Gut Pathogens最新文献

{"title":"Multi-omics profiling and bile-acid exposure assays implicate a gut microbiome-parasite axis linked to persistent Entamoeba histolytica carriage.","authors":"Yasuaki Yanagawa, Naoko Yoshida, Takashi Makiuchi, Akira Kawashima, Haruka Uemura, Takahiro Aoki, Daisuke Mizushima, Hiroyuki Gatanaga, Koji Watanabe","doi":"10.1186/s13099-026-00845-1","DOIUrl":"10.1186/s13099-026-00845-1","url":null,"abstract":"<p><strong>Background: </strong>Asymptomatic Entamoeba histolytica (Eh) carriage is a major transmission reservoir, yet how the gut ecosystem-particularly microbiota-derived metabolites such as secondary bile acids-supports persistent colonization remains unclear. We investigated whether gut microbiome-metabolite features are associated with Eh carriage and could influence parasite phenotypes METHODS: We integrated shotgun metagenomics from a prospectively screened outpatient cohort (n=36) with functional in vitro assays. An ordinal stepwise model across detection states (Eh-, Eh_qPCR, Eh_Cyst) was used to identify candidate microbial features, followed by bile-acid exposure assays and transcriptomic profiling to evaluate impacts on parasite fitness and metronidazole susceptibility in vitro RESULTS: Microbiome profiling suggested taxon-specific shifts rather than wholesale dysbiosis. Community-level beta diversity showed no significant separation, whereas genus richness was higher in Eh_Cyst (unadjusted p=0.046). Multivariable modeling yielded concordant directional but non-significant trends (all q>0.9), highlighting Firmicutes genera including Coprococcus, Ruminococcus, and Catenibacterium as candidate taxa. We then evaluated deoxycholic acid (DCA), a microbiota-modified secondary bile acid. In vitro, 100 μM DCA extended Eh survival under nutrient-limited conditions and reduced metronidazole susceptibility after pretreatment. Transcriptomic profiling showed that DCA induced a distinct response, including an 8.34-fold induction of the ABC transporter P-glycoprotein-2 and upregulation of lipid remodeling and stress-response genes, supporting a bile acid-driven adaptive program consistent with intestinal persistence CONCLUSIONS: Our findings suggest that secondary bile acids, exemplified by DCA, can reprogram Eh gene expression and attenuate metronidazole susceptibility in vitro. In the context of cyst-associated microbiome signatures, this supports the plausibility of a microbiome-bile acid-parasite axis that may promote persistence in asymptomatic carriers and could influence treatment efficacy.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13523215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148257842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence of Helicobacter pylori infection and the associated demographic and histopathological characteristics in patients diagnosed with chronic gastritis in three histopathology laboratories in Uganda.","authors":"Okello Malcom Mark, Omega Phillip, Asiimwe Ivan, Byebei Eunice Chepkurui, Wanyenze Ester Fiona, Mawanda Anatoli, Boaz Mwesigwa, Musoke Sharrif, Lukande Robert, Bukirwa Phiona, Kalungi Sam","doi":"10.1186/s13099-026-00847-z","DOIUrl":"10.1186/s13099-026-00847-z","url":null,"abstract":"<p><strong>Background: </strong>Helicobacter pylori is the principal infectious driver of chronic gastritis, a precursor to several gastric lesions. Data on tissue-based prevalence and associated histopathology in Uganda remain limited. H. pylori affect over half the global population, leading to chronic gastritis and subsequent complications with increased risk of gastric cancer in about 1-3% of patients. This study investigated H. pylori prevalence, its demographic and histopathological associations among chronic gastritis patients in three histopathology laboratories in Uganda.</p><p><strong>Methods: </strong>A cross-sectional study analyzed 150 formalin-fixed paraffin-embedded tissue blocks of patients diagnosed with chronic gastritis between September 2018 to August 2021. The histopathology analysis was done using H&E and modified Giemsa stains. Data was analyzed with STATA version 17, determining prevalence through proportions, assessing associations using Chi-square tests and Fisher exact test. Significance was set at p ≤ 0.05 with 95% confidence intervals.</p><p><strong>Results: </strong>The study included 150 patients (male-to-female ratio 1.5:1; mean age 48 years, SD = 17, range 12-89). H. pylori prevalence was 29.3%. Significant associations were observed with chronic inflammation (p < 0.001), neutrophil activity (p < 0.001), glandular atrophy (p < 0.001) and intestinal metaplasia (p < 0.001).