Shymaa Enany

Acinetobacter baumannii, particularly in its multidrug-resistant (MDR) and carbapenem-resistant (CRAB) forms, has become a major global health concern due to its ability to survive in hospital environments, acquire resistance rapidly, and cause severe infections with high mortality. Conventional diagnostic and therapeutic strategies remain slow, imprecise, and difficult to implement, especially in resource-limited settings, highlighting the need for innovative approaches. Advances in artificial intelligence (AI) and machine learning (ML) offer powerful tools to strengthen every stage of Acinetobacter infection management. This narrative review synthesizes current evidence on how AI enhances early detection, improves species-level identification, predicts antimicrobial resistance from genomic data, accelerates drug discovery, and supports real-time hospital surveillance and outbreak control. AI-driven methods enable faster triage, more accurate differentiation between colonization and true infection, robust prediction of resistance phenotypes, and efficient identification of synergistic antibiotic combinations. Moreover, AI-supported drug discovery pipelines have recently yielded novel agents such as abaucin, demonstrating the potential of computational approaches to explore new chemical spaces. Despite these promising advances, challenges persist regarding data quality, generalizability across settings, interpretability, and ethical considerations including privacy and algorithmic bias. Successful integration of AI into clinical practice will require rigorous model validation, equitable data governance, and strong collaboration between clinicians, microbiologists, and data scientists. Overall, AI represents a transformative opportunity to reduce the clinical and economic burden of Acinetobacter infections and to strengthen global antimicrobial resistance surveillance.

Background: The nasal passages’ microbial communities are vital to human health and can influence infection processes. In this study, ten nasal samples were obtained, five from mothers and five from their 1- to 2-year-old infants. We studied the proteins of the nasal passage microbiota using the metaproteomic technique. The ten nasal samples collected were initially subjected to in-solution digestion, followed by a series of purification steps to ensure sample quality. Subsequent analysis was performed using LC–MS/MS, and the workflow was finalized with comprehensive data processing and bioinformatic analysis utilizing the UniProt database. The preliminary observations indicated that eight proteins showed differential abundance between the maternal and infant cohorts. Results: The eight proteins detected in our exploratory study were found to be of particular importance, as they may be implicated in bacterial pathogenesis, can represent potential drug targets, and may be associated with pathways related to drug resistance. These proteins include amidohydrolase, SLEI domain protein (pf07620 family), histidine kinase (EC 2.7.13.3), RND transporter, GLPGLI family protein, penicillin-binding protein, MFS transporter, and a protein kinase domain-containing protein. Conclusions: These observations provide preliminary evidence of how metaproteomics can elucidate the protein interactions within bacterial communities and their interactions with the host, potentially advancing our understanding of infection processes and guiding the development of targeted therapies.

Colorectal cancer (CRC) incidence is increasing in many low- and middle-income countries, including Egypt, partly due to urbanization and lifestyle changes. Metaproteomic approaches remain underutilized in these settings. In this study, we applied fecal metaproteomics in Egyptian CRC patients to characterize disease-associated protein expression patterns, explore host–microbiota functional interactions, and identify metabolic pathways that are altered in the CRC gut environment. Stool samples from 10 CRC patients and 10 healthy controls were analyzed. A total of 441 differentially expressed proteins (DEPs) were identified, of which 406 were consensus proteins overlapping across fold-change analysis, Wilcoxon testing, and PLS-DA. Differential microbial protein expression was primarily associated with core metabolic functions, including carbohydrate, amino acid, and nucleotide transport. Notably, proteins from Segatella copri were markedly suppressed in CRC patients. Functional analysis revealed upregulation of microbial proteins related to DPP-4 and cysteine metabolism, suggesting a possible role of microbiome-derived enzymes in colorectal cancer–associated metabolic and immune modulation, without direct evidence of host translocation.

Multidrug-resistant Klebsiella pneumoniae (MDR-KP) poses a significant clinical challenge due to limited therapeutic options and high mortality. This study investigated the antimicrobial efficacy of gamma-irradiation-synthesized gentamicin-conjugated silver nanoparticles (Gent-Ag NPs), copper oxide nanoparticles (CuO NPs), and bimetallic Ag-CuO NPs against three MDR-KP isolates in comparison with the gamma-irradiated gentamicin alone. Gent-Ag, Gent-CuO, and bimetallic Gent-Ag-CuO NPs were synthesized via gamma-radiation-induced reduction and characterized by different analytical methods to confirm their shape, size, surface morphology, particle size distribution, and crystallinity using HRTEM, SEM, DLS, and XRD, respectively. Comparative analysis demonstrated that Gent-Ag NPs exhibited superior antimicrobial activity, while Gent-CuO NPs showed diminished efficacy. SEM imaging analysis showed that Gent-Ag-CuO NPs effectively damaged and weakened the bacterial surfaces. It should be noted that the complete lys of K. pneumoniae cells is depicted by the white holes seen inside the bacteria. These findings suggest potential therapeutic applications of Ag-based NPs against MDR-KP, warranting further validation with larger sample sizes.

