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The gut microbiota produces high concentrations of antimicrobial short-chain fatty acids (SCFAs) that restrict the growth of invading microorganisms. The enteric pathogen Salmonella enterica serovar (S.) Typhimurium triggers inflammation in the large intestine to ultimately reduce microbiota density and bloom, but it is unclear how the pathogen gains a foothold in the homeostatic gut when SCFA-producing commensals are abundant. Here, we show that S. Typhimurium invasion of the ileal mucosa triggers malabsorption of dietary amino acids to produce downstream changes in nutrient availability in the large intestine. In gnotobiotic mice engrafted with a community of 17 human Clostridia isolates, S. Typhimurium virulence factors triggered marked changes in the cecal metabolome, including an elevated abundance of amino acids. In an ex vivo fecal culture model, we found that two of these amino acids, lysine and ornithine, countered SCFA-mediated growth inhibition by restoring S. Typhimurium pH homeostasis through the inducible amino acid decarboxylases CadA and SpeF, respectively. In a mouse model of gastrointestinal infection, S. Typhimurium CadA activity depleted dietary lysine to promote cecal ecosystem invasion in the presence of an intact microbiota. From these findings, we conclude that virulence factor-induced malabsorption of dietary amino acids in the small intestine changes the nutritional environment of the large intestine to provide S. Typhimurium with resources needed to counter growth inhibition by microbiota-derived SCFAs.

Salmonella translocate to the gut epithelium via microfold cells lining the follicle-associated epithelium (FAE). How Salmonella localize to the FAE is not well characterized. Here we use live imaging and competitive assays between wild-type and chemotaxis-deficient mutants to show that Salmonella enterica serotype Typhimurium (S. Typhimurium) localize to the FAE independently of chemotaxis in an ex vivo mouse caecum infection model. Electrical recordings revealed polarized FAE with sustained outward current and small transepithelial potential, while the surrounding villus is depolarized with inward current and large transepithelial potential. The distinct electrical potentials attracted S. Typhimurium to the FAE while Escherichia coli (E. coli) localized to the villi, through a process called galvanotaxis. Chloride flux involving the cystic fibrosis transmembrane conductance regulator (CFTR) generated the ionic currents around the FAE. Pharmacological inhibition of CFTR decreased S. Typhimurium FAE localization but increased E. coli recruitment. Altogether, our findings demonstrate that bioelectric cues contribute to S. Typhimurium targeting of specific gut epithelial locations, with potential implications for other enteric bacterial infections.

Enteric pathogens such as Salmonella enterica serovar Typhimurium experience spatial and temporal changes to the metabolic landscape throughout infection. Host reactive oxygen and nitrogen species non-enzymatically convert monosaccharides to alpha hydroxy acids, including L-tartrate. Salmonella utilizes L-tartrate early during infection to support fumarate respiration, while L-tartrate utilization ceases at later time points due to the increased availability of exogenous electron acceptors such as tetrathionate, nitrate, and oxygen. It remains unknown how Salmonella regulates its gene expression to metabolically adapt to changing nutritional environments. Here, we investigated how the transcriptional regulation for L-tartrate metabolism in Salmonella is influenced by infection-relevant cues. L-tartrate induces the transcription of ttdBAU, genes involved in L-tartrate utilization. L-tartrate metabolism is negatively regulated by two previously uncharacterized transcriptional regulators TtdV (STM3357) and TtdW (STM3358), and both TtdV and TtdW are required for the sensing of L-tartrate. The electron acceptors nitrate, tetrathionate, and oxygen repress ttdBAU transcription via the two-component system ArcAB. Furthermore, the regulation of L-tartrate metabolism is required for optimal fitness in a mouse model of Salmonella-induced colitis. TtdV, TtdW, and ArcAB allow for the integration of two cues, i.e., substrate availability and availability of exogenous electron acceptors, to control L-tartrate metabolism. Our findings provide novel insights into how Salmonella prioritizes the utilization of different electron acceptors for respiration as it experiences transitional nutrient availability throughout infection.ImportanceBacterial pathogens must adapt their gene expression profiles to cope with diverse environments encountered during infection. This coordinated process is carried out by the integration of cues that the pathogen senses to fine-tune gene expression in a spatiotemporal manner. Many studies have elucidated the regulatory mechanisms of how Salmonella sense metabolites in the gut to activate or repress its virulence program; however, our understanding of how Salmonella coordinates its gene expression to maximize the utilization of carbon and energy sources found in transitional nutrient niches is not well understood. In this study, we discovered how Salmonella integrates two infection-relevant cues, substrate availability and exogenous electron acceptors, to control L-tartrate metabolism. From our experiments, we propose a model for how L-tartrate metabolism is regulated in response to different metabolic cues in addition to characterizing two previously unknown transcriptional regulators. This study expands our understanding of how microbes combine metabolic cues to enhance fitness during infection.

