Colonization with Carbapenemase producing Enterobacterales (CPE) and associated alteration in microbiota composition in a tertiary care hospital in Egypt

Inflammatory bowel diseases are characterized by chronic intestinal inflammation and alterations in the gut microbiota composition. Bacteroides fragilis, which secretes outer membrane vesicles (OMVs) with polysaccharide A (PSA), can moderate the inflammatory response and possibly alter the microbiota composition. In this study, we created a murine model of chronic sodium dextran sulfate (DSS)-induced intestinal colitis and treated it with B. fragilis OMVs. We monitored the efficiency of OMV therapy by determining the disease activity index (DAI) and performing histological examination (HE) of the intestine before and after vesicle exposure. We also analyzed the microbiota composition using 16S rRNA gene sequencing. Finally, we evaluated the volatile compound composition in the animals' stools by HS-GC/MS to assess the functional activity of the microbiota. We observed more effective intestinal repair after OMV treatment according to the DAI and HE. A metabolomic study also revealed changes in the functional activity of the microbiota, with a predominance of phenol and pentanoic acid in the control group compared to the group treated with DSS and the group treated with OMVs (DSS OMVs). We also observed a positive correlation of these metabolites with Saccharibacteria and Acetivibrio in the control group, whereas in the DSS group, there was a negative correlation of phenol and pentanoic acid with Lactococcus and Romboutsia. According to the metabolome and sequencing data, the microbiota composition of the DSS-treated OMV group was intermediate between that of the control and DSS groups. OMVs not only have an anti-inflammatory effect but also contribute to the recovery of the microbiota composition.IMPORTANCEBacteroides fragilis vesicles contain superficially localized polysaccharide A (PSA), which has unique immune-modulating properties. Isolated PSA can prevent chemically induced colitis in a murine model. Outer membrane vesicles (OMVs) also contain digestive enzymes and volatile metabolites that can complement the anti-inflammatory properties of PSA. OMVs showed high therapeutic activity against sodium dextran sulfate-induced colitis, as confirmed by histological assays. 16S rRNA sequencing of fecal samples from different inflammatory stages, supplemented with comprehensive metabolome analysis of volatile compounds conducted by HS-GC/MS, revealed structural and functional alterations in the microbiota composition under the influence of OMVs. Correlation analysis of the OMV-treated and untreated experimental animal groups revealed associations of phenol and pentanoic acid with Lactococcus, Romboutsia, Saccharibacteria, and Acetivibrio.

Although prednisolone treatment is effective in Cronkhite–Canada syndrome (CCS), its mechanisms of action are poorly understood. We performed analyses of cytokine expression and fecal microbiota in a patient with the concurrent occurrence of CCS and rectal cancer, in whom regression of polyposis was achieved by prednisolone. Regression of CCS polyps was accompanied by downregulation of proinflammatory cytokine expression and alterations in microbiota composition; a decrease in Bacteroides fragilis and Peptostreptococcus anaerobius with the promotion of inflammation. We could not completely exclude the possibility that alterations in fecal microbiota composition might be influenced by the presence of advanced cancer. However, this case suggests that the administration of PSL might lead to the regression of CCS polyps through alterations in gut microbiota composition and suppression of proinflammatory cytokine responses.

Alterations in gut microbiota composition are associated with metabolic syndrome and chronic inflammatory diseases such as inflammatory bowel disease. One feature of inflammation-associated gut microbiotas is enrichment of motile bacteria, which can facilitate microbiota encroachment into the mucosa and activate pro-inflammatory gene expression. Here, we set out to investigate whether elicitation of mucosal anti-flagellin antibodies by direct administration of purified flagellin might serve as a general vaccine against subsequent development of chronic gut inflammation. We show, in mice, that repeated injection of flagellin elicits increases in fecal anti-flagellin IgA and alterations in microbiota composition, reduces fecal flagellin concentration, prevents microbiota encroachment, protects against IL-10 deficiency-induced colitis, and ameliorates diet-induced obesity. Flagellin’s impact on the microbiota is B-lymphocyte dependent and, in humans, obese subjects exhibit increased levels of fecal flagellin and reduced levels of fecal flagellin-specific IgA, relative to normal weight subjects. Thus, administration of flagellin, and perhaps other pathobiont antigens, may confer some protection against chronic inflammatory diseases.