</p><p><strong>Conclusion: </strong>H. pylori positivity was associated with more severe chronic inflammation and active neutrophilic infiltration, glandular atrophy and intestinal metaplasia.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13281601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148251261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive genomic insights into lineages, virulence, and antibiotic resistance profiles of Campylobacter jejuni entailing a global One Health scenario.","authors":"Shamsul Qumar, Mohamad Hamad, Raed AbuOdeh, Ghalia Khoder, Niyaz Ahmed","doi":"10.1186/s13099-026-00848-y","DOIUrl":"10.1186/s13099-026-00848-y","url":null,"abstract":"<p><strong>Background: </strong>Campylobacter species are among the leading causes of bacterial gastroenteritis worldwide, with poultry recognized as a major reservoir for several life-threatening foodborne and zoonotic infections. The overuse and possible misuse of antimicrobials in the livestock sector in different countries of the world have contributed to the emergence of multidrug-resistant Campylobacter jejuni strains with significant public health concerns. To better understand the evolution, host adaptation, and antimicrobial resistance (AMR) of C. jejuni, we performed a global comparative genomic analysis of 1,125 high-quality genomes from human and chicken hosts, including five newly sequenced isolates representing broiler chicken samples.</p><p><strong>Results: </strong>Pangenome analysis of 1,125 C. jejuni genomes identified 4,489 orthologous gene clusters, of which 1,360 constitute the conserved core genome. The findings indicate a weakly open pangenome approaching saturation, suggesting limited gene acquisition. Phylogenomic analysis revealed three major clades with limited geographic clustering, consistent with global dissemination and evolutionary divergence. Human isolates were distributed across all clades, whereas chicken isolates were primarily restricted to clade one. Sequence typing identified 290 STs across 30 clonal complexes, with ST-48 enriched in chickens while ST-50 predominated in humans, reflecting potential host adaptation and epidemiological structuring. All five in-house isolates were multidrug-resistant, producing extended-spectrum β-lactamases (ESBLs) that conferred β-lactam resistance. Additionally, three isolates exhibited resistance to macrolides and tetracycline, further underscoring their broad resistance phenotype. Genome-wide AMR profiling of 1,125 C. jejuni isolates identified 31 well-characterized resistance genes, including those encoding RND and MATE efflux systems, penicillin-binding proteins, and metallo- and serine-beta-lactamase families, underscoring their intrinsic role in the core resistome. The most common resistance mutations were gyrA p.T86I (60.3%) and 23S r2075A>G (4%), conferring resistance to fluoroquinolones and clarithromycin. Analysis of the 1,125 genomes, including the five new isolates, revealed 126 key virulence genes, with cytolethal distending toxin (cdtA, cdtB, and cdtC) and capsule biosynthesis clusters present in over 85% and 93% of the isolates, respectively.</p><p><strong>Conclusion: </strong>These findings provide comprehensive insights into the evolution, transmission dynamics, host adaptation, antimicrobial resistance, and pathogenic potential of C. jejuni. Poultry serves as a critical reservoir contributing to the emergence and dissemination of high-risk, pathogenic, and drug-resistant lineages, underscoring the importance of monitoring and controlling AMR in livestock to protect public health.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13312522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148251241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated analysis of gastric microbiome and clinical features for the diagnosis of gastric neoplasms.","authors":"Donghoon Kang, Youngjin Shin, Yu Kyung Cho, Jae Myung Park, Seung-Hyun Jung, Myung-Gyu Choi","doi":"10.1186/s13099-026-00843-3","DOIUrl":"10.1186/s13099-026-00843-3","url":null,"abstract":"<p><strong>Background: </strong>Gastric cancer (GC) progression is closely associated with microbial dysbiosis. However, microbial alterations in the intermediate stage of gastric adenoma (GA) remain under-characterized. This study investigated stage-specific microbiome changes and evaluated predictive models integrating microbial and clinical features.