Potential Pathogens Research Articles

Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study

This study aimed to evaluate the usefulness of amplicon-based real-time metagenomic sequencing applied to cerebrospinal fluid (CSF) for identifying the causative agents of bacterial meningitis. We conducted a 16S rRNA amplicon sequencing using a nanopore-based platform, alongside routine polymerase chain reaction (PCR) testing or bacterial culture, to compare its clinical performance in pathogen detection on CSF samples. Among 17 patients, nanopore-based sequencing, multiplex PCR, and bacterial culture detected potential bacterial pathogens in 47.1%, 0%, and 47.1% samples, respectively. Nanopore-based sequencing demonstrated a sensitivity of 50.0%, specificity of 55.6%, positive predictive value of 50.0%, negative predictive value of 55.6%, and overall accuracy of 47.1%, compared to the gold standard method for bacterial culture. In 44.4% (4/9) of culture-negative cases, nanopore-based sequencing detected potentially causative pathogens, whereas four (23.5%) patients were positive only in culture. Using nanopore-based sequencing alongside bacterial culture increased the positivity rate from 47.1 to 70.6%. However, these values may be overestimated due to challenges in distinguishing significant pathogens from background noise. Meanwhile, the bioinformatics module in EPI2ME reduced the turn-around time to 10 min. Nanopore-based metagenomic sequencing is expected to serve as a complementary tool for pathogen detection in CSF samples by facilitating rapid and accurate diagnosis.

Complete genome sequences of Castellaniella ginsengisoli associated with mortality events in avian species.

Castellaniella ginsengisoli is a potential bacterial pathogen that affects chickens. We present 22 complete genome sequences of clinical isolates to facilitate the genomic analysis and the development of diagnostic tools.

S100A13-driven interaction between pancreatic adenocarcinoma cells and cancer-associated fibroblasts promotes tumor progression through calcium signaling

BackgroundCancer-associated fibroblasts (CAFs) are key components of the pancreatic adenocarcinoma (PAAD) tumor microenvironment (TME), where they promote tumor progression and metastasis through immunosuppressive functions. Although significant progress has been made in understanding the crosstalk between cancer cells and CAFs, many underlying mechanisms remain unclear. Recent studies have highlighted the importance of calcium signaling in enhancing interactions between tumor cells and the surrounding stroma, with the S100 family of proteins serving as important regulators. While the roles of some S100 proteins have been extensively studied, others, such as S100A13, remain less well understood.MethodsBioinformatic analysis was employed to predict the pathogenic potential of CAFs and S100A13. Stable S100A13 knockdown CAFs were generated using a short hairpin RNA system. Cellular viability and apoptosis rates were evaluated through CCK-8 and flow cytometry tests, respectively. Additionally, the wound healing and migration assays were conducted to assess the invasive and metastatic capabilities. Transcriptome analysis was conducted to identify differential gene expression and associated signaling pathways in PAAD cells derived from an indirect culture system. Furthermore, the protumoral role of S100A13 in PAAD was further verified using both 3D bioprinting and cell line-based xenograft tumor models.ResultsIn this study, we identified a strong association between S100A13, a calcium-binding protein, and CAFs in PAAD. Gene expression analysis revealed that S100A13 was highly expressed in CAFs and correlated with poor prognosis. Knockdown of S100A13 in CAFs reduced the metastatic potential of PAAD cells. In addition, S100A13 depletion impaired cell motility and calcium signaling pathways within the TME. Furthermore, silencing S100A13 in CAFs markedly slowed PAAD progression in both tumor spheroids and Balb/c nude mice.ConclusionsTogether, our findings underscore the critical role of CAFs-derived S100A13 in PAAD progression and suggest that targeting S100A13 may offer a promising therapeutic strategy for PAAD.