Tic disorders (TDs) are childhood-onset neurodevelopmental disorders characterized by complex neurochemical dysregulation, and inflammation plays a critical role in TD pathogenesis. Yinhua Gouteng Decoction (YHGTD), a traditional Chinese medicinal formula, has demonstrated clinical efficacy in TD management. However, the specific pharmacological mechanisms underlying its effects remain unclear. In this study, we investigated the neuroprotective and anti-inflammatory effects of YHGTD in a 3,3'-iminodipropionitrile (IDPN)-induced TD rat model. A rat model of IDPN-induced was established. Behavioral assessments, striatal histopathology, and quantification of striatal dopamine (DA) levels and dopamine receptor (DR) expression were measured to assess the effects of YHGTD on tic symptoms and dopaminergic function. Microglial activation was examined by immunofluorescence staining, while IL-1β, TNF-α, and IL-6 in serum, striatum, and colon were quantified using ELISA or qPCR. In addition, 16S rRNA sequencing was used to analyze alterations in the gut microbiota composition. Western blotting was performed to assess TLR4/MyD88/NF-κB pathway activation in the striatum and colon. YHGTD significantly improved motor and stereotypical behaviors in TD rats, decreased spontaneous activity, total travel distance, prolonged rest time, and normalized movement trajectories. It attenuated striatal neuropathology, elevated DA levels, and downregulated the expression of DRD1 and DRD2. YHGTD also suppressed microglial activation and reduced the levels of IL-1β, TNF-α, and IL-6 in the striatum, serum, and colon. Furthermore, YHGTD restored gut microbial homeostasis and reduced the abundance of proinflammatory bacterial taxa. Finally, we found that YHGTD downregulated the TLR4/MyD88/NF-κB signaling pathway in both the striatum and colon. YHGTD alleviated TD symptoms through neuroprotective and anti-inflammatory mechanisms, accompanied by alterations in the microbiota composition, supporting its potential as a therapeutic option for TD.

ObjectivesRecent evidence suggests that the gut microbiota may play a crucial role in the pathogenesis of ankylosing spondylitis (AS). This systematic review aims to examine the existing literature to explore changes in gut microbiota composition between AS patients and healthy controls (HC) to identify microbial signatures associated with AS. Understanding these alterations could enhance our knowledge of the mechanisms underlying AS.MethodsWe queried PubMed, Web of Science, Scopus, Embase, and Cochrane databases through May 2024 to identify studies comparing stool microbiota composition in AS patients and healthy controls (HC). Following PRISMA guidelines, our search yielded 1,163 studies. We included studies comparing microbiota in AS patients and HC. We excluded duplicates, animal studies, case reports, conference abstracts, non-English articles, irrelevant studies, non-full-text manuscripts, and Mendelian randomization studies, as these do not provide direct observational data on microbiota composition and could introduce methodological heterogeneity.ResultsAfter screening 184 studies, 18 manuscripts were included: 14 prospective cohort studies, 2 case-control studies, and 2 cross-sectional studies (Figure 1). These studies covered a total of 900 ankylosing spondylitis (AS) patients and 734 healthy controls (HC). The majority of the participants were male, with 73.8% in the AS group and 66.7% in the HC group, and most participants (73.4%) were of Asian descent. HLA-B27 status was reported in 13 studies, with a 92.3% positive rate among the AS patients. Notably, none of the AS or HC participants, except for 1 study, had received antibiotics in the 3 months prior to enrollment. At the phylum level, 12 studies (66.6%) reported significant changes in microbiota composition (Figure 2). Actinobacteria, Firmicutes, and Proteobacteria were increased in 8, 6, and 5 studies, respectively, while Bacteroidetes, Fusobacteria, and Verrucomicrobia were decreased in 5, 3, and 3 studies, respectively. At the genus level, 16 studies (88.8%) observed changes. Prevotella, Escherichia-Shigella, Streptococcus, and Collinsella were increased in 6, 6, 5, and 4 studies, respectively, while Bacteroides, Lachnospira, and Dialister were decreased in 9, 4, and 4 studies, respectively. Prevotella and Collinsella have been linked to inflammatory diseases in previous studies, suggesting their potential involvement in the inflammatory processes observed in AS patients. On the other hand, a reduction in Lachnospira has been associated with increased inflammation, indicating its potential protective role in inflammatory conditions.Figure 1: Alterations in Microbiota Composition at the Phylum Level in AS Patients Compared to Healthy ControlsFigure 2: Alterations in Microbiota Composition at the Genus Level in AS Patients Compared to Healthy ControlsConclusionOur findings reveal significant differences in gut microbiota composition between AS patients and healthy controls, indicating a role of microbiota in AS pathogenesis. These findings highlight the potential for microbiota-targeted therapies in AS treatment.

