Salmonella Pathogenicity Island 1 Research Articles

Comparative Genomic Analysis Reveals the Emergence and Dissemination of Different Salmonella enterica serovar Gallinarum biovar Gallinarum Lineages in Brazil

Salmonella enterica serovar Gallinarum biovar Gallinarum is a pathogenic bacterium that causes fowl typhoid (FT), affecting chicken flocks worldwide. This study aimed to evaluate the emergence, dissemination and genomic profile of S. Gallinarum lineages from Brazil. Twelve whole-genomes sequences (WGS) of different S. Gallinarum strains isolated from Brazilian poultry farms (2014 to 2018) were obtained and used to construct a dataset with other 31 previously published data (five more from Brazil). Brazilian strains phylogenetic diversity, temporal evolution and antimicrobial resistance/virulence genomic profile were evaluated. Sixteen (94.1%) Brazilian strains were from sequence type ST78 and one (5.9%) was from ST331. All S. Gallinarum strains clustered into five different clades/lineages (I to V), all circulating in South America and four (I, II, III, IV) in Brazil. The time of most recent common ancestor (tMRCA) of all strains was many centuries ago, but the lineages detected in South America (II and V) had tMRCA in recent decades. IncFIC(FII), IncFII(S) and ColRNAI were plasmid replicons frequently found in the lineages from Brazil, but antimicrobial resistance genes were scarce. Only two resistance genes (aac(6’)-Iaa and mdf(A)) were detected in most strains, while other two (blaTEM-106 and fosA3) were present in some isolates. It was also observed important differences in the virulence genomic profile of the different lineages, highlighting lineage IV, which does not carry the very important Salmonella pathogenicity island 1 (SPI1) genes cluster. In summary, this study reveals the emergence and dissemination of four different lineages of S. Gallinarum in Brazil.

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

BackgroundThe 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.ResultsOut 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.ConclusionsOur study reports emergence of a highly MDR- CIPRS. 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.

Activation of ferritin light chain (FTL) by transcription factor salmonella pathogenicity island 1 modulates glycolysis to drive metastasis of ovarian cancer cells

ABSTRACT Background Ovarian cancer (OC) is the most lethal gynecological cancer often diagnosed at an advanced stage due to a lack of effective biomarkers. Ferritin light chain (FTL) is implicated in the development of various cancers, but its impact on OC remains unknown. Research design and methods Bioinformatics methods were utilized to analyze FTL. Quantitative real-time polymerase chain reaction, western blot, and immunohistochemistry were employed for expression detection, and cell counting kit- 8, and transwell assays were for cell biological functions assessment. Extracellular acidification rate, oxygen consumption rate, and glycolytic metabolite contents were measured. Dual-luciferase and chromatin immunoprecipitation assay validated binding relationship. Xenografted tumor models in nude mice verified the role of FTL in vivo. Results Cell function experiments revealed that FTL facilitated proliferation, migration, and invasion of OC cells. Rescue experiments unveiled that 2-Deoxy-D-glucose attenuated stimulation on OC cell metastasis and glycolysis by FTL overexpression. Salmonella pathogenicity island 1 (SPI1) up-regulated FTL expression to promote glycolysis and metastasis. FTL knockdown inhibited tumor growth and suppressed glycolysis and cell metastasis in vivo, while SPI1 overexpression attenuated these effects. Conclusions This study demonstrated pro-metastatic mechanisms of transcription factor SPI1/FTL axis in OC and suggested it as a potential target for treating OC metastasis.

Suppression of amber stop codons impairs pathogenicity in Salmonella.

Translation terminates at UAG (amber), UGA (opal), and UAA (ochre) stop codons. In nature, readthrough of stop codons can be substantially enhanced by suppressor tRNAs. Stop-codon suppression also provides powerful tools in synthetic biology and disease treatment. How stop-codon suppression affects bacterial pathogenesis is poorly understood. Here, we show that suppression of UAG codons, but not UGA or UAA codons, attenuates expression of Salmonella Pathogenicity Island 1 (SPI-1) genes, which are required for virulence. Consistently, amber suppression abolishes Salmonella infection of macrophages. Systematic genetic and biochemical analyses further show that amber suppression decreases the activity, but not the level, of the master SPI-1 regulator HilD. Our work thus demonstrates an unexpected selectivity of stop codons in regulating Salmonella virulence.