Pathogens threatening agriculture and biodiversity in South Africa: A horizon scanning approach

There is mounting evidence that invasive alien species (IAS) have adverse effects on plant health and the global economy, posing a significant threat to biodiversity and ecosystem functioning. Identifying and assessing emerging IAS, such as plant pathogens, is a proactive approach that might assist in prioritising potential pathogen threats before they become established or widespread, negatively affecting plant health, crop production, animal production, animal health by affecting pastures and food security in South Africa. We collected information from the CABI Invasive Species Compendium and Crop Protection Compendium on plant pathogens that are present in neighbouring countries and are likely to be introduced throughout the Republic of South Africa using an expert-elicitation horizon scanning study. Pathogens with the highest score were determined based on their strong capability on the chance of entry, establishment, economic impact, and biodiversity destruction. The current study revealed that only 17 pathogens (6 fungi, 7 viruses, 2 bacteria and 2 phytoplasma) had been prioritised due to their potential to enter the country and have been reported in the neighbouring countries. Maize lethal necrosis disease, Candidatus Liberibacter asiaticus, Candidatus Phytoplasma palmae, Fusarium oxysporum f.sp. cubense tropical race 4, and Maize chlorotic mottle virus have the highest potential to enter and establish in the country. The most effective phytosanitary actions for the high scoring pathogen were to conduct surveillance for their potential presence in South Africa and risk analysis, especially for organisms recorded in neighbouring countries.

How likely is it that a virus or bacteria is causing a patient’s symptoms? A new approach to interpret the outcome from multi-pathogen PCR

Background Whether a detected virus or bacteria is a pathogen that may require treatment, or is merely a commensal ‘passenger’, remains confusing for many infections. This confusion is likely to increase with the wider use of multi-pathogen PCR. Objectives To propose a new statistical procedure to analyse and present data from case-control studies clarifying the probability of causality. Methods We conducted a case-control study in US outpatient settings that enrolled patients aged 18 to 75 years with acute lower respiratory tract infection and controls without respiratory symptoms. Patients underwent multi-pathogen PCR testing. The positive etiologic predictive value was calculated to estimate the probability that each potential pathogen was the cause of symptoms. The outcome was illustrated using a modified forest plot and by classifying pathogens into five categories clarifying the probability for causality. Results We enrolled 618 adult cases and 497 asymptomatic controls. The modified forest plot and the classification of risk for causality aimed to facilitate understanding. Pathogens likely to be causative when present included influenza A and B, SARS-CoV-2, rhinovirus, and parainfluenza viruses, while Staphylococcus aureus is almost always commensal. Broad confidence intervals for the positive etiologic predictive value made it difficult to draw conclusions for potential pathogens with low prevalence. Conclusion This pilot study shows that the proposed statistical approach is likely to be practical for analysing larger case-control studies or for a meta-analysis of multiple studies. This method may help when interpreting the results from multi-pathogen PCR.

Comparison of pathogenicity factors of avian pathogenic and extraintestinal pathogenic Escherichia coli isolates originating from broiler chickens

ABSTRACT 1. E. coli is an opportunist pathogen of animals, including food-producing ones and humans. Chickens may be a notable source of pathogenic and antimicrobial resistant E. coli for transmission to humans. 2. This study compared virulence-associated genes (VGs) and antimicrobial resistance (AMR) in avian pathogenic E. coli (APEC) and extraintestinal pathogenic E. coli (ExPEC) isolates from broiler chickens, specifically APEC isolates in liver samples (n = 78) and ExPEC or non-ExPEC isolates in litter samples (n = 34). Virulence was evaluated by PCR for feoB, hlyF, iroN, iss, iutA and ompT genes, while AMR was evaluated by using antimicrobials from seven classes and detecting blaSHV, blaTEM, blaOXA, qnrB, stcM, mrc1, mrc2, sul1 and tetA genes. 3. The APEC isolates were found in 100% of livers, while ExPEC and non-ExPEC isolates were found in 44% and 56% of the litter samples. The predominant VG was feoB (100%), followed by ompT (63%), iutA (60%), iss (58%) and hlyF (43%). Surprisingly, iroN, omp T and iutA had higher prevalences in APEC isolates (85%, 96% and 96%, respectively) than in ExPEC isolates (73%, 87% and 73%, respectively) and non-ExPEC isolates (0% for all). The presence of all VG in 33% of isolates indicated high pathogenicity. 4. The isolates were phenotypically resistant to ampicillin (93%), ceftazidime (72%) and nalidixic acid (82%). All APEC and ExPEC isolates (100%) were multidrug resistant (MDR), while 63% of non-ExPEC isolates were MDR. Genotypic AMR testing revealed that 53% and 52% of all isolates had stcM and tetA, respectively. No isolate was positive for blaSHV, blaOXA, mrc1 or mrc2, which suggested the benefits of colistin for treating carbapenem-resistant enteric pathogens, due to the high resistance detected to meropenem (47%). 5. Given the potential pathogenicity of E. coli isolates, improving biosecurity practices in chicken flocks should be prioritised to eliminate transmission to humans through the food chain.