Abdominal aortic aneurysm (AAA) is a cardiovascular disease characterized by accumulation of immune cells, inflammation, and degradation of medial layer of the abdominal aorta. While the link between altered microbiota composition and atherosclerosis had been established, only a few studies suggested that altered gut microbiota composition may contribute to AAA, but mechanisms remain unknown. Cytokines are crucial regulators of inflammation in AAA, however, whether cytokines control microbial homeostasis in the intestine to regulate AAA has not been examined. Interleukin (IL)-27 is known to regulate various immune and inflammatory diseases in context-dependent manner. Here, we found that Apoe -/- Il27ra -/- mice were protected from gut dysbiosis and contain less pro-inflammatory bacterial genera in their colons. Unexpectedly, microbiota depletion by broad-spectrum antibiotics (Abx) accelerated AAA development in Apoe -/- Il27ra -/- mice while Apoe -/- controls were protected from the disease. Our bulk RNAseq data on suprarenal aortas revealed that multiple pro-inflammatory and collagen/ECM degradation pathways were upregulated, while extracellular matrix and cell junction organization pathways were downregulated in Ang II-infused Apoe -/- Il27ra -/- mice with depleted microbiota. We found that numbers of circulating mature myeloid cells, and the level of pro-inflammatory serum metabolites were microbiota-dependent and correlated with AAA development. Moreover, fecal microbiota transplant (FMT) from Apoe -/- Il27ra -/- mice which contain less pro-inflammatory bacterial genera in their colon, but not from Apoe -/- mice, attenuated AAA incidence in Ang II-infused Apoe -/- recipients, indicating that protection from the disease can be transferred with microbiota. Collectively, our findings provide novel insight into the mechanisms of how IL27R signaling regulates AAA development by controlling intestinal microbiota and microbiota-derived metabolites, which in turn modulate pathogenic myeloid cell production and activation driving AAA.