Salmonella pathogenicity Island 1 undergoes decay in serovars adapted to swine and poultry.

Human salmonellosis is a high-priority foodborne disease worldwide. The main reservoir of Salmonella is livestock, mainly swine and poultry that are infected both by generalist serovars and serovars adapted to them. The most widespread livestock-adapted serovars are attenuated in both their primary hosts and humans. We previously identified a lineage of the swine-adapted Salmonella Derby carrying mutations in Salmonella Pathogenicity Island-1(SPI-1) giving attenuation. To evaluate if SPI-1 decay is a general feature of swine-adapted serovars, we analyzed the Enterobase global population of Salmonella serovars most frequently isolated from swine. We found that deleterious mutations in SPI-1 are accumulated more in swine-adapted (S. Derby and Salmonella Rissen) than in generalist (Salmonella Typhimurium, I 1,4,[5],12:i:-, and Salmonella Infantis) serovars. The genomes carrying such mutations are widespread in the population of S. Derby and S. Rissen, indicating that the occurrence and fixation of deleterious mutations in SPI-1 are frequent. Similarly, also poultry-adapted Salmonella Kentucky has accumulated deleterious mutations in SPI-1, leading to over 70% of mutated genomes of this serovar compared with negligible proportions of mutated genomes in the generalist serovars from poultry. Although in vitro attenuation of S. Derby carrying mutated SPI-1 had been previously demonstrated, we showed the same phenotype for mutated S. Rissen. Considering also the known attenuation of S. Kentucky, our population-scale findings provide evidence of progressive evolution toward the attenuation of serovars adapted to the main animal reservoirs of human salmonellosis through the food chain. Intensive farming with a high density of animals could be a possible driver of this evolution.IMPORTANCEThis study shows at the global population level of Salmonella that the main attenuated serovars adapted to food-producing animals are undergoing convergent evolution toward further attenuation through the decay of SPI-1, considered critically important for the intestinal phase of Salmonella infection. The drivers of this evolution are unknown, but they could be attributed, at least in part, to the intensive farming of livestock with its high densities. On one side, our results contribute to the knowledge of the interaction between livestock populations and their host-adapted serovars of Salmonella. On the other side, the study provides scientific background for reconsidering the microbiological criteria adopted by the food safety legislation of many countries that ask for the absence of Salmonella in foods, regardless of any virulence evaluation of the detected strain. In this respect, the study provides molecular bases to investigate the virulence of different lineages within these host-adapted serovars.

RECSALMO: Rapid typing and characterization tool for whole genome sequencing data of Salmonella

Salmonella is one of the most prevalent foodborne pathogens. Endemic events involving Salmonella now occur more frequently and must be handled efficiently and quickly. Whole genome sequencing (WGS) cost and speed have improved significantly during the past decades, with the number of bioinformatics tools based on WGS data also increasing. This research presented the “RECSALMO” tool, designed specifically to analyze Salmonella genome assemblies. This tool can quickly type and characterize a collection of Salmonella genomes, providing extensive information and assist related healthcare personnel to effectively and timely manage a Salmonella epidemic. The essential outputs of the tool include sequence-based typing comprising serotyping, MLST and cgMLST, antibiotic resistance genes with their associated classes/subclasses of antibiotic drugs, Salmonella pathogenicity islands (SPIs) from SPI-1 to SPI-17, and spacer profiles (CRISPR locus 1 and 2). Moreover, the tool generates SNP-based trees, CRISPR-based dendrograms and pie charts of serotypes and ST indexes. Due to the superior resolution, quick operational time, and low processing cost of WGS, RECSALMO is considered a practical bioinformatics tool for comprehensive and rapid examination of Salmonella genomes.