</p><p><strong>Methods: </strong>We analyzed 231 subjects (129 GA, 73 GC, 29 healthy controls [HC]) using 16 S ribosomal DNA sequencing of paired oral, non-lesional gastric mucosa (GM), and gastric lesion (GL) samples. Random Forest models were constructed using microbial genera and clinical features, validated via leave-one-out cross-validation.</p><p><strong>Results: </strong>Stepwise microbial dysbiosis was observed during GC progression. Alpha diversity was significantly lower in GC-GL than in HC-GM and GA-GL. Helicobacter pylori infection was associated with reduced alpha diversity in GL samples. Genera such as Streptococcus, Neisseria, and Haemophilus were enriched in GC-GL, while Phocaeicola, Faecalibacterium, and Bifidobacterium were depleted. A gastric neoplasm prediction model incorporating 33 microbial genera and six clinical variables (age, sex, BMI, hypertension, smoking, and atrophy) demonstrated superior predictive performance (AUC = 0.830) in distinguishing gastric neoplasms from HCs, compared to models using either microbial genera (AUC = 0.790) or clinical variables (AUC = 0.715) alone. The combined model also accurately distinguished between GA and GC (AUC = 0.807).</p><p><strong>Conclusions: </strong>The gastric microbiome profile changes dynamically during GC progression, highlighting its potential role in tumor development. Integrating microbial signatures with clinical features enables robust classification of gastric neoplasms and may serve as a valuable adjunctive tool for diagnosis and risk stratification in endoscopic practice.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13520268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148239198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Burden of intestinal protozoan parasites coinciding with Helicobacter pylori infection in patients with gastrointestinal symptoms.","authors":"Amel Youssef Shehab, Mona Mohamed Tolba, Ali Ali Mohammed Alrabeei, Heba S Ibrahim, Hend El-Taweel","doi":"10.1186/s13099-026-00841-5","DOIUrl":"10.1186/s13099-026-00841-5","url":null,"abstract":"<p><strong>Aim: </strong>Protozoal infections are underdiagnosed contributors to gastrointestinal disease. As their symptoms frequently overlap with those of Helicobacter pylori infection, a leading cause of gastrointestinal illness, coinfections may be overlooked. This study aimed to determine the prevalence of intestinal protozoal infections among patients referred for H. pylori stool testing and to explore their association with clinical symptoms and risk factors.</p><p><strong>Methods: </strong>A cross-sectional study was conducted on 150 patients presenting with gastrointestinal complaints. Stool samples were examined using comprehensive parasitological techniques, along with ELISA for Entamoeba histolytica/dispar and H. pylori antigens.</p><p><strong>Results: </strong>Intestinal protozoa were detected in 36.9% of participants, most commonly Blastocystis spp. (33.3%), followed by E. dispar (5.3%) and E. coli (2.7%). Giardia lamblia, Dientamoeba fragilis, and Cyclospora cayetanensis were detected in only four patients. All Entamoeba infections were negative for E. histolytica-specific antigen. H. pylori antigen was positive in 35.3% of participants. The prevalence of intestinal protozoa did not differ significantly between H. pylori-positive and H. pylori-negative patients (39.6% vs. 34%); however, Blastocystis spp. was significantly associated with higher H. pylori antigen concentrations. Both protozoal and H. pylori infections were significantly associated with the source of drinking water but showed no significant association with age or sex. Abdominal pain was the predominant symptom among all patients, regardless of H. pylori or protozoal infection status. Notably, 78% of patients referred for H. pylori testing had not concurrently undergone parasitological examination, of whom 37.6% were subsequently found to have protozoal infections.</p><p><strong>Conclusion: </strong>This study demonstrates a high prevalence of intestinal protozoal infections, predominantly Blastocystis spp., among patients undergoing H. pylori evaluation, and identifies a significant association between Blastocystis and elevated H. pylori antigen levels. The overlapping symptoms and frequent underdiagnosis of protozoal infections in clinical practice support the incorporation of routine parasitological examination alongside H. pylori testing in patients presenting with gastrointestinal symptoms, with the potential to improve diagnostic accuracy and patient management.