Salmonella enterica serotype Typhimurium (Salmonella) resides and multiplies intracellularly in cholesterol-rich compartments called Salmonella-containing vacuoles (SCVs) with actin-rich tubular extensions known as Salmonella-induced filaments (SIFs). SCV maturation depends on host-derived cholesterol, but the transport mechanism of low-density lipoprotein (LDL)-derived cholesterol to SCVs remains unclear. Here we find that peroxisomes are recruited to SCVs and function as pro-bacterial organelle. The Salmonella effector protein SseI is required for the interaction between peroxisomes and the SCV. SseI contains a variant of the PTS1 peroxisome-targeting sequence, GKM, localizes to the peroxisomes and activates the host Ras GTPase, ADP-ribosylation factor-1 (ARF-1). Activation of ARF-1 leads to the recruitment of phosphatidylinsolitol-5-phosphate-4 kinase and the generation of phosphatidylinsolitol-4-5-bisphosphate on peroxisomes. This enhances the interaction of peroxisomes with lysosomes and allows for the transfer of lysosomal cholesterol to SCVs using peroxisomes as a bridge. Salmonella infection of peroxisome-depleted cells leads to the depletion of cholesterol on the SCVs, resulting in reduced SIF formation and bacterial proliferation. Taken together, our work identified peroxisomes as a target of Salmonella secretory effectors, and as conveyance of host cholesterol to enhance SCV stability, SIF integrity, and intracellular bacterial growth. Synopsis: Salmonella effector SseI recruits peroxisomes to serve as bridge for the transport of lysosomal cholesterol to the SCV. SseI is targeted to peroxisomes via a PTS1-like motif. SseI activates ARF-1 resulting in the activation of PI5P4K (PIP4K) and PIP2 generation on peroxisomes. PIP2 strengthens the interaction of peroxisomes with SCVs using Syt7 as the tethering protein on SCVs. Peroxisomes serve as bridge for the transport of cholesterol from lysosomes to the SCV. Salmonella effector SseI recruits peroxisomes to serve as bridge for the transport of lysosomal cholesterol to the SCV. [ABSTRACT FROM AUTHOR]

Salmonella infections can lead to intestinal inflammation and metabolic disorders in birds. However, whether arachidonic acid (ARA) metabolism is involved in Salmonella -induced intestinal inflammation remains unclear. This experiment investigated the changes in cecal flora and ARA metabolism in Hainan Wenchang chickens infected with S. Typhimurium using 16s rDNA sequencing and targeted metabolomics. The results showed that the levels of ARA metabolites were increased in the cecum tissue of Wenchang chickens after infection with S. Typhimurium , including prostaglandin E2 (PGE2), prostaglandin F2α (PGF2α), lipoxin A4 (LXA4), ± 8(9)-EET, ± 11(12)-EET, and ± 8,9-DiHETrE. The content of key enzymes for ARA production and metabolism (Phospholipase A2 PLA2 and Cyclooxygenase-2 COX-2) in chicken cecum tissues was increased after S. Typhimurium infection. The relative mRNA levels of inflammatory factors were also increased after infection, including Interferon-γ (IFN-γ), Transforming growth factor-β1 (TGF-β1), Interleukin-4 (IL-4), and Interleukin-6 (IL-6). In HD11 cells, the use of a cyclooxygenase (COX) inhibitor reduced the increased levels of COX-2 and PGF2α induced by S. Typhimurium infection and effectively reduced the inflammatory response. In addition, the number of beneficial genera (e.g., Bifidobacterium , Lactobacillus , and Odorobacterium) in the cecum of Wenchang chickens was significantly reduced after infection with S. Typhimurium. The present study revealed the structure of cecal flora in S. Typhimurium -infected Wenchang chickens. In addition, this study demonstrated that S. Typhimurium activates the ARA cyclooxygenase metabolic pathway, which in turn mediates the development of intestinal inflammation in Wenchang chickens. The results can provide data support and theoretical support for the prevention and control of avian salmonellosis. [ABSTRACT FROM AUTHOR]