Comparative genomics analysis of Salmonella Enteritidis isolated from clinical cases associated with chicken

Salmonella Enteritidis is a major foodborne pathogen, and the emergence of multidrug-resistant (MDR) S. Enteritidis poses a serious public health challenge. In this study, we report the genomic characterization of five S. Enteritidis isolates from clinical. These isolates exhibited resistance to seven classes of antimicrobials with four of the five characterized as MDR. Isolate 33 A exhibited resistance to colistin and polymyxin B, while no associated antimicrobial resistance genes (ARGs) were identified in its genome. Isolate 21 A and 44 A were extended-spectrum beta-lactamases-producing (ESBLs). Whole genome sequencing analysis revealed the presence of multiple mobile genetic elements (MGEs), including plasmids, prophages, and genomic islands, which may have facilitated the acquisition and dissemination of ARGs. Notably, several ARGs, including blaCTX−M−55, blaTEM−141, blaTEM−1B, aph(3’)-IIa, aph(3’’)-Ib, aph(6)-Id, tet(A), floR, fosA3, and sul2, were identified on plasmids. In addition, chromosomal point mutations in gyrA (D87G and D87Y) and acrB (F28L and L40P) were also observed in each isolate. Multiple virulence genes associated with the type III secretion system were identified on Salmonella pathogenicity islands (SPIs) SPI-1 and SPI-2. Phylogenetic analysis revealed that the five isolates, along with a clinical and chicken origin isolates in the database, clustered together, suggesting a probable common source of infection. Our findings highlight the intricate genetic mechanisms behind MDR in S. Enteritidis, emphasizing the ongoing necessity for surveillance and appropriate antimicrobial usage. This contributes to our understanding of S. Enteritidis transmission within the food chain.

The Salmonella pathogenicity island 1-encoded small RNA InvR mediates post-transcriptional feedback control of the activator HilA in Salmonella.

Salmonella Pathogenicity Island 1 (SPI1) encodes a type three secretion system (T3SS) essential for Salmonella invasion of intestinal epithelial cells. Many environmental and regulatory signals control SPI1 gene expression, but in most cases, the molecular mechanisms remain unclear. Many of these regulatory signals control SPI1 at a post-transcriptional level and we have identified a number of small RNAs (sRNAs) that control the SPI1 regulatory circuit. The transcriptional regulator HilA activates expression of the genes encoding the SPI1 T3SS structural and primary effector proteins. Transcription of hilA is controlled by the AraC-like proteins HilD, HilC, and RtsA. The hilA mRNA 5' untranslated region (UTR) is ~350-nuclotides in length and binds the RNA chaperone Hfq, suggesting it is a likely target for sRNA-mediated regulation. We used the rGRIL-seq (reverse global sRNA target identification by ligation and sequencing) method to identify sRNAs that bind to the hilA 5' UTR. The rGRIL-seq data, along with genetic analyses, demonstrate that the SPI1-encoded sRNA InvR base pairs at a site overlapping the hilA ribosome binding site. HilD and HilC activate both invR and hilA. InvR in turn negatively regulates the translation of the hilA mRNA. Thus, the SPI1-encoded sRNA InvR acts as a negative feedback regulator of SPI1 expression. Our results suggest that InvR acts to fine-tune SPI1 expression and prevent overactivation of hilA expression, highlighting the complexity of sRNA regulatory inputs controlling SPI1 and Salmonella virulence.

Whole-Genome Sequencing Analysis of Antimicrobial Resistance, Virulence Factors, and Genetic Diversity of Salmonella from Wenzhou, China.

Salmonella species are important foodborne pathogens worldwide. Salmonella pathogenicity is associated with multiple virulence factors and enhanced antimicrobial resistance. To determine the molecular characteristics and genetic correlations of Salmonella, 24 strains of Salmonella isolated from different sources (raw poultry, human stool, and food) in the Wenzhou area were investigated to determine the distribution of antimicrobial resistance and virulence determinants using whole-genome sequencing (WGS). Aminoglycoside resistance genes were detected in all samples. Over half of the samples found antimicrobial resistance genes (ARGs) and point mutations for several clinically frequently used antibiotic, beta-lactams, tetracyclines, and quinolones. Of these strains, 62.5% were predicted to be multidrug-resistant (MDR). The quinolone-modifying enzyme gene aac(6')-Ib-cr, detected in five samples (S1-S4 and S10), was located on integrons. The analysis of Salmonella pathogenicity island (SPI) profiles suggests that serotypes with close genetic relationships share the same distribution of virulence factors, revealing a link between genotype and SPI profiles. cgMLST analysis indicated that five isolates S14-S18 were closely related to strains originating from the United Kingdom, suggesting that they may share a common origin. Data from this study may enrich the molecular traceability database for Salmonella and provide a basis for effective public health policies.