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13274104/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148198754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Longitudinal dynamics of gut microbiota and mycobiota in pneumonia-derived sepsis: evidence of taxonomic stability and trans-kingdom network reorganization.","authors":"Fangyi Li, Xinyi Xu, Minggen Zhou, Shangming Du, Zhijie He, Zhongsheng Xia, Qikui Chen, Jieyao Li, Song Tang, Wa Zhong, Jihao Xu","doi":"10.1186/s13099-026-00838-0","DOIUrl":"10.1186/s13099-026-00838-0","url":null,"abstract":"<p><strong>Background: </strong>Gut microbial dysbiosis has been implicated in sepsis-related organ dysfunction. However, the longitudinal dynamics of the gut microbiota and mycobiota-and particularly their cross-kingdom ecological organization-in pneumonia-derived sepsis remain incompletely understood.</p><p><strong>Methods: </strong>Patients with pneumonia-derived sepsis were prospectively enrolled. Fecal samples and clinical data (SOFA scores and inflammatory markers) were collected on Day 1 and Day 7. Gut bacterial and fungal communities were profiled using 16 S rRNA and ITS1 sequencing. Longitudinal and outcome-stratified analyses were performed. Trans-kingdom co-occurrence networks and module-based topological analyses were constructed, and associations with clinical parameters were explored.</p><p><strong>Results: </strong>Global analyses indicated relative compositional stability in the gut microbiota and mycobiota between Day 1 and Day 7, with no significant differences in alpha or beta diversity. The dominant bacteria were Bacillota, Bacteroidota, and Pseudomonadota at the phylum level, and Enterococcus, Bacteroides, and Escherichia-Shigella at the genus level; Escherichia-Shigella showed a decreasing trend and Bacteroides an increasing trend, though neither reached statistical significance (Padj > 0.05). Ascomycota dominated the fungal community, with Candida, Fusarium, and Oligophagozyma as the core genera, with no obvious temporal shifts. However, outcome-based stratification revealed that fungal Chao1 richness increased significantly post-treatment, specifically in the bad-outcome group (P < 0.05). The most notable findings emerged from the trans-kingdom interactome. In the favorable-outcome group, a specific modular configuration (ModM1) was identified post-treatment, containing four microbiota hubs (Parabacteroides, Mediterraneibacter, Serratia, and Enterococcus). While the aggregate abundance of ModM1 lacked clinical correlation, its hub genus, Mediterraneibacter-a prevalent anaerobe-showed a negative association with PCT and TNF-α. Additionally, the fungal-integrated ModM8 showed a potential positive association with IL-8. Conversely, the bad-outcome group showed a lack of such hub-anchored coordination.</p><p><strong>Conclusions: </strong>In this small exploratory cohort, early pneumonia-derived sepsis appeared to exhibit relative taxonomic stability but subtle reorganization of cross-kingdom ecological connectivity. Microbial shifts appeared to manifest primarily as changes in network embedding rather than abundance. These observations provide exploratory insights that require further validation regarding topological integration, especially fungal involvement in inflammatory modules, for understanding host-microbiome interactions in critical illness. Larger longitudinal studies are warranted.</p><p><strong>Trial registration: </strong>ClinicalTrials.gov, NCT04525677, registered on 14 July 2020.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13459335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148101361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bone marrow mesenchymal stem cells synergize with fusobacterium nucleatum to drive colorectal tumorigenesis via gut microbiome dysbiosis.","authors":"Keyi Zhang, Caihan Duan, Jiawei Chen, Qi He, Yu Jin, Jun Liu, Rong Lin, Chaoqun Han","doi":"10.1186/s13099-026-00839-z","DOIUrl":"10.1186/s13099-026-00839-z","url":null,"abstract":"<p><strong>Background: </strong>The oncogenic role of F. nucleatum (Fn) in colorectal cancer (CRC) is increasingly recognized, yet its interaction with host stromal components, such as bone marrow mesenchymal stem cells (BMSCs), remains poorly understood. Building on our previous discovery that BMSC-derived Wnt3a promotes Fn-driven tumorigenesis, this study aims to investigate the synergistic interplay between BMSCs and F. nucleatum in CRC pathogenesis via the gut microbiome.