Background: Rheumatoid arthritis (RA) is a chronic inflammatory disabling autoimmune disorder. Little is known regarding the association between the gut microbiome and etiopathogenesis of RA. We aimed to dissect the differences in gut microbiomes associated with RA in comparison to healthy individuals and, in addition, to identify the shifts in the bacterial community in association with disease activity; Methods: In order to identify compositional shifts in gut microbiomes of RA patients, V3-V4 hypervariable regions of 16S rRNA were sequenced using Illumina MiSeq. In total, sixty stool samples were collected from 45 patients with RA besides 15 matched healthy subjects; Results: Notably, RA microbiomes were significantly associated with diverse bacterial communities compared with healthy individuals. Likewise, a direct association between bacterial diversity and disease activity was detected in RA patients (Kruskal Wallis; p = 0.00047). In general, genus-level analysis revealed a positive coexistence between RA and Megasphaera, Adlercreutzia, Ruminococcus, Bacteroides, Collinsella, and Acidaminococcus. Furthermore, Spearman correlation analysis significantly stratified the most dominant genera into distinct clusters that were mainly based on disease activity (r ≥ 0.6; p ≤ 0.05). The predictive metabolic profile of bacterial communities associated with RA could support the potential impact of gut microbiomes in either the development or recovery of RA; Conclusions: The overall shifts in bacterial composition at different disease statuses could confirm the cross-linking of certain genera either to causation or progression of RA.

The emergence of bla_KPC-2 and bla_NDM-1 producing Klebsiella pneumoniae represents a great problem in many Egyptian hospitals. One hundred and twenty-six K. pneumoniae isolates from patients admitted to Assiut University Hospital were identified by an API20E kit. Carbapenemase-producing K. pneumoniae (CPKP) was detected by the modified carbapenem inactivation method (mCIM), the EDTA-modified carbapenem inactivation method (eCIM), and an E-test. Based on the polymerase chain reaction, all isolates were negative for bla-_VIM-1 and bla-_IMP-1, fifteen of these isolates were positive for both bla_KPC-2 and bla_NDM-1, two isolates were positive for bla_KPC-2 only, and twenty-eight isolates were positive for bla-_NDM-1 only. Although one isolate was positive for the string test, all CPKP isolates were negative for capsular genes. Only 71.1% of CPKP transferred their plasmids to their corresponding transconjugants (E. coli J53). The resistance patterns of the clinical isolates and their transconjugates were similar, except for 12 isolates, which showed differences with their transconjugates in the resistance profile of four antibiotics. Molecular typing of the plasmids based on replicon typing showed that Inc FIIK and FII plasmids predominated in isolates and their transconjugants carrying bla_KPC-2 and/or bla_NDM-1. Conjugative Inc FII plasmids play an important role in the spread of CPKP, and their recognition is essential to limit their spread.

Spreading of NDMI-producing klebsiella pneumoniaehas become a great trouble in many Egyptian hospitalized patients. Localizing the source of these isolates is an important step to prevent their spread in this country. This study included 33 NDMI-producing klebsiella pneumoniae that collected from different clinical specimens of patients admitted to different wards at Assiut University Hospitals in Egypt and confirmed to produce blaNDM1 gene by polymerase chain reaction. Isolates were typed by Enterobacterial Repetitive Intergenic Consensus (ERIC). Respiratory samples (51%) were the predominant samples and chestdepartment was the major ward (48.48%) that isolates recovered. ERIC gel profile showed that several identical isolates were found especially in chest ward and between different medical wards of this hospital suggested clonal transmission of NDMI-producing K. pneumoniae. Also, there are differences in the number and size of ERIC-PCR profiles indicated the genetic diversity among NDMI-producing K. pneumoniae isolates. The results of this study may help in tracing and controlling NDM-1-producing K. pneumoniae outbreak by applying effective infection control measures especially in the chest ward of this hospital.

Background: Rotavirus gastroenteritis (RVGE) remains a leading cause of severe infant diarrhea worldwide, with growing evidence supporting the role of the gut microbiome in modulating the disease. However, the interplay between early-life demographic factors, the gut microbiome, and their combined impact on RVGE clinical severity remains inadequately characterized, particularly in specific geographic populations. Aim: We aimed to investigate how demographic determinants shape gut microbiome composition and function in RVGE and how these features relate to clinical severity. Methods: In our comprehensive case–control study of 165 infants (120 RVGE cases and 45 healthy controls, aged 0–12 months), we utilized 16S rRNA sequencing combined with advanced statistical modeling and machine learning to investigate how demographic factors influence microbiome composition and clinical outcomes. Results: RVGE cases exhibited significantly reduced bacterial diversity (Kruskal–Wallis, Static = 14.85, p < 0.001) and distinct patterns, with community structure most strongly associated with dehydration severity (PERMANOVA; R² = 0.15, p < 0.001). Substantial taxonomic alterations were identified characterized by depletion of beneficial commensals including Akkermansia (LDA score = 3.8, p < 0.001), Faecalibacterium (Random Forest AUC = 0.82, p < 0.001), and Bifidobacterium (r = −0.42 with breastfeeding, p < 0.001), alongside enrichment of inflammation-associated taxa such as Escherichia-Shigella (WBC; r = 0.49, p < 0.001, and CRP; r = 0.56, p < 0.001), Streptococcus (LDA score = 4.2, p < 0.001), and Staphylococcus. Proteobacteria was the top potential biomarker of severe outcomes (Random Forest AUC = 0.85), with abundance positively correlated with systemic inflammation (CRP: r = 0.51, p = 0.003). Functional predictions revealed increased lipopolysaccharide biosynthesis (ko00540) and reduced butanoate metabolism (ko00650, p < 0.001) in severe disease. Importantly, demographic factors significantly modulated clinical outcomes: cesarean-delivered, formula-fed infants presented the most dysbiotic profiles and experienced 3.2-fold longer hospitalization (95% CI: 1.8–5.6, p < 0.001) than vaginally delivered, breastfed infants did. Conclusions: Collectively, these findings demonstrate that early-life demographic factors potentially shape the gut microbiome composition and function, may influence RVGE severity and recovery trajectories, thus providing candidate biomarkers for risk stratification and identifying targets for microbiota-based interventions.

Ventilator-associated pneumonia is a common nosocomial infection occurring in patients receiving mechanical ventilation especially in pediatric intensive care units (PICUs). Klebsiella pneumoniae is a multidrug resistant nosocomial pathogen that plays an important role in respiratory tract infection among critically ill patients. This study included 51 pediatric patients had VAP admitted to the Pediatric Intensive Care Unit (PICU) at Assiut university children's hospital through 12-month period from May 2014 to May 2015, using quantitative endotracheal aspirate (EA) culture. K. pneumoniae were isolated by culturing onto blood and MacConkey`s agar plates then incubated aerobically at 35°C for 2448 hrs. and identified by morphology and biochemical tests. K. pneumoniae 19 (37.25%) was the most isolated bacteria that causing VAP in PICU. Antimicrobial susceptibility testing showed that K. pneumoniae isolates were resistant to all commercial available antimicrobial agents that used in the PICU.