Development of a conditional plasmid for gene deletion in non-model Fusobacterium nucleatum strains.

Fusobacterium nucleatum is an opportunistic pathogen with four subspecies: nucleatum (FNN), vincentii (FNV), polymorphum (FNP), and animalis (FNA), each with distinct disease potentials. Research on fusobacterial pathogenesis has mainly focused on the model strain ATCC 23726 from FNN. However, this narrow focus may overlook significant behaviors of other FNN strains and those from other subspecies, given the genetic and phenotypic diversity within F. nucleatum. While ATCC 23726 is highly transformable, most other Fusobacterium strains exhibit low transformation efficiency, complicating traditional gene deletion methods that rely on non-replicating plasmids. To address this, we developed a conditional plasmid system in which the RepA protein, essential for replication of a pCWU6-based shuttle plasmid, is controlled by an inducible system combining an fdx promoter with a theophylline-responsive riboswitch. This system allows plasmid replication in host cells upon induction and plasmid loss when the inducer is removed, forcing chromosomal integration via homologous recombination in the presence of the antibiotic thiamphenicol. We validated this approach by targeting the galK gene, successfully generating mutants in FNN (ATCC 23726, CTI-2), FNP (ATCC 10953), FNA (21_1A), and the closely related species Fusobacterium periodonticum. Incorporating a sacB counterselection marker in this conditional plasmid enabled the deletion of the radD gene in non-model strains. Interestingly, while radD deletion in 23726, 10953, and 21_1A abolished coaggregation with Actinomyces oris, the CTI-2 mutant retained this ability, suggesting the involvement of other unknown adhesins. This work significantly advances gene deletion in genetically recalcitrant F. nucleatum strains, enhancing our understanding of this pathogen.IMPORTANCEFusobacterium nucleatum is implicated in various human diseases, including periodontal disease, preterm birth, and colorectal cancer, often linked to specific strains and reflecting the species' genetic and phenotypic diversity. Despite this diversity, most genetic research has centered on the model strain ATCC 23726, potentially missing key aspects of other strains' pathogenic potential. This study addresses a critical gap by developing a novel conditional plasmid system that enables gene deletion in genetically recalcitrant strains of F. nucleatum. We successfully deleted genes in the FNN clinical strain CTI-2, the FNA strain 21_1A, and F. periodonticum for the first time. Our findings, particularly the varying behavior of the radD gene production in coaggregation across strains, underscore the complexity of F. nucleatum and the need for broader genetic studies. This work advances our understanding of F. nucleatum virulence at the strain level and provides a valuable tool for future bacterial genetics research.

Prevalence and pathogenic potential of Shewanella species in oysters and seawater collected from the Chesapeake Bay and Maryland Coastal Bays

Shewanella is a genus of Gram-negative marine bacteria with some species associated with human and shellfish illnesses. This study evaluated the abundance of Shewanella species in oysters and seawater from the Chesapeake and Maryland Coastal Bays at four sites between 2019 and 2021. Physicochemical parameters such as temperature, salinity, dissolved oxygen, turbidity, pH, chlorophyll-a, rainfall within the last 48 h, total dissolved solids, and atmospheric pressure were also recorded to evaluate if there was a correlation between environmental parameters and the level of Shewanella. The highest total Shewanella counts were 1.8 × 107 CFU/g in oysters and 4.0 × 102 CFU/mL in seawater. 16S rRNA sequencing was performed on 1,344 representative isolates of which 890 (713 oyster, 177 seawater) were confirmed as Shewanella within 16 species. The top four species isolated from oysters and seawater were S. khirikhana a known shrimp pathogen (49%), S. marisflavi (19%), S. loihica (11%), and S. algae (8%). Testing for alpha and beta hemolysis were performed on all confirmed Shewanella isolates. Beta hemolysis was observed in 405 (46%) of the isolates of which 313 were in oysters and 92 in seawater. In oysters, beta-hemolysis was most prevalent in S. khirikhana (233 of 344 isolates, 68%), while in seawater 64 of 92 isolates (70%) were beta-hemolytic strains. Beta-hemolysis suggests that these could be potentially pathogenic strains. Correlations were performed between physicochemical attributes of the seawater and Shewanella counts. Only seawater temperature and dissolved oxygen correlated with Shewanella counts (r = 0.45 and − 0.41), respectively. No correlations were observed between the physicochemical parameters and Shewanella abundances in oysters. Results suggest that virulent strains of Shewanella may be present in oysters and seawater from the Chesapeake and Maryland Coastal Bays, perhaps as a consequence of rising seawater temperatures.