Epigallocatechin gallate protects mice from Salmonella enterica ser. Typhimurium infection by modulating bacterial virulence through quorum sensing inhibition.

Salmonella enterica ser. Typhimurium is a common pathogen that poses a considerable public health threat, contributing to severe gastrointestinal diseases and widespread foodborne illnesses. The virulence of S. Typhimurium is regulated by quorum sensing (QS) and the type III secretion system (T3SS). This study investigated the inhibitory effects and anti-QS activity of epigallocatechin gallate (EGCG), which is a bioactive ingredient found in green tea, on the virulence of S. Typhimurium. In vitro bacterial experiments demonstrated that EGCG inhibited the production of autoinducers, biofilm formation, and flagellar activity by downregulating the expression of AI-1, AI-2, Salmonella pathogenicity islands (SPI)-1, SPI-2, and genes related to flagella, fimbriae, and curli fibers. In a mouse model of S. Typhimurium-induced enteritis, EGCG considerably reduced intestinal colonization by S. Typhimurium and alleviated intestinal damage. In conclusion, EGCG protects the intestines of mice infected with S. Typhimurium by inhibiting QS-induced virulence gene expression, demonstrating its potential as a therapeutic agent for controlling S. Typhimurium infections.

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.

Critical role of msgA in invasive capacity and intracellular survivability of Salmonella.

Salmonella enterica serovar Typhimurium is a common foodborne pathogen, it has a complex pathogenic mechanism that involves invasive capacity and intracellular survivability. The virulence of Salmonella is primarily studied through its pathogenicity islands. In contrast, virulence genes located outside the Salmonella pathogenicity islands (SPIs) have received less attention. Macrophage survival gene (MsgA) is positioned at a region independent of the SPIs and conserved in Salmonella. Our research indicates that MsgA is a novel global regulator influencing the metabolic pathways and SPIs. Further research into the function of MsgA will enhance the understanding of Salmonella pathogenesis and promote the application of Salmonella for medical treatment.

Comparison of global transcriptomes for nontyphoidal Salmonella clinical isolates from pediatric patients with and without bacteremia after their interaction with human intestinal epithelial cells in vitro

BackgroundNontyphoidal Salmonella (NTS) outbreaks of invasive diseases are increasing. Whether the genetic diversity of invasive NTS correlates with the clinical characteristics and bacteremia development in NTS infections remains unclear. In this study, we compared the global transcriptomes between bacteremic and nonbacteremic NTS strains after their interaction with human intestinal epithelial cells in vitro. MethodsWe selected clinical isolates obtained from stool and blood samples of patients with or without bacteremia and patients with high and low C-reactive protein (CRP) levels. The bacterial RNA samples were isolated after coculturing with Caco-2 cells for RNA sequencing and subsequent analyses. ResultsCRP is an unreliable predictive maker for NTS bacteremia with a median CRP level of 1.6 mg/dL. Certain Salmonella Pathogenicity Island (SPI)-1 genes (sipC, sipA, sicA, sipD, and sipB), SPI-2 genes (ssaP, ssrA, and ssaS), and six SPI-4 genes (siiA, siiB, siiC, siiD, siiE, and siiF) remained upregulated in the bacteremic blood-derived strains but significantly downregulated in the nonbacteremic strains after their interaction with Caco-2 cells. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis identified that arginine biosynthesis, ascorbate and aldarate metabolism, and phosphotransferase system pathways were activated in bacteremic NTS strains after Caco-2 cell priming. ConclusionCRP levels were not correlated with bacteremia development. Significant regulation of certain SPI genes in bacteremic NTS strains after Caco-2 cell priming; bacteremia development might be influenced by the host immune response and the extent to which specific metabolism pathways in NTS strains can be prevented from invading the bloodstream.