Background: Endogenous antimicrobial peptides and proteins are essential for shaping and maintaining a healthy gut microbiota, contributing to anti-inflammatory responses and resistance to pathogen colonization. Salmonella enterica subsp. enterica serovar Typhimurium (ST) infection is one of the most frequently reported bacterial diseases worldwide. Manipulation of the gut microbiota through exogenous antimicrobial peptides may protect against ST colonization and improve clinical outcomes. Results: This study demonstrated that oral administration of the antimicrobial peptide AP2 (2 µg /mouse), an optimized version of native apidaecin IB (AP IB), provided protective effects against ST infection in mice. These effects were evidenced by reduced ST-induced body weight loss and lower levels of serum inflammatory cytokines. A 16 S rRNA-based analysis of the cecal microbiota revealed that AP2 significantly modulated the gut microbiota, increasing the relative abundance of Bifidobacterium while decreasing that of Akkermansia at the genus level. Furthermore, the transplantation of fecal microbiota from AP2-treated donor mice, rather than from Control mice, significantly reduced cecal damage caused by ST and decreased the concentration of ST by one order of magnitude after infection. Conclusions: These findings reveal a novel mechanism by which exogenous antimicrobial peptides mitigate Salmonella Typhimurium infection through the modulation of gut microbiota. [ABSTRACT FROM AUTHOR]

Identifying and characterizing virulence proteins secreted by Gram-negative bacteria are fundamental for deciphering microbial pathogenicity as well as aiding the development of therapeutic strategies. Effector predictors utilizing pre-trained protein language models (PLMs) have shown sound performance by leveraging extensive evolutionary and sequential protein features. However, the accuracy and sensitivity of effector prediction remain challenging. Here, we introduce a model named Contrastive-learning of Language Embedding and Biological Features (CLEF) leveraging contrastive learning to integrate PLM representations with supplementary biological features. Biologically information is captured in learned contextualized embeddings to yield meaningful representations. With cross-modality biological features, CLEF outperforms state-of-the-art (SOTA) models in predicting type III, type IV, and type VI secreted effectors (T3SEs/T4SEs/T6SEs) in enteric pathogens. All experimentally verified effectors in Enterohemorrhagic Escherichia coli and 41 of 43 experimentally verified T3SEs of Salmonella Typhimurium are recognized. Moreover, 12 predicted T3SEs and 11 predicted T6SEs are validated by extensive experiments in Edwardsiella piscicida. Furthermore, integrating omics data via CLEF framework enhances protein representations to illustrate effector-effector interactions and determine in vivo colonization-essential genes. Collectively, CLEF provides a blueprint to bridge the gap between in silico PLM's capacity and experimental biological information to fulfill complicated tasks. Identifying and characterizing secreted virulence proteins are fundamental for deciphering microbial pathogenicity. Here, the authors introduce a practical training framework to improve protein language model representations by integrating biological features and prior information through contrastive learning. [ABSTRACT FROM AUTHOR]