Background Fecal microbiota transplantation (FMT) can effectively decolonize multidrug-resistant organisms but its efficacy is variable. We evaluated the impact of FMT treatment at eliminating carbapenemase-producing Enterobacterales (CPE) carriage compared to spontaneous decolonization and identified microbial signatures of successful decolonization. Methods Prospective study, with patients colonized with CPE receiving a single dose of FMT via the nasogastric route. CPE-colonized patients who did not meet our inclusion criteria or decided not to participate in the study comprised the control group where spontaneous decolonization was evaluated. Primary endpoint was complete elimination of CPE carriage 2 weeks after FMT. A secondary endpoint for decolonization was set at 3 months post-FMT. Successful decolonization was defined by 2+ consecutive negative rectal swabs as determined by both culture and PCR. Shotgun metagenomic sequencing was performed to assess gut microbiota composition of donors and recipients before and after FMT. Results Twenty patients colonized with CPE were included, 72.5 ± 18.8 years. Median duration of carriage of CPE before FMT was 62.5 days (IQR 48.75-122.5). At 3 months post-FMT, 40% (n=8/20) of patients were successfully decolonized, while 20% (n=4/20) meeting the 2-week primary endpoint. Kaplan-Meier curves between patients in the FMT cohort and those in the control group (n=82) revealed the same rate of decolonization over time (p=0.9). Microbiota composition analyses post-FMT revealed significantly higher bacterial species richness and alpha diversity in responders versus non-responders (Fig1A,B), and specific taxa including Faecalibacterium prausnitzii, Parabacteroides distasonis, Collinsella aerofaciens, Alistipes finegoldii and Blautia_A sp900066335 were associated with response (Fig.2). Furthermore, CPE abundance levels at baseline were significantly higher in non-responders than in responders (Fig.3). Box and whisker plots of the percent relative abundance for the indicated species in samples from patients with CRE clearance on day 14 (teal), and patients without CRE clearance on day 14 (orange). The median (±interquartile range) is plotted for each species in each group. Whiskers extend to the lowest and highest values no greater than 1.5x the interquartile range from the closest hinge. The displayed taxa were significantly altered between patients with and without CRE clearance at day 14 across all samples, with q-values below 0.01 (MaAslin2 log-transformed linear model). Box and whisker plots indicating the cumulative percent relative abundance of CRE species in samples from patients with CRE clearance on day 14 (teal) and patients without CRE clearance on day 14 (orange). The median (±interquartile range) is plotted for each group at the indicated timepoints. Whiskers extend to the lowest and highest values no greater than 1.5x the interquartile range from the closest hinge. Patients with CRE clearance on day 14 have significantly lower CRE relative abundance than patients without CRE clearance on day 14 at baseline and 1 week post-FMT (Wilcoxen Rank-Sum test with FDR adjustment). Conclusion FMT administration led to complete CPE eradication in a subset of colonized patients but did not achieve statistical significance. Response to FMT was not donor-dependent and correlated with the transfer of specific bacteria taxa and CPE colonization levels. Disclosures Andrea Watson, PhD, Vedanta Biosciences: Advisor/Consultant|Vedanta Biosciences: Honoraria Gianluca Galazzo, PhD, Vedanta Biosciences: Advisor/Consultant|Vedanta Biosciences: Honoraria Ed J. Kuijper, Prof. Dr., Vedanta Biosciences: Advisor/Consultant Silvia Caballero, PhD, Vedanta Biosciences: Advisor/Consultant|Vedanta Biosciences: Board Member|Vedanta Biosciences: Ownership Interest

The hospital sink drain biofilm resistome is independent of the corresponding microbiota, the environment and disinfection measures.

Feeding frequency has been shown to affect growth and body composition of the host associated with gut microbiota. It remains unknown whether adjusting feeding frequency could effectively regulate both skeletal muscle development and whole-body lipid metabolism and thus affect carcass composition and feed conversion efficiency. Therefore, this study aimed to explore the effects of feeding frequency on muscle growth, fat deposition, cecal microbiota composition, and bile acid composition in finishing pigs. Sixteen Sichuan-Tibetan black pigs, with an initial weight of 121.50 ± 1.60 kg, were divided into two groups and fed either two meals (M2) or four meals (M4) per day. The trial lasted 30 days. The muscle fiber characteristics, lipid metabolism in adipose tissue, and cecal microbiota and bile acid composition were determined. The present study revealed that pigs fed four meals exhibited a lower feed-to-gain ratio, abdominal fat weight, and average backfat thickness (p < 0.05), as well as a higher loin eye area (p = 0.09) and myofiber diameter in the longissimus muscle than their counterparts. The mRNA expression of slow-twitch fiber and myogenesis-associated genes in the longissimus muscle was upregulated, while lipid metabolism-related genes in the backfat were downregulated in the M4 group compared to the M2 group (p < 0.05). The M4 pigs exhibited higher abundances of Firmicutes, Actinobacteriota, Bacillus, Clostridium_sensu_1, and Romboutsia, and lower abundances of Spirochaetota, Verrucomicrobiota, Treponema, and Muribaculaceae in the cecal content than the M2 pigs (p < 0.05). A higher feeding frequency increased the levels of primary bile acids and decreased the concentrations of taurine-conjugated bile acids in the cecal content of pigs (p < 0.05). Our research suggested that the M4 feeding pattern, compared to the M2 pattern, promoted muscle growth and reduced fat deposition by enhancing fast- to slow-twitch fiber conversion and myogenesis in the muscle and repressing lipid metabolism in adipose tissue, associated with altered microbiota composition and bile acid profiles.