Unusual Case of 20year Male-Resistant Typhoid Fever

A very common infectious disease but still emerging as extensive resistant known as resistant typhoid fever, caused by gram negative Salmonella enterica serovar Typhi(S.Typhi). This bacteria invades human cells by evading host defence system with the help of virulence plasmids and clustered genes called as salmonella pathogenicity islands(SPIs).These factor help bacteria to bind with plasmid mediated antimicrobial resistance gene and enable bacterium to become resistant strain or extensively resistant. After usage of multiple drugs for enteric fever made us to introduce tetracycline as last resort drug.

Genetic Characteristics of Multidrug-Resistant Salmonella Isolated from Poultry Meat in South Korea.

Given the lack of genetic characterization data for multidrug-resistant (MDR) Salmonella in South Korean poultry, we analyzed 53 MDR Salmonella strains from 1232 poultry meat samples (723 chicken, 509 duck) using whole-genome sequencing. Five serotypes were identified: S. Infantis (30/53, 56.6%), S. Enteritidis (11/53, 20.8%), S. Virchow (9/53, 17.0%), S. Agona (2/53, 3.8%), and S. Indiana (1/53, 1.9%). Sequence types (STs) included ST32, ST11, ST16, ST13, and ST17, with three major clusters, each having two subclusters. Eight core genome sequence types (cgSTs) were identified: 225993, 2268, 58360, 150996, 232041, 96964, 117577, and 267045. Salmonella Infantis and S. Enteritidis had two (117577, 267045) and three (225993, 2268, 58360) cgSTs, respectively, whereas S. Virchow showed allelic differences in identical cgSTs. The S. Enteritidis subcluster was classified as chicken or duck. Twenty-eight antimicrobial resistance genes (ARGs), 10 plasmid replicons, 11 Salmonella pathogenicity islands (SPIs), and 230 virulence genes were identified, showing distinct profiles by cluster and subcluster. Salmonella Infantis, the primary MDR Salmonella, carried the IncFIB (pN55391) plasmid, 10-11 ARGs, nine SPIs, and approximately 163 virulence genes. Three major MDR Salmonella serotypes (S. Infantis, S. Enteritidis, and S. Virchow) had specific genetic profiles that can inform epidemiological surveillance.

Modulation of Salmonella virulence by a novel SPI-2 injectisome effector that interacts with the dystrophin-associated protein complex.

In Salmonella enterica, the injectisome machinery encoded by Salmonella pathogenicity island 2 (SPI-2) is conserved among the five subspecies and delivers proteins (effectors) into host cells, which are required for Salmonella virulence. The identification and functional characterization of SPI-2 injectisome effectors advance our understanding of the interplay between Salmonella and its host(s). Using an optimized method for preparing secreted proteins and a clinical isolate of the invasive non-typhoidal Salmonella enterica serovar Enteritidis strain D24359, we identified 22 known SPI-2 injectisome effectors and one new effector-SseM. SseM modulates bacterial growth during murine infection and has a sequence corresponding to a postsynaptic density-95/discs large/zonula occludens-1 (PDZ)-binding motif that is essential for interaction with the PDZ-containing host protein β-2-syntrophin and other components of the dystrophin-associated protein complex (DAPC). To our knowledge, SseM is unique among Salmonella effectors in containing a functional PDZ-binding motif and is the first bacterial protein to target the DAPC.

Genomic insights into antimicrobial resistant Salmonella in internationally traded chicken meat: First baseline findings in the United Arab Emirates