Nowadays, due to the harmful effects of chemical preservatives in food products and antibiotic resistance too, the efforts of researchers to use natural and safe antimicrobial compounds, including plant essential oils, have increased. In the present study, after collecting the Badrashboo plant from the fields around Urmia city and drying it, extracting the essential oil from the plant was carried out using a Clevenger device, and the antimicrobial effects of this essential oil against some Gram -positive and Gram -negative food - borne pathogenic bacteria were determined by methods: Disk Diffusion Agar (DDA), Well Diffusion Agar (WDA), Minimum inhibitory concentration (MIC), Minimum bactericidal concentration (MBC) and interaction with four common broad -spectrum antibiotics including Vancomycin, Erythromycin, Chloramphenicol and Gentamicin were performed. The results of the DDA and WDA tests showed that the essential oil of Badreshbo had significant antimicrobial effects on all the tested bacteria in this study. The gram -positive bacteria were more sensitive than the gram -negative bacteria in front of this essential oil. The results of the MIC test of the essential oil for Salmonella typhimurium, Escherichia coli, Pseudomonas aeruginosa, Shigella dysentery, Staphylococcus aureus, Bacillus cereus, and Listeria monostogenes were 2.5, 1.25, 1.25, 0.625, 0.312, 1.25 and 1.25 mg/ml. The MBC of the mentioned strains were 5, 5, 2.5, 5, 2.5, 2.5, and 2.5 mg/mL, respectively. Also, the results of the study of the interaction effect of Badreshbo essential oil with the mentioned antibiotics indicate synergistic effects of the essential oil with all four antibiotics tested. Therefore, considering the significant antimicrobial effects observed for Badrashbo essential oil in this study, it can be used in the food and pharmaceutical industries. [ABSTRACT FROM AUTHOR]

Salmonella enterica serovar Typhimurium is a prevalent food-borne pathogen that is usually associated with gastroenteritis infection. S. Typhimurium is also a major cause of bloodstream infections in sub-Saharan Africa, and is responsible for invasive non-typhoidal Salmonella (iNTS) disease. The pathogen also causes bloodstream infection in Colombia, but there has been a lack of information about the S. Typhimurium isolates that were responsible. Here, we investigated the genomic characteristics of 270 S. Typhimurium isolates from bloodstream infection patients in Colombia, collected between 1997 and 2017. We used whole-genome sequencing to analyse multidrug-resistant (MDR) profiles, plasmid distribution, and to define phylogenetic relationships. The study identified the distinct sequence types and phylogenetic clusters of S. Typhimurium prevalent in Colombia. The majority of isolates (90.8%) were ST19, which is distinct from the iNTS-associated S. Typhimurium in sub-Saharan Africa (ST313). The two prominent clusters of MDR S. Typhimurium were either DT104 or closely related to the LT2 reference strain. We used a phylogenetic approach to associate the Colombian clusters with global S. Typhimurium isolates from public databases. By putting the Colombian S. Typhimurium isolates in the context of the global spread of DT104, ST313 and LT2-related variants, we found that the Colombian clusters were introduced to the country via multiple independent events that were consistent with international transmission. We suggest that the acquisition of quinolone and chloramphenicol resistance by the Colombian S. Typhimurium isolates was driven by horizontal gene transfer. Three ST313 isolates that caused bloodstream infection in Colombia were identified. These ST313 isolates were related to the Malawian ST313 lineage 3 & UK ST313, and shared a similarly high invasiveness index. To our knowledge, this is the first report of ST313 in Colombia. Author summary: Salmonella Typhimurium is a serovar of the bacterial species Salmonella enterica. S. Typhimurium usually infect humans through contaminated food or drink to cause self-limited diarrhoea. However, S. Typhimurium can also cause invasive non-typhoidal Salmonellosis (iNTS) disease, a dangerous bloodstream infection. In sub-Saharan Africa, most of the iNTS-associated S. Typhimurium isolates belonged to sequence type ST313. It was not known what type of S. Typhimurium caused iNTS in Colombia. Whole genome sequencing (WGS) has been widely used to monitor Salmonella infection in European and Northern American countries. However, WGS data from Latin American countries such as Colombia has been very limited. Here, we analysed 270 Colombian S. Typhimurium isolates from bloodstream infection patients with iNTS disease. Using WGS and bioinformatic analyses, we answered many questions about the Colombian S. Typhimurium isolates. The majority of the iNTS-associated isolates in Colombia belonged to ST19, rather than the ST313 sequence type responsible for bloodstream infections in sub-Saharan Africa. We compared the three ST313 isolates from Colombia and Malawi. The Colombian ST313 cluster was closely related to Malawian ST313 L3, and both appeared to have adaptations to an extraintestinal lifestyle. We suggest that the limited number of ST313 bloodstream infections in Colombia reflects the highly immune-competent population, in contrast to the substantial numbers of immune-compromised people in sub-Saharan Africa. We identified ST19 multi-drug resistance clusters linked to globally-distributed S. Typhimurium isolates. One MDR cluster (Cluster 2) is likely to have spread from Europe or North America. We propose that a second MDR cluster (Sub-cluster 7.3) recently emerged in Colombia, and acquired plasmid-associated resistance genes prior to transmission to Ecuador. [ABSTRACT FROM AUTHOR]