</p><p><strong>Methods: </strong>Based on the established Apc^Min/+ mouse model of CRC, animals were randomly assigned to four experimental groups: control, Fn-only, BMSCs-only, and Fn+BMSCs co-treatment group. Gut microbiota composition was continuously analyzed over 8 weeks by metagenomic sequencing. Metagenomic functions were predicted using PICRUSt2.</p><p><strong>Results: </strong>The Fn+BMSCs co-treatment group exhibited the highest enrichment of F. nucleatum and the greatest reduction in microbial diversity. Fn+BMSCs co-treatment induced a distinct pro-tumorigenic shift, marked by a decline in symbiont Lactobacillus and an increase in pathobiont Escherichia-Shigella. Metagenomic analysis revealed a unique enhancement of butanoate metabolism in the Fn+BMSC co-treatment group. Furthermore, a profoundly elevated LPS level was discovered in the Fn+BMSCs co-treatment group, indicating hyperactivation of the pro-inflammatory and proliferative TLR4/NF-κB pathway.</p><p><strong>Conclusions: </strong>Our findings demonstrate that BMSCs synergize with F. nucleatum to create a tumorigenicmicroenvironment by driving microbial dysbiosis, reprogramming metabolic pathways, and amplifying pro-inflammatory signaling. Our findings reveal that BMSCs fuel CRC progression via multiple mechanisms: by altering the gut microbiome ecology and, as previously discovered, by providing oncogenic Wnt3a signals. Targeting the synergistic BMSC-Fn axis may thus offer a novel therapeutic strategy for CRC.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13459635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148054130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antimicrobial resistance and genomic characteristics of nontyphoidal Salmonella strains from diarrheal patients in Shandong, China.","authors":"Ruyue Fan, Peibin Hou, Bin Hu, Ying Yang, Na Sun, Dandi Li, Yuan Gao, Hao Song, Wenjuan Liu, Tingting Miao, Kai Guo, Weiwei Li, Yunchang Guo, Shaofei Yan, Xinpeng Li","doi":"10.1186/s13099-026-00840-6","DOIUrl":"10.1186/s13099-026-00840-6","url":null,"abstract":"<p><strong>Background: </strong>Nontyphoidal Salmonella (NTS) is a major cause of foodborne illness worldwide. This study aimed to determine the antimicrobial susceptibilities of clinical NTS isolates from Shandong, China, and to characterize the genomic determinants of antimicrobial resistance and virulence genotypes using whole-genome sequencing (WGS).</p><p><strong>Methods: </strong>A total of 125 NTS strains were isolated and identified from diarrhea patients in Shandong, China. Antimicrobial susceptibility testing (AST) was performed for all isolates. Antimicrobial resistance genes (ARGs), virulence factor genes (VFGs), and plasmid replicons, serotypes, sequence types (STs) were determined through WGS analysis.</p><p><strong>Results: </strong>The NTS isolates in this study showed high resistance to ampicillin (AMP, 73.6%), tetracycline (TET, 62.4%), and chloramphenicol (CHL, 56.8%), among them the multidrug resistance (MDR) rate was 59.2%. In total, 28 serotypes, and 30 STs were identified, with ST34 serotype 1,4,[5],12:i:- being the most prevalent. Genomic analysis revealed 63 ARGs and 171 VFGs across all isolates. Type VI secretion system-associated genes were identified in Salmonella Liverpool (S. Liverpool). Plasmid replicons, especially Col(pHAD28), pKPC-CAV1321, and IncHI2, were more frequently present among MDR isolates. Among dominant serotypes, S. Enteritidis carried the highest number of VFGs but relatively few ARGs compared with other dominant serotypes.</p><p><strong>Conclusion: </strong>These findings indicate a substantial MDR burden and diverse genomic features among clinical NTS isolates in Shandong, China. The deep understanding of resistance and virulence characteristics from NTS genome can be quite supportive for continuous surveillance and antimicrobial stewardship.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13459773/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148015254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic diversity, antibiotic resistance, and maturation‑dependent adhesion of F18 enterotoxigenic Escherichia coli strains in porcine intestinal cells.","authors":"Dongqi Liu, Nicholas L F Gallina, Chenhai Li, Nicole Irizarry-Tardi, Mahmoud Sayedahmed, Jathya C Karunathilaka, Nathan Horn, Weicang Wang, Ahmed AbdelKhalek, Arun K Bhunia","doi":"10.1186/s13099-026-00837-1","DOIUrl":"10.1186/s13099-026-00837-1","url":null,"abstract":"<p><strong>Background: </strong>Enterotoxigenic Escherichia coli (ETEC) strains expressing F4 and F18 fimbriae are major causes of neonatal and post‑weaning diarrhea in swine. Although epithelial maturation influences susceptibility in vivo, its impact on ETEC-host interactions remains poorly defined. This study characterizes the genomic diversity, virulence traits, and antibiotic resistance profiles of emerging F18 ETEC isolates using whole-genome sequencing and a differentiated porcine intestinal cell model.