Non-typhoidal Salmonella is among the most prevalent foodborne zoonoses, challenging food safety and One Health worldwide. A dearth of knowledge exists regarding non-typhoidal Salmonella prevalence and genomic features within the United Arab Emirates (UAE), one of the top markets in chicken meat consumption worldwide. In this study, Salmonella was detected in 16 out of 254 (6.30 %, 95 % confidence interval: 3.64 %, 10.03 %) samples of imported frozen chicken carcasses sampled from UAE retails. Among the recovered serotypes, S. Minnesota; ST 548 (10/16) emerged as the most prevalent, trailed by S. Heidelberg; ST 15 (4/16), and then S. Kentucky; ST 198, and ST 152 (2/16). Antimicrobial resistance (AMR) was most prevalent against tetracycline (93.7 %), followed by ampicillin (68.7 %), and extended-spectrum cephalosporins (ceftriaxone and cefoxitin) (56.2 %); with 68.7 % (11/16) of the isolates classified as multidrug resistant (MDR). Whole-genome sequencing (WGS) analysis revealed the existence of 14 AMR genes, among which the blaCMY-2, an AmpC cephalosporinases resistance gene, presented in 10 of the 16 isolates. Among the ten out of the eleven MDR Salmonella isolates, both IncC and Col(pHAD28) plasmid incompatibility types were concurrently featured. The range of virulence genes varied from 149 to 165 genes, with an average of 168 genes per isolate. Except for one isolate, all other isolates possessed type III secretion system (TTSS) related genes known to be encoded by the Salmonella pathogenicity island-1 (SPI-1). This study contributes to our global understanding of Salmonella epidemiology, specifically focusing on the Middle East. The insights gained from this study are significant in shaping import risk analyses aimed at mitigating Salmonella exposure risks through globally traded chicken. The research underscores the value of WGS as a crucial tool for substantiating evidence-based food safety hazard assessment.

Structure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands

Salmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due to its potential health risks and significant impact on public health. This study provides evolutionary classification of proteins from Salmonella enterica pangenome. We classified 17,238 domains from 13,147 proteins from 79,758 Salmonella enterica strains and studied in detail domains of 272 proteins from 14 characterized Salmonella pathogenicity islands (SPIs). Among SPIs-related proteins, 90 proteins function in the secretion machinery. 41% domains of SPI proteins have no previous sequence annotation. By comparing clinical and environmental isolates, we identified 3682 proteins that are overrepresented in clinical group that we consider as potentially pathogenic. Among domains of potentially pathogenic proteins only 50% domains were annotated by sequence methods previously. Moreover, 36% (1330 out of 3682) of potentially pathogenic proteins cannot be classified into Evolutionary Classification of Protein Domains database (ECOD). Among classified domains of potentially pathogenic proteins the most populated homology groups include helix-turn-helix (HTH), Immunoglobulin-related, and P-loop domains-related. Functional analysis revealed overrepresentation of these protein in biological processes related to viral entry into host cell, antibiotic biosynthesis, DNA metabolism and conformation change, and underrepresentation in translational processes. Analysis of the potentially pathogenic proteins indicates that they form 119 clusters or novel potential pathogenicity islands (NPPIs) within the Salmonella genome, suggesting their potential contribution to the bacterium’s virulence. One of the NPPIs revealed significant overrepresentation of potentially pathogenic proteins. Overall, our analysis revealed that identified potentially pathogenic proteins are poorly studied.

Detection of Salmonella Pathogenicity Islands and Antimicrobial-Resistant Genes in Salmonella enterica Serovars Enteritidis and Typhimurium Isolated from Broiler Chickens.

Rapid growth in commercial poultry production is one of the major sources of Salmonella infections that leads to human salmonellosis. The two main Salmonella enterica serovars associated with human salmonellosis are enteritidis and typhimurium. The aim of this study was to determine the prevalence of S. enterica serovars Enteritidis and S. Typhimurium as well as their Salmonella pathogenicity islands (SPI) and antibiotic resistance profiles in broiler chicken feces from slaughterhouses. A total of 480 fecal samples from broiler chickens that were grouped into 96 pooled samples were identified to have Salmonella spp. using the invA gene, whilst the Spy and sdfI genes were used to screen for the presence of S. Enteritidis and S. Typhimurium serovars, respectively, by polymerase chain reaction (PCR) assays. The isolates were also screened for the presence of Salmonella pathogenicity islands (SPIs) using PCR. The disc diffusion assay was performed to determine the antibiotic resistance profiles of the isolates. A total of 36 isolates were confirmed as Salmonella spp. through amplification of the invA gene. Out of 36 confirmed Salmonella spp. a total of 22 isolates were classified as S. Enteritidis (n = 8) and were S. Typhimurium (n = 14) serovars. All (n = 22) S. Enteritidis and S. Typhimurium isolates possessed the hilA (SPI-1), ssrB (SPI-2) and pagC (SPI-11) pathogenicity islands genes. Amongst these serovars, 50% of the isolates (n = 11/22) were resistant to tetracycline and nalidixic acid. Only 22% of the isolates, S. Typhimurium (13.6%) and S. Enteritidis (9.1%) demonstrated resistance against three or more antibiotic classes. The most detected antibiotic resistance genes were tet(K), mcr-1, sulI and strA with 13 (59.1%), 9 (40.9%), 9 (40.9%) and 7 (31.8%), respectively. The findings of this study revealed that S. Typhimurium is the most prevalent serotype detected in chicken feces. To reduce the risk to human health posed by salmonellosis, a stringent public health and food safety policy is required.