Therapeutic potential of the neutralizing monoclonal antibody 45G3 against encephalomyocarditis virus

Encephalomyocarditis virus (EMCV), a potential zoonotic pathogen, poses significant socioeconomic and public health challenges across various host species. Although EMCV rarely triggers severe clinical symptoms in humans, its widespread prevalence and unique biological characteristics underscore the need for continuous surveillance and the development of effective therapeutics and prophylactics. In this study, we evaluated the neutralizing effects of a monoclonal antibody derived from the spleens of mice immunized with EMCV virus-like particles (VLPs), both in vitro and in vivo. Using recombinant DNA technology, we engineered a baculovirus system to express EMCVs P12A and 3C, facilitating the production of VLPs in Sf9 cells. These VLPs serve as antigens to immunize mice, leading to the isolation of the monoclonal antibody 45G3. This antibody exhibited high specificity for EMCV conformational epitopes, excluding linear epitopes, and demonstrated potent in vitro neutralizing activity, with an IC50 of 0.01873 μg/mL. Immunoelectron microscopy (IEM) revealed a strong direct interaction between the 45G3 antibody and EMCV particles. Virus adsorption inhibition assays demonstrated that 45G3 effectively blocked viral attachment, thereby preventing further infection of host cells. These findings further support the notion of a robust interaction between the virus and the antibody. Moreover, in vivo assessments revealed that 45G3 significantly reduced viral loads in treated mice and improved survival outcomes following EMCV exposure. Additionally, posttreatment analysis revealed reduced tissue damage and a markedly decreased inflammatory response in the brain, indicating that the 45G3 antibody effectively blocked viral infection, thereby mitigating tissue damage and enhancing survival. These findings position 45G3 as a promising candidate for EMCV management and provide a strong foundation for the future development of antiviral drugs targeting this widespread virus.

Evaluation of the recovery effects of antibiotic-resistant lactiplantibacillus plantarum subsp. Plantarum ATCC14917 on the antibiotic-disturbed intestinal microbiota using a mice model.

Supplementing Lactobacillus alongside antibiotic treatment was a curative strategy to modulate gut microbiota and alleviate antibiotic-associated dysbiosis. But the lactobacilli that are used as probiotics are sensitive or have a low level of resistance to antibiotics, so they usually cannot achieve their beneficial effect, since they are killed by the applied antibiotics. This work aimed to develop the highly resistant Lactiplantibacillus plantarum subsp. plantarum ATCC14917 to cephalexin and evaluate its recovery effects of antibiotic-resistant L. plantarum on the antibiotic-disturbed intestinal microbiota using a mice model. After successive growth in LSM broth containing a gradually increasing concentration of cephalexin for 70 days, the minimum inhibitory concentration (MIC) of L. plantarum ATCC14917 to cephalexin significantly increased from 16 μg·mL-1 to 8192 μg·mL-1, but stabilized on 4096 μg·mL-1. After sequencing and sequence analysis, no mutated genes were detected on mobile elements, showing that horizontal transfer of mutated genes could not occur. Compared to the control group (Con), feeding mice with cephalexin (1mg·mL-1; Cep) led to a decrease in alpha diversity. However, concurrently used cephalexin and L. plantarum (Cep+LpR) increased the alpha diversity in both microbial richness and diversity. The Cep+LpR group showed a lowest distance with the Con group than either Cep or Cep+LpS groups, suggesting that resistant L. plantarum treatment was more effective than the original strain for the recovery of intestinal microbiota. Compared to the cephalexin-treated group, concurrent ingestion of cephalexin together with resistant L. plantarum significantly increased the proportion of beneficial bacteria, decreased Firmicutes/Bacteroidetes ratio and abundance of potential pathogens. The use of antibiotic-resistant Lactiplantibacillus plantarum ATCC14917 contributed to a much faster and richer recovery of the gut microbiota disturbed by antibiotic treatment compared to original strain.