</p><p><strong>Methods: </strong>Six ETEC genomes: three F18 strains (3EC1, 27EC1, 3247EC), a porcine F4 strain, human ETEC H10407, and the historical F18 strain E. coli Nysø were analyzed by comparative genomics for virulence factors, toxin genes, and antimicrobial resistance (AMR) determinants. Genome sequences were submitted to the Type (Strain) Genome Server (TYGS) for whole genome-based taxonomic classification. Antibiotic susceptibility was phenotypically confirmed by microdilution and disk diffusion assays. Adhesion assays were performed using IPEC‑1, IPEC‑J2, and Caco‑2 cells conditioned to Early (6 days post‑confluence, DPC), Mid (9 DPC), and Late (16 DPC) maturation states. Expression of F18‑binding receptors (FUT1, FUT2) was quantified by RT‑qPCR.</p><p><strong>Results: </strong>IPEC‑1 cells exhibited significantly higher FUT1 and FUT2 expression than IPEC‑J2, corresponding to approximately two‑fold stronger adhesion by most F18 isolates. Strain 3EC1 showed a distinct adhesion peak at 9 DPC, approaching F4 levels, while F4 and H10407 consistently displayed the highest adhesion across all models. Phylogenetic analysis placed 27EC1 and 3247EC in a clade with the F4 strain, whereas 3EC1 clustered with human H10407 and the ancestral E. coli Nysø strain. Comparative genomic analysis revealed substantial heterogeneity among F18 strains in fimbrial loci, flagellin, lipopolysaccharide biosynthesis genes, and AMR genes. Strain 3EC1 uniquely carried stx2e, and 3EC1 and 3247EC were positive for non‑classical EAST1 variants. All F18 isolates encoded hlyE and were β‑hemolytic. Strain 3247EC harbored the largest AMR gene repertoire (28 resistance genes), with all three F18 isolates demonstrating resistance to multiple antibiotic classes.</p><p><strong>Conclusions: </strong>The IPEC‑1/IPEC‑J2 maturation model recapitulates age‑dependent susceptibility to ETEC, driven by FUT1/FUT2 expression levels. The co-occurrence of strong adhesion capacity, stx2e, and extensive antimicrobial resistance in F18 strains underscores the evolution in virulence and the public health relevance of AMR surveillance in swine. This integrated genomic and cell-based platform provides a refined model for studying porcine ETEC pathogenesis and informing the development of targeted intervention strategies.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13371446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147963521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fungi and colorectal cancer: from dysregulation to clinical translation.","authors":"Wu Yinhang, Han Shuwen, Zhuang Jing, Feng Min","doi":"10.1186/s13099-026-00835-3","DOIUrl":"10.1186/s13099-026-00835-3","url":null,"abstract":"<p><p>Research on the gut microbiota has primarily focused on bacterial communities. However, the role of fungi-the second-largest eukaryotic component of the gut microbiome-in the development and progression of colorectal cancer (CRC) has been less extensively studied compared to bacteria. Recent studies have revealed significant fungal dysbiosis in the intestines of CRC patients, where the enrichment of specific pathogenic fungi (e.g., Aspergillus spp.) is closely associated with tumor progression, while the reduction of certain commensal fungi may weaken their protective effects. This fungal imbalance not only directly promotes tumorigenesis through carcinogenic mechanisms but also indirectly accelerates CRC progression by reshaping the bacteria-fungi interaction network and the host immune microenvironment. This article reviews the structural alterations of fungal communities in CRC, the changing patterns of specific fungal species, the relationship between fungal dysbiosis and clinicopathological features, the potential molecular mechanisms of fungi in CRC pathogenesis, the significance of cross-kingdom microbial interactions, as well as the potential diagnostic and therapeutic applications of fungi in CRC and the challenges and prospects of novel fungal-modulating therapeutic strategies.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147814154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}