Identification of differentially expressed mRNAs as novel predictive biomarkers for gastric cancer diagnosis and prognosis.

Gastric cancer (GC) has a high mortality rate worldwide. Despite significant progress in GC diagnosis and treatment, the prognosis for affected patients still remains unfavorable. To identify important candidate genes related to the development of GC and identify potential pathogenic mechanisms through comprehensive bioinformatics analysis. The Gene Expression Omnibus database was used to obtain the GSE183136 dataset, which includes a total of 135 GC samples. The limma package in R software was employed to identify differentially expressed genes (DEGs). Thereafter, enrichment analyses of Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were performed for the gene modules using the clusterProfile package in R software. The protein-protein interaction (PPI) networks of target genes were constructed using STRING and visualized by Cytoscape software. The common hub genes that emerged in the cohort of DEGs that was retrieved from the GEPIA database were then screened using a Venn Diagram. The expression levels of these overlapping genes in stomach adenocarcinoma samples and non-tumor samples and their association with prognosis in GC patients were also obtained from the GEPIA database and Kaplan-Meier curves. Moreover, real-time quantitative polymerase chain reaction (RT-qPCR) and western blotting were performed to determine the mRNA and protein levels of glutamic-pyruvic transaminase (GPT) in GC and normal immortalized cell lines. In addition, cell viability, cell cycle distribution, migration and invasion were evaluated by cell counting kit-8, flow cytometry and transwell assays. Furthermore, we also conducted a retrospective analysis on 70 GC patients diagnosed and surgically treated in Wenzhou Central Hospital, Dingli Clinical College of Wenzhou Medical University, The Second Affiliated Hospital of Shanghai University between January 2017 to December 2020. The tumor and adjacent normal samples were collected from the patients to determine the potential association between the expression level of GPT and the clinical as well as pathological features of GC patients. We selected 19214 genes from the GSE183136 dataset, among which there were 250 downregulated genes and 401 upregulated genes in the tumor samples of stage III-IV in comparison to those in tumor samples of stage I-II with a P-value < 0.05. In addition, GO and KEGG results revealed that the various upregulated DEGs were mainly enriched in plasma membrane and neuroactive ligand-receptor interaction, whereas the downregulated DEGs were primarily enriched in cytosol and pancreatic secretion, vascular smooth muscle contraction and biosynthesis of the different cofactors. Furthermore, PPI networks were constructed based on the various upregulated and downregulated genes, and there were a total 15 upregulated and 10 downregulated hub genes. After a comprehensive analysis, several hub genes, including runt-related transcription factor 2 (RUNX2), salmonella pathogenicity island 1 (SPI1), lysyl oxidase (LOX), fibrillin 1 (FBN1) and GPT, displayed prognostic values. Interestingly, it was observed that GPT was downregulated in GC cells and its upregulation could suppress the malignant phenotypes of GC cells. Furthermore, the expression level of GPT was found to be associated with age, lymph node metastasis, pathological staging and distant metastasis (P < 0.05). RUNX2, SPI1, LOX, FBN1 and GPT were identified key hub genes in GC by bioinformatics analysis. GPT was significantly associated with the prognosis of GC, and its upregulation can effectively inhibit the proliferative, migrative and invasive capabilities of GC cells.