P1320 Oral highly-virulent pathogenic isolates aggravated colitis through gut microbiota-equol-ERβ axis

Abstract Background We isolated potential oral pathogens from IBD patients saliva and analyzed their virulence differences, hoping to elucidate the mechanism of different disease patterns in IBD patients. Methods A series of in vitro and in vivo experiments, whole-genome sequencing, 16S rRNA sequencing and non-targeted metabolomics sequencing were used to explore the pathogenicity of Streptococcus mutans (S.m) isolates. Results Our previous study indicated that the abundance of streptococcus in ulcerative colitis (UC) patients saliva was higher than healthy people. After over 1 year follow-up, we found that UC patients with poor disease state had higher proportion of S.m in saliva, and 31 S.m strains were further isolated from 25 UC saliva. Whole-genome sequencing showed that the virulence genes of S.m strains were related to immunity, metabolism and exotoxins. 9 strains with greater pro-inflammatory effects and barrier destroying ability were obtained based on microbe-cell co-culture. Subsequent animal experiments suggested that pro-inflammatory S.m strains significantly exacerbated intestinal inflammation of DSS mice, while non-pro-inflammatory S.m strains didn’t induce above effects. The pro-inflammatory effects of pro-inflammatory S.m strains on DSS mice disappeared after the depletion of gut microbiota by antibiotics, and fecal bacteria transplantation (FMT) found that the intestinal inflammation of DSS mice transplanted with pro-inflammatory strains groups feces was more severe than that of non-proinflammatory mice, suggesting that intestinal microbiota is essential for the proinflammatory effects of S.m strains. 16S rRNA sequencing showed that α diversity of intestinal microbiota of pro-inflammatory strains groups mice was lower than that of non-proinflammatory mice. The level of equol was lower in pro-inflammatory groups compared to non-pro-inflammatory groups through non-targeted metabolomics sequencing. Subsequently, we further confirmed S-equol/R-equol both ameliorated DSS mice colitis, while estrogen receptor β (ERβ) antagonist inhibited the protective effect of equol partially. Molecular docking also confirmed the combination of equol and ERβ protein, of which the binding sites were GLU-305, Ph-356 and HIE-475. Conclusion This study found for the first time that the pro-inflammatory effects of S.m isolates are different, which may be related to gut microbiota-equol-ERβ axis.

P0213 Salivary Veillonella parvula from Crohn’s Disease Patients Exacerbates Intestinal Inflammation

Abstract Background The gut microbiota plays a significant role in the development of inflammatory bowel disease (IBD). There is a close interaction between the oral and gut microbiota. However, the role of the "oral-gut" microbial axis in the development of IBD is not yet clear. Methods 1. Analyzed oral-gut microbiota patterns in 97 IBD patients using 16S rDNA sequencing and bioinformatics methods. 2. A mouse colitis model with DSS was used. It was gavaged with oral microbiota from CD patients to assess the impacts on colitis and gut microbiota. 3. Isolated specific differential bacteria, Veillonella, from CD patient saliva and evaluated their effects on DSS-induced colitis in mice. Results 1. IBD patients had a reduced core gut microbiota, lower diversity (P < 0.05), and increased abundance of potential pathogens such as Escherichia-Shigella. 2. CD patients showed more correlations between saliva and fecal microbiota, with the most significant correlation between Veillonella in saliva and Escherichia-Shigella in fecal (P=0.00018) . 3. The mice which were gavaged with saliva from CD patients showed significant weight loss (P < 0.0001), reduced colon length (P=0.03), increased histopathological scores (P=0.01), decreased expression of colonic mucosal barrier proteins ZO-1 and E-cadherin, and exacerbated gut microbiota dysbiosis . 4. The mice which were gavaged with Veillonella parvula from CD patients showed significant weight loss (P < 0.0001), reduced colon length (P=0.02), increased histopathological scores (P=0.02), decreased expression of colonic mucosal barrier proteins ZO-1 and E-cadherin, and exacerbated gut microbiota dysbiosis. Conclusion The interplay between the oral and gut microbiota potentially influences the progression of IBD, with oral bacteria such as Veillonella possibly intensifying intestinal inflammation in IBD patients by disrupting the gut microbiota balance. Targeted modulation of the gut microbiota and interference with oral-gut microbial interactions may offer a promising therapeutic strategy for managing IBD.

Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance

Microbial species must compete for space and nutrients to persist in the gastrointestinal (GI) tract, and our understanding of the complex pathobiont-microbiota interactions is far from complete. Klebsiella pneumoniae, a problematic, often drug-resistant nosocomial pathogen, can colonize the GI tract asymptomatically, serving as an infection reservoir. To provide insight on how K. pneumoniae interacts with the resident gut microbiome, we conduct a transposon mutagenesis screen using a murine model of GI colonization with an intact microbiota. Among the genes identified were those encoding a type VI secretion system (T6SS), which mediates contact-dependent killing of gram-negative bacteria. From several approaches, we demonstrate that the T6SS is critical for K. pneumoniae gut colonization. Metagenomics and in vitro killing assays reveal that K. pneumoniae reduces Betaproteobacteria species in a T6SS-dependent manner, thus identifying specific species targeted by K. pneumoniae. We further show that T6SS gene expression is controlled by several transcriptional regulators and that expression only occurs in vitro under conditions that mimic the gut environment. By enabling K. pneumoniae to thrive in the gut, the T6SS indirectly contributes to the pathogenic potential of this organism. These observations advance our molecular understanding of how K. pneumoniae successfully colonizes the GI tract.

Acquisition of innate B cell properties and generation of autoreactive IgA antibodies by follicular B cells during homeostatic proliferation

The physiologic process of homeostatic proliferation serves to restore the pool of peripheral lymphocytes in response to lymphopenia. However, functional changes in B cell responses during homeostatic proliferation are still only insufficiently characterized. Mature peripheral B cells consist of functionally distinct B cell subsets, such as adaptive follicular B cells (FoBs) and the innate B cell subsets, marginal zone B cells (MZBs) and B1a B cells. During homeostatic proliferation, B cells undergo antigen-independent clonal expansion and differentiation into antibody-producing plasma cells (PCs). However, it is still largely unknown which B cell lineages are involved in the formation of antibodies in response to lymphopenia and what functional properties these antibodies have. Employing adoptive transfer of different mature B cell subsets into lymphopenic Rag2-/- hosts, we here show that not only innate B cells – MZBs and B1a cells – but also adaptive FoBs were capable to differentiate into PCs and to produce IgM and class-switched IgA serum antibodies in a T cell-independent fashion during homeostatic proliferation. In light of the poor reactivity of FoBs to innate stimulation in vitro, the observed high expansion capacity of FoBs, their sustained repopulation of lymphoid and intestinal organs and their particularly prominent ability to induce class-switched auto-/polyreactive IgA antibodies in this antigen- and T cell-independent system was rather unexpected. These properties, which are more typical for innate B cells, were associated with a striking plasticity of FoBs that transdifferentiate into MZB-like cells under lymphopenic conditions. Together, our study indicates that the reconstitution of antibodies in response to lymphopenia-induced homeostatic B cell proliferation is mainly elicited by innate MZB-like B cell responses via antigen- and T cell-independent pathways resulting in the selection of autoreactive IgA antibodies. In addition, our data point to the pathogenic potential of the conversion of conventional adaptive B cells, which are the most common population of mature B cells, into innate-like B cells and the production of autoreactive IgA antibodies during homeostatic proliferation. This process could also manifest as clinical complication of therapy-induced lymphopenia in the context of transplantation and cancer in human patients.

DOP068 Vedolizumab counteracts Parkinson’s disease-related brain pathology driven by gut-primed IBD T cells