ABSTRACTParkinson’s disease (PD) is known to be associated with altered gastrointestinal function and microbiota composition. To date, the effect of PD medication on the gastrointestinal function and microbiota, at the site of drug absorption, the small intestine, has not been studied, although it may represent an important confounder in reported microbiota alterations observed in PD patients. To this end, healthy (non-PD) wild-type Groningen rats were employed and treated with dopamine, pramipexole (in combination with levodopa-carbidopa), or ropinirole (in combination with levodopa-carbidopa) for 14 sequential days. Rats treated with dopamine agonists showed a significant reduction in small intestinal motility and an increase in bacterial overgrowth in the distal small intestine. Notably, significant alterations in microbial taxa were observed between the treated and vehicle groups; analogous to the changes previously reported in human PD versus healthy control microbiota studies. These microbial changes included an increase in Lactobacillus and Bifidobacterium and a decrease in Lachnospiraceae and Prevotellaceae. Markedly, certain Lactobacillus species correlated negatively with levodopa levels in the systemic circulation, potentially affecting the bioavailability of levodopa. Overall, the study highlights a significant effect of PD medication intrinsically on disease-associated comorbidities, including gastrointestinal dysfunction and small intestinal bacterial overgrowth, as well as the gut microbiota composition. The results urge future studies to take into account the influence of PD medication per se when seeking to identify microbiota-related biomarkers for PD.IMPORTANCE Parkinson’s disease (PD) is the second most common neurodegenerative disorder and is known to be associated with altered gastrointestinal function and microbiota composition. We previously showed that the gut bacteria harboring tyrosine decarboxylase enzymes interfere with levodopa, the main treatment for PD (S. P. van Kessel, A. K. Frye, A. O. El-Gendy, M. Castejon, A. Keshavarzian, G. van Dijk, and S. El Aidy, Nat Commun 10:310, 2019). Although PD medication could be an important confounder in the reported alterations, its effect, apart from the disease itself, on the microbiota composition or the gastrointestinal function at the site of drug absorption, the small intestine, has not been studied. The findings presented here show a significant impact of commonly prescribed PD medication on the small intestinal motility, small intestinal bacterial overgrowth, and microbiota composition, irrespective of the PD. Remarkably, we observed negative associations between bacterial species harboring tyrosine decarboxylase activity and levodopa levels in the systemic circulation, potentially affecting the bioavailability of levodopa. Overall, this study shows that PD medication is an important factor in determining gastrointestinal motility and, in turn, microbiota composition and may, partly, explain the differential abundant taxa previously reported in the cross-sectional PD microbiota human studies. The results urge future studies to take into account the influence of PD medication on gut motility and microbiota composition when seeking to identify microbiota-related biomarkers for PD.

Emerging evidence suggests that microbiota dysbiosis plays a critical role in the pathogenesis of endometrial cancer (EC), a leading cause of cancer-related deaths in women globally. However, few studies have simultaneously examined both the upper and lower genital tract microbiota in such individuals. In this study, we investigated alterations in microbiota composition across different parts of the female genital tract in a Chinese cohort of EC patients. Samples from 59 individuals (22 endometrial cancer patients; 8 endometrial hyperplasia patients, and 29 benign controls) were collected. In addition, a total of 58 vaginal swabs, 39 fallopian swabs, 16 peritoneal fluid samples, 36 urine swabs, and 34 endometrium samples were finally recruited. The composition of bacterial communities was determined by 16S ribosomal RNA Miseq sequencing. Specific taxa were significantly enriched in the EC group, including Akkermansia muciniphila, Acinetobacter, and Pseudomonas in the vagina, and Pseudomonas, Bacillus, Streptomyces, and Burkholderia-Caballeronia-Paraburkholderia in the endometrium. Meanwhile, Acinetobacter was positively correlated with fasting plasma glucose, while Pseudomonas was correlated with estrogen and progesterone receptor expression. An effective random forest model enabled us to distinguish EC patients from benign controls. Moreover, specific alterations in the composition and diversity of the reproductive tract microbiota in endometrial cancer patients were identified. Our findings suggest a potential link between microbiome alterations and estrogen and glucose metabolism in EC. However, further investigation is needed to elucidate the molecular mechanisms underlying these associations.

