards Institute standard. The Salmonella serotypes were identified by slide agglutination (Kauffman-White-Le-Minor Scheme) and/or the Whole Genome Sequencing for the Salmonella in silico Serovar Typing Resource-based identification.

RESULTS

Of the cases included in this study, 4.6% (n = 154) had at least one Salmonella isolate, corresponding to 55 different serovars. Salmonella isolation was highest from exotic animal species (n = 40, 1.20%), followed by porcine (n = 26, 0.78%), and canine (n = 23, 0.69%). Salmonella subsp. enterica serovar Typhimurium was predominant among exotic mammals, porcine and caprine samples, whereas S. Enteritidis was mostly identified in bovine and canine samples. S. Typhimurium of porcine origin was frequently resistant (>70.0%) to ampicillin. In contrast, S. Typhimurium isolates from porcine and caprine samples were susceptible (>70.0%) to florfenicol. S. Oranienburg from equine samples was susceptible to chloramphenicol, but frequently resistant (>90.0%) to azithromycin. In avian samples, S. Copenhagen was susceptible (>90.0%) to florfenicol, whereas Muenchen was frequently resistant (>90.0%) to florfenicol. S. subsp. diarizonae serovar IIIb:61:k:1,5 of ovine origin was resistant (50.0% isolates) to sulfadimethoxine. No significant changes were observed in the antibiotic resistance profiles across the study years.

CONCLUSIONS

This report provides data for surveillance studies, distribution of Salmonella serotypes and their antimicrobial resistance among veterinary specimens of Atlantic Canada.

Antimicrobial resistance and genome characteristics of Salmonella enteritidis from Huzhou, China

Salmonella enteritidis is a main pathogen responsible for sporadic outbreaks of gastroenteritis, and therefore is an important public health problem. This study investigated the drug resistance and genomic characteristics of S. enteritidis isolated from clinical and food sources in Huzhou, Zhejiang Province, China, from February 1, 2021, to December 30, 2023. In total, 43 S. enteritidis strains isolated during the study period were subjected to virulence gene, drug resistance gene, genetic correlation, antibiotic resistance, and multilocus sequence typing analyses. All 43 isolates were identified as ST11, and contained 108 virulence-related genes. Drug sensitivity analysis of the 43 isolates showed resistance rates of 100% to nalidixic acid and 90.70% to ampicillin and ampicillin/sulbactam. Multidrug resistance is a serious issue, with 81.40% of strains resistant to three or more antibacterial drugs. Genome sequencing indicated that S. enteritidis possessed 23 drug resistance genes, of which 14 were common to all 43 isolates. Phylogenetic analysis based on core genome single-nucleotide polymorphisms divided the 43 S. enteritidis strains into three clusters, with the 10 samples from an outbreak forming an independent branch located in cluster 3.

Tackling salmonellosis: A comprehensive exploration of risks factors, impacts, and solutions

Salmonellosis, caused by Salmonella species, is one of the most common foodborne illnesses worldwide with an estimated 93.8 million cases and about 155,00 fatalities. In both industrialized and developing nations, Salmonellosis has been reported to be one of the most prevalent foodborne zoonoses and is linked with arrays of illness syndromes such as acute and chronic enteritis, and septicaemia. The two major and most common Salmonella species implicated in both warm-blooded and cold-blooded animals are Salmonella bongori and Salmonella enterica. To date, more than 2400 S. enterica serovars which affect both humans and animals have been identified. Salmonella is further classified into serotypes based on three primary antigenic determinants: somatic (O), flagella (H), and capsular (K). The capacity of nearly all Salmonella species to infect, multiply, and survive in human host cells with the aid of their pathogenic and virulence arsenals makes them deadly and important public health pathogens. Primarily, food-producing animals such as poultry, swine, cattle, and their products have been identified as important sources of salmonellosis. Additionally, raw fruits and vegetables are among other food types that have been linked to the spread of Salmonella spp. Based on the clinical manifestation of human salmonellosis, Salmonella strains can be categorized as either non-typhoidal Salmonella (NTS) and typhoidal Salmonella. The detection of aseptically collected Salmonella in necropsies, environmental samples, feedstuffs, rectal swabs, and food products serves as the basis for diagnosis. In developing nations, typhoid fever due to Salmonella Typhi typically results in the death of 5%-30% of those affected. The World Health Organization (WHO) calculated that there are between 16 and 17 million typhoid cases worldwide each year, with scaring 600,000 deaths as a result. The contagiousness of a Salmonella outbreak depends on the bacterial strain, serovar, growth environment, and host susceptibility. Risk factors for Salmonella infection include a variety of foods; for example, contaminated chicken, beef, and pork. Globally, there is a growing incidence and emergence of life-threatening clinical cases, especially due to multidrug-resistant (MDR) Salmonella spp, including strains exhibiting resistance to important antimicrobials such as beta-lactams, fluoroquinolones, and third-generation cephalosporins. In extreme cases, especially in situations involving very difficult-to-treat strains, death usually results. The severity of the infections resulting from Salmonella pathogens is dependent on the serovar type, host susceptibility, the type of bacterial strains, and growth environment. This review therefore aims to detail the nomenclature, etiology, history, pathogenesis, reservoir, clinical manifestations, diagnosis, epidemiology, transmission, risk factors, antimicrobial resistance, public health importance, economic impact, treatment, and control of salmonellosis.

High-throughput fitness experiments reveal specific vulnerabilities of human-adapted Salmonella during stress and infection

Salmonella enterica is comprised of genetically distinct 'serovars' that together provide an intriguing model for exploring the genetic basis of pathogen evolution. Although the genomes of numerous Salmonella isolates with broad variations in host range and human disease manifestations have been sequenced, the functional links between genetic and phenotypic differences among these serovars remain poorly understood. Here, we conduct high-throughput functional genomics on both generalist (Typhimurium) and human-restricted (Typhi and Paratyphi A) Salmonella at unprecedented scale in the study of this enteric pathogen. Using a comprehensive systems biology approach, we identify gene networks with serovar-specific fitness effects across 25 host-associated stresses encountered at key stages of human infection. By experimentally perturbing these networks, we characterize previously undescribed pseudogenes in human-adapted Salmonella. Overall, this work highlights specific vulnerabilities encoded within human-restricted Salmonella that are linked to the degradation of their genomes, shedding light into the evolution of this enteric pathogen.