Abstract Background The gut-brain axis has been increasingly recognized as a critical pathway linking Inflammatory Bowel Diseases (IBD) with neurodegenerative diseases. Chronic inflammation resulting from IBD can extend beyond the gut, and epidemiological data have also linked to the increased prevalence of neurodegenerative conditions like Parkinson’s disease (PD). However, the exact mechanisms underlying this interconnection are largely unclear. We therefore investigated how gut-primed T cells from IBD patients may drive neurodegenerative processes seen in PD. Methods Peripheral blood T cells from IBD patients were analyzed for co-expression of gut-homing integrin α4β7 and brain-homing integrin β1. Using gut-specific photoconversion in a Kaede T cell Transfer Colitis mouse model, we assessed the infiltration of gut-primed T cells into the brain tissue. To model and elucidate the interplay of T cells with the brain tissue ex vivo, we developed an innovative three-dimensional co-culture system involving human stem cell-derived Brain Organoids (hBrO) and peripheral blood T cells from IBD patients and controls. Vedolizumab, an anti-α4β7 integrin antibody, was used to assess its potential in blocking T cell accumulation and subsequent neurotoxicity in hBrO cultures. Results Gut-primed T cells from IBD patients co-expressed brain-homing integrins, suggesting that they are able to enter brain tissue. Clear evidence of gut-to-brain T cell trafficking was obtained in the Kaede T cell Transfer Colitis mouse model, confirming the capacity of gut-primed T cells to migrate across the blood-brain barrier under conditions of chronic intestinal inflammation. In the hBrO co-culture model, neurons expressed MAdCAM-1, and MAdCAM-1 expression in neurons was also found in single cell RNA sequencing of postmortem brain tissue. Consistently, α4β7+ IBD T cells accumulated specifically in the vicinity of neurons, leading to neuronal cell death and aSyn aggregation (a hallmark of PD) in hBrO. In line, Vedolizumab treatment reduced IBD T cell accumulation in hBrO and preserved neural cell integrity. Conclusion Our data, for the first time, show a T cell trafficking-driven axis of gut-to-brain communication with pathogenic potential for the central nervous system in the context of IBD. Moreover, our findings suggest that neurotoxic T cell-neuron interaction is mediated by MADCAM1 and α4β7 integrin. Thus, our study reveals a novel pathway, by which IBD T cells may contribute to neurodegeneration, linking chronic gut inflammation to brain tissue pathology and synucleinopathy. Blocking α4β7-mediated T cell-induced neurotoxicity and aSyn pathology presents a potential therapeutic approach for IBD patients at risk of neurodegenerative diseases such as PD.

Large-scale genetic characterization of Parkinson's disease in the African and African admixed populations.

Elucidating the genetic contributions to Parkinson's disease (PD) etiology across diverse ancestries is a critical priority for the development of targeted therapies in a global context. We conducted the largest sequencing characterization of potentially disease-causing, protein-altering and splicing mutations in 710 cases and 11,827 controls from genetically predicted African or African admixed ancestries. We explored copy number variants (CNVs) and runs of homozygosity (ROHs) in prioritized early onset and familial cases. Our study identified rare GBA1 coding variants to be the most frequent mutations among PD patients, with a frequency of 4% in our case cohort. Out of the 18 GBA1 variants identified, ten were previously classified as pathogenic or likely pathogenic, four were novel, and four were reported as of uncertain clinical significance. The most common known disease-associated GBA1 variants in the Ashkenazi Jewish and European populations, p.Asn409Ser, p.Leu483Pro, p.Thr408Met, and p.Glu365Lys, were not identified among the screened PD cases of African and African admixed ancestry. Similarly, the European and Asian LRRK2 disease-causing mutational spectrum, including LRRK2 p.Gly2019Ser and p.Gly2385Arg genetic risk factors, did not appear to play a major role in PD etiology among West African-ancestry populations. However, we found three heterozygous novel missense LRRK2 variants of uncertain significance overrepresented in cases, two of which - p.Glu268Ala and p.Arg1538Cys - had a higher prevalence in the African ancestry population reference datasets. Structural variant analyses revealed the presence of PRKN CNVs with a frequency of 0.7% in African and African admixed cases, with 66% of CNVs detected being compound heterozygous or homozygous in early-onset cases, providing further insights into the genetic underpinnings in early-onset juvenile PD in these populations. Novel genetic variation overrepresented in cases versus controls among screened genes warrants further replication and functional prioritization to unravel their pathogenic potential. Here, we created the most comprehensive genetic catalog of both known and novel coding and splicing variants potentially linked to PD etiology in an underserved population. Our study has the potential to guide the development of targeted therapies in the emerging era of precision medicine. By expanding genetics research to involve underrepresented populations, we hope that future PD treatments are not only effective but also inclusive, addressing the needs of diverse ancestral groups.

Metabolic tug-of-war: Microbial metabolism shapes colonization resistance against enteric pathogens.

A widely recognized benefit of gut microbiota is that it provides colonization resistance against enteric pathogens. The gut microbiota and their products can protect the host from invading microbes directly via microbe-pathogen interactions and indirectly by host-microbiota interactions, which regulate immune system function. In contrast, enteric pathogens have evolved mechanisms to utilize microbiota-derived metabolites to overcome colonization resistance and increase their pathogenic potential. This review will focus on recent studies of metabolism-mediated mechanisms of colonization resistance and virulence strategies enteric pathogens use to overcome them, along with how induction of inflammation by pathogenic bacteria changes the landscape of the gut and enables alternative metabolic pathways. We will focus on how intestinal pathogens counteract the protective effects of microbiota-derived metabolites to illustrate the growing appreciation of how metabolic factors may serve as crucial virulence determinants and overcome colonization resistance.