Inflammatory bowel diseases encompass gastrointestinal illnesses typified by chronic inflammation, loss of epithelial integrity and gastrointestinal microbiota dysbiosis. In an effort to counteract these characteristic perturbations, we used stem cells and/or a probiotic therapy in a murine model of Dextran Sodium Sulfate induced colitis to examine both their efficacy in ameliorating disease and impact on niche-specific microbial communities of the lower GI tract. Colitis was induced in C57BL/6 mice by administering 3% DSS in drinking water for 10 days prior to administering one of three treatment plans: daily probiotic (VSL#3) supplementation for 3 days, a single tail vein injection of 1x106 murine mesenchymal stem cells, or both. Ileal, cecal and colonic sections were collected for microbiota and histological analyses. Microbiota profiling revealed distinct bacterial community compositions in the ileum, cecum and colon of control untreated animals, all of which were predicted in silico to be enriched for a number of discrete KEGG pathways, indicating compositional and functional niche specificity in healthy animals. DSS-treatment perturbed community composition in all three niches with ileal communities exhibiting the greatest change relative to control animals. Each treatment group exhibited treatment-specific alterations in microbiota composition in the lower GI tract, though disease scores were only improved in VSL#3-treated animals. The ileal microbiota were most profoundly altered in composition in this group of animals and characterized by significant Enterobacteriaceae enrichment compared with colitic mice (P < 0.05).

In recent years, especially after the development of sophisticated metagenomic studies, research on the intestinal microbiota has increased, radically transforming our knowledge about the microbiome and its association with health maintenance and disease development in humans. Increasing evidence has shown that a permanent alteration in microbiota composition or function (dysbiosis) can alter immune responses, metabolism, intestinal permeability, and digestive motility, thereby promoting a proinflammatory state. Such alterations can mainly impair the host's immune and metabolic functions, thus favoring the onset of diseases such as diabetes, obesity, digestive, neurological, autoimmune, and neoplastic diseases. This comprehensive review is a compilation of the available literature on the formation of the complex intestinal ecosystem and its impact on the incidence of diseases such as obesity, non-alcoholic steatohepatitis, irritable bowel syndrome, inflammatory bowel disease, celiac disease, and digestive neoplasms. Alterations in the composition and function of the gastrointestinal microbiota (dysbiosis) have a direct impact on human health and seem to have an important role in the pathogenesis of several gastrointestinal diseases, whether inflammatory, metabolic, or neoplastic ones.

Effects of diet shift on the gut microbiota of the critically endangered Siberian Crane

Heart failure (HF) represents a major health problem affecting millions of people worldwide. In the latest years, many efforts have been made to search for more effective strategies to prevent and modify the course of this disease, but results are still not satisfying. HF represents a complex clinical syndrome involving many other systems, including the gastrointestinal system. Although the relationship between the gut and HF is far from being fully understood, based on recent evidence highlighting the putative role of the gastrointestinal system in different cardiovascular diseases, it is conceivable that the gut-heart link may represent the basis for novel therapeutic approaches in the HF context as well. This intricate interplay involving typical hemodynamic changes and their consequences on gut morphology, permeability, and function, sets the stage for alterations in microbiota composition and is able to impact mechanisms of HF through different routes such as bacterial translocation and metabolic pathways. Thus, the modulation of the gut microbiota through diet, probiotics, and fecal transplantation has been suggested as a potential therapeutic approach. More interestingly, another effect of alteration in microbiota composition reflects in the upregulation of cotransporters (NHE3) with consequent salt and fluid overload and worsening visceral congestion. Therefore, the inhibitors of this cotransporter may also represent a novel therapeutic frontier. By review of recent data on this topic, we describe the current state of the complex interplay between the gastrointestinal and cardiac systems in HF, and the relevance of this knowledge in seeking new therapeutic strategies.