Background: Salmonella enterica Serovar Typhimurium (S. Typhimurium) infection can cause inflammation and oxidative stress in the body, leading to gastroenteritis, fever and other diseases in humans and animals. More and more studies have emphasized the broad prospects of probiotics in improving inflammation and oxidative stress, but the ability and mechanism of Lactobacillus acidophilus (LA) to alleviate the inflammatory/oxidative reaction caused by pathogens are still unclear. Methods and results: In this study, we treated the mice with LA for 14 days, infected them with S. Typhimurium for 24 h, and sacrificed the mice to collect samples. We found that the early intervention of LA alleviated the pathological injury and reversed the down-regulation of the duodenal and hepatic tight junction protein mRNA levels caused by S. Typhimurium infection. Compared with S. Typhimurium group, LA early intervention increased the expression of antioxidant enzymes, but decreased the levels of serum malondialdehyde (MDA), interleukin-8 and tumor necrosis factor-α (TNF-α). Additionally, LA early intervention significantly increased Nrf2 mRNA expression in the liver and decreased Keap1 mRNA expression in the duodenum compared to the S. Typhimurium group. Furthermore, early LA treatment reduced the abundance of Bacteroides acidificiens , increased the abundance of Akkermansia , and alleviated the decrease in SCFAs levels in the cecum of S. Typhimurium-infected mice. Spearman correlation analysis showed that there was a certain correlation between cecal flora and serum indicators and short chain fatty acids. Conclusion: Taken together, the results indicate that LA early intervention may alleviates S. Typhimurium-induced inflammation and oxidative responses in mice by activating the p62-Keap1-Nrf2 signaling pathway and regulating the gut microbial community. Significance and impact of the study: Exploring the ability of LA to resist animal oxidative stress and microflora regulation caused by pathogenic microbes, so as to provide more options for developing healthy disease-resistant feed additives. [ABSTRACT FROM AUTHOR]

Background: Salmonella enterica serovar Typhimurium is one of the most common serovars of Salmonella associated with clinical cases. It not only leads to diarrhea and mortality raised in livestock and poultry farming, but also poses a risk to food safety. Results: In this study, a lytic bacteriophage named ZK22 was isolated and identified from sewage. It exhibited favorable capability against 20 strains of S. Typhimurium. The genome of ZK22 consisted of a double-stranded DNA with a total length of 47,066 base pairs and a GC content of 45.71%. A total of 78 coding sequences were predicted, with no virulence genes or drug resistance genes predicted. Based on blastn similarity analysis, ZK22 belongs to the genus Skatevirus of the class Caudoviricetes, as a long-tailed Siphovirus. Biological characteristics of ZK22 indicated that the optimal multiplicity of infection (MOI) of bacteriophage ZK22 to S. Typhimurium was 10− 2 (PFU/cell), with an incubation period of around 10 min and the burst size of 393 PFU/cell. The physicochemical resistance results of ZK22 demonstrated that it maintained stability under temperatures ranging from 4 °C to 70 °C and under pH conditions ranging from 3 to 12. After inoculating S. Typhimurium at 37 °C, co-culture mixed with the optimal multiplicity of infection exhibited the lowest OD600 within 12 h, demonstrating the exceptional antibacterial effect. Inoculation of phage ZK22 in mice infected with S. Typhimurium was performed to assess its therapeutic efficacy in vivo. The results showed that phage ZK22 at a dose of 108 PFU/mL increased the survival rates of infected mice, effectively suppressed the dissemination and colonization of the host bacteria in the mice, and alleviated the inflammatory response caused by the infection. Conclusions: In summary, bacteriophage ZK22 presents favorable application prospects as a potential biological agent for the control of Salmonella infections in livestock and poultry farming. [ABSTRACT FROM AUTHOR]