Occurrence of <i>Salmonella</i> and presumptive <i>Bacillus cereus</i> in sesame products from Swiss retail stores

Sesame products such as tahini (tahin) or halva (halwa or helva), originating from Arabic cuisine, are becoming increasingly popular in Switzerland. Pathogens, such as Salmonella, can contaminate sesame products, as evidenced by various product recalls. In this study, the occurrence of Salmonella and Bacillus cereus group members was investigated in 100 sesame products (25 sesame seeds, 16 halva, 19 different sesame pastes, 7 sesame bars, 25 hummus, and 8 other products containing sesame) collected from Swiss retail stores. None of the products were positive for Salmonella, whereas B. cereus group members could be detected with bacterial counts between 1×102 and 9×102 CFU/g in 11 out of 100 (11%) products. The 11 isolates identified by matrix-assisted laser desorption ionization-time of flight were whole-genome sequenced with Illumina technology to confirm the identity of the pathogen, determine its toxin gene profile, and perform panC typing. Most of the isolates harbored genes encoding the enterotoxins Nhe, Hbl, and CytK. The isolates were assigned to diverse B. cereus group members, including one identified as B. cytotoxicus. In addition, one of the isolates matched genetically with the Thurigiensis strain used in biopesticide products. In conclusion, none of the investigated sesame products contained significant levels of Salmonella or B. cereus group members. However, as B. cereus with pathogenic potential was detected in multiple samples, proper storage is crucial to prevent its growth and ensure consumer safety, especially for products with high water activity such as hummus.

Genomic, Evolutionary, and Pathogenic Characterization of a New Polerovirus in Traditional Chinese Medicine Viola philippica.

Viola philippica, a medicinal herbaceous plant documented in the Chinese Pharmacopoeia, is a promising candidate for research into plant-derived pharmaceuticals. However, the study of newly emerging viruses that threaten the cultivation of V. philippica remains limited. In this study, V. philippica plants exhibiting symptoms such as leaf yellowing, mottled leaves, and vein chlorosis were collected and subjected to RNA sequencing to identify potential viral pathogens. A novel polerovirus, named Viola Philippica Polerovirus (VPPV), was identified in V. philippica. VPPV possesses a linear, positive-sense, single-stranded RNA genome consisting of 5535 nucleotides (nt) and encodes seven highly overlapping open reading frames (ORFs). Two potential recombination events were identified within ORF2, ORF3a, and ORF3, providing insights into the genetic diversity and evolution history of this novel polerovirus. An infectious cDNA clone of VPPV was successfully constructed and shown to infect Nicotiana benthamiana. Using a PVX-based heterologous expression system, the VPPV P0 protein was shown to trigger a systemic hypersensitive response (HR)-like reaction in N. benthamiana, indicating that P0 functions as the main pathogenicity determinant. These findings contributed to the detection and understanding of pathogenic mechanisms and control strategies for VPPV in V. philippica.

Whole-exome sequencing identifies novel mutation in intrahepatic cholestasis of pregnancy: A case report and literature review.

Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disease characterized by pruritus and elevated total bile acid (TBA) levels. The most serious impact of ICP is sudden unexplained intrauterine fetal death, especially when an associated TBA ≥ 100 µmol/L is confirmed.We report a case of a 27-year-old female patient with early-onset severe refractory ICP. Whole-exome sequencing and mutation analyses were performed to obtain genetic data on the patient and her mother. Sanger sequencing was performed to screen the mutation site. Computer-based algorithms were applied to predict the pathogenesis of the identified mutation. Subsequently, we conducted a literature review to characterize the pathological features and perinatal management of severe refractory ICP, especially ICP with genetic susceptibility.A heterozygous mutation in the ABCD3 gene: c.130C > T/p.Pro44Ser was detected in this patient. Through the analysis of pathogenicity prediction software, the mutations were disease-causing. This is the first report to identify the novel p.Pro44Ser mutations of ABCD3 gene in ICP patients.Our report provides new insights into the genetic architecture of ICP involving ABCD3 variants. Early-onset severe refractory ICP is rare and mutations in bile acid metabolism genes might accentuate the phenotype. Emphasized perinatal management and screening for potential pathogenicity sites of variants that drive specific recognition of ICP is necessary.