Background Global health security is increasingly threatened by emerging viral syndemics, where infectious viruses interact synergistically with socio-economic-structural vulnerabilities. Traditional reactive surveillance are increasingly insufficient to address the complexity of these interconnected crises. This systematic review aims to synthesize evidence for the "Silicon Shield," a proactive computational framework integrating mathematical modelling and artificial intelligence (AI) to bridge a unified computational framework, and critical literature gaps for pandemic preparedness and response. Methods Following updated PRISMA 2020 guidelines, we searched PubMed, Scopus, and Web of Science (January 1990-July 2026) using Medical Subject Headings (MeSH). We evaluated the convergence of mechanistic frameworks (SIR, SEIR, ABM) with deep learning architectures (CNNs, Transformers, pLMs). Analysis prioritized Uncertainty Quantification (UQ) via Bayesian updating and causal inference through Directed Acyclic Graphs (DAGs) to mitigate ecological biases when modelling biosocial determinants. Results Synthesizing 371 sources, we formalize the "Silicon Shield" three-layer architecture: Data Pipes, Model Pipelines, and Decision Interfaces. Integrating real-time genomic and mobility data enables anomaly detection via ViraMiner and TCINet. EVEscape forecasts immune escape, while Social Vulnerability Indices (SVI) optimize resource allocation. The framework yields predictive performance, improved AUROC and probabilistic metrics including Weighted Interval Score (WIS) and Continuous Ranked Probability Score (CRPS). Explainable AI (xHAIM) translates outputs into clinical decision support. Conclusions The convergence of AI and mathematical modelling facilitates a fundamental transformation into a proactive global health defence system. Implementing the "Silicon Shield" requires interdisciplinary collaboration, standardized clinical validation, and a focus on global health equity to effectively mitigate future emerging virus syndemic threats.
Background Bartonella henselae and Bartonella quintana are among the most clinically relevant Bartonella species infecting humans. While B. henselae is a zoonotic pathogen maintained in animal reservoirs, B. quintana is considered a human-restricted bacterium transmitted via the human body louse. Both species can cause a wide range of manifestations, particularly in immunocompromised individuals such as those with HIV/AIDS. This study aimed to estimate the prevalence of IgG and IgM seropositivity to these two species and to identify determinants of seropositivity. Methods This cross-sectional study included 200 participants, comprising 97 HIV-positive patients, 53 patients with AIDS, and 50 healthy individuals as the control group.IgG antibodies against B. henselae and B. quintana were measured in all participants using an indirect immunofluorescence assay (IFA). In addition, IgM antibodies were assessed in a randomly selected subset of 48 participants. Results The overall seroprevalence of B. henselae and B. quintana IgG was 24.0% and 22.0%, respectively, while IgM seropositivity was 18.8% and 22.9%. No significant differences were observed in B. quintana IgG prevalence among control, HIV, and AIDS groups. Individuals with a history of drug abuse had a more than threefold increased likelihood of IgG positivity. For B. henselae, IgG prevalence was higher in the control and AIDS groups compared to HIV-positive individuals, though not statistically significant. Conclusion The significant prevalence of IgG antibodies against both Bartonella species and the presence of IgM antibodies in the selected study group, especially in HIV patients, demonstrate the clinical importance of these pathogens in at-risk populations. These findings emphasize the need for clinical vigilance in symptomatic immunocompromised patients.
An 80-year-old man with diffuse large B-cell lymphoma developed pulmonary nocardiosis caused by Nocardia gipuzkoensis, with a concomitant central nervous system lesion. The isolate was identified as N. gipuzkoensis by secA1 gene sequencing. To our knowledge, this is the first reported human infection caused by N. gipuzkoensis in Japan.
Background Multiple detections of Rift Valley fever virus (RVFV) infections in humans, animals and mosquito vectors suggest permanent circulation of RVFV in Senegal. This study investigated the spatial and temporal dynamics of RVFV circulation in central (Sahelian) and southeastern (Sudanian) Senegal from March 2021 to June 2024. Methods A total of 976 initially seronegative sheep and goats from sentinel herds in 10 districts and 2 areas were monitored for 40 months. Serum samples were collected quarterly and tested by ELISA, while mosquitoes were collected monthly and screened for RVFV RNA by RT-PCR. Results Active RVFV circulation was detected in both areas during the four years preceding the 2025 outbreak. Overall, 2,989 sera were tested, and 7.2% (95% CI: 5.6–9.0%) of animals seroconverted, while no RVFV RNA was detected from 65,830 mosquitoes. Seroconversion was higher in goats than in sheep (OR = 2.6; 95% CI: 1.5-4.6; p < 0.001) and during the rainy than the dry season (dry: 9.1% vs rainy: 5.6, p=0.023). Conclusion Enzootic RVFV circulation preceded the 2025 outbreak. Sentinel herd surveillance, integrated with entomological and environmental monitoring, may improve RVFV risk assessment within a One Health framework.
Neisseria gonorrhoeae is the second most prevalent bacterial sexually transmitted infection and a major contributor to the global antimicrobial resistance crisis. The World Health Organization (WHO) has designated N. gonorrhoeae as a high-priority pathogen due to its resistance to nearly all empirically recommended therapies. While dual