Campylobacter species are considered to be the leading bacterial cause of human gastroenteritis globally. Consumption of undercooked or contaminated food, such as chicken, is the main cause of human campylobacteriosis. Despite this significant zoonotic link, comparative data on virulence determinants in Campylobacter isolates across avian and human sources remain limited. This study aimed to characterize the prevalence and expression of virulence determinants in Campylobacter jejuni and Campylobacter coli isolates from chicken and human sources in Ismailia governorate, Egypt. A total of twenty C. jejuni and C. coli isolates (ten of each species) were screened for 14 virulence genes using PCR. All isolates harbored virB11, iam, racR, and tetO. Chicken isolates exhibited a significantly higher prevalence: C. jejuni (chicken): pldA, dnaJ, flaA (100%), cdtB (80%), ciaB (60%), and wlaN (0%); C. coli (chicken): pldA, dnaJ (100%), flaA (60%), cdtB (60%), ciaB (40%), and wlaN (20%). In contrast, human isolates showed a markedly lower prevalence: C. jejuni (human): dnaJ, flaA, and cdtB (20%); C. coli (human): dnaJ, flaA, and cdtB (40%). Crucially, pldA, ciaB, and wlaN were absent in all human isolates. plda and dnaJ genes showed statistically significant prevalence differences. qPCR revealed a significant upregulation (p < 0.05) of dnaJ, virB11, flaA, and iam in chicken isolates compared to human isolates, with log₂ fold changes of 3.52, 2.84, 2.43, and 1.90 for C. jejuni and 3.06, 2.38, 1.51, and 1.32 for C. coli. Differential expressions of racR, cdtB, and tetO were not significant, with log2 fold changes ranging from −0.51 to 0.14. Ganglioside mimicry genes (Cst11, wlaN, Waac, ggt, and cgtB) and the carbon storage regulator gene (csrA) were absent in all human isolates. These findings underscore the significant variability in virulence gene profiles in chicken and human C. jejuni and C. coli isolates and highlight the importance of molecular characterization in the risk assessment and epidemiological surveillance of Campylobacter infections.

The number of colorectal cancer (CRC) patients is steadily growing worldwide, particularly in developing nations. Nonetheless, recent advances in early detection studies and therapy alternatives have reduced CRC mortality in affluent countries, despite rising incidence. Gut microbiota and their metabolites may contribute to tumor growth and reduced therapeutic efficacy. This preliminary study sought to uncover metabolic fingerprints in colorectal cancer patients. It also emphasizes the correlation between the gut microbiome, microbial metabolism, and altered metabolites in CRC. In this study, stool samples from 20 CRC patients and matched healthy controls were enrolled. Untargeted metabolomics approach based on an ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-MS/MS) were applied. Statistical approaches, pathway enrichment analysis, and network analysis were employed to unleash CRC perturbed metabolic pathways and putative biomarkers. The study identified a distinct manually curated metabolite profile that is substantially linked to CRC. The steroidogenesis, aspartate, tryptophan (Trp), and urea cycle were the most significant pathways that concurrently contributed to CRC.Prominently, among other pathways, Trp metabolism was identified as a critical pathway, indicating a possible connection between the development of CRC and gut microbiota. In a nutshell the notable resulted metabolites reveal auspicious biomarkers for the initial diagnosis as well as surveilling of CRC progression. This preliminary study highlights the potential involvement that gut bacteria may contribute in CRC patients. Further investigation into the composition of the gut microbiome associated with this metabolic profile may lead to the identification of novel biomarkers for early detection and possible targets for treatment.

Introduction: Raw milk and dairy products can cause a variety of diseases due to environmental pollution. The objectives of this study were to identify the genetic variables, evaluate antibiotic resistance, and isolate microorganisms from raw milk and dairy products. Methodology: Three hundred samples of raw milk were collected from farmers and marketplaces in Gamasa, Mansoura, and Damietta cities in Egypt. Various bacterial species were isolated using selective culture media, of which 101 (33.6%) were Staphylococcus species, 11 (3.6%) were Escherichia coli, and 1 (0.3%) was Salmonella. The isolates were confirmed by biochemical tests. The disk diffusion method was used to test antibiotic susceptibility. Additionally, resistance genes and virulence factors in 4 randomly selected Staphylococcus species samples were identified through MinION nanopore sequencing (Oxford Nanopore Technologies, Oxford, UK). Results: Staphylococcus species showed resistance to antibiotics, including ampicillin (89%) and colistin (94%). Whole genome sequencing was used to identify the molecular traits of antibiotic-resistant Staphylococcus species. The genes associated with resistance to antibiotics in Staphylococcus species were examined. Four Staphylococcus samples were randomly selected for extracting DNA and nanopore sequencing. Staphylococcus species exhibited remarkable resistance to colistin because of the presence of putative serine protease proteins (colistinase) or resistance-nodulation-division (RND) efflux pumps (ACRB gene). Conclusions: The identification of resistant bacterial strains in unpasteurized milk and dairy products highlights the critical need for strict regulations to limit the overuse of antibacterial treatments in dairy herd management.

The assessment of research performance is widely seen as a vital tool in upholding the highest standards of quality, with selection and competition believed to drive progress. Academic institutions need to take critical decisions on hiring and promotion, while facing external pressure by also being subject to research assessment^1–4. Here we present an outlook on research assessment for career progression with specific focus on promotion to full professorship, based on 314 policies from 190 academic institutions and 218 policies from 58 government agencies, covering 32 countries in the Global North and 89 countries in the Global South. We investigated how frequently various promotion criteria are mentioned and carried out a statistical analysis to infer commonalities and differences across policies. Although quantitative methods of assessment remain popular, in agreement with what is found in more geographically restricted studies^5–9, they are not omnipresent. We find differences between the Global North and the Global South as well as between institutional and national policies, but less so between disciplines. A preference for bibliometric indicators is more marked in upper-middle-income countries. Although we see some variation, many promotion policies are based on the assumption of specific career paths that become normative rather than embracing diversity. In turn, this restricts opportunities for researchers. These results challenge current practice and have strategic implications for researchers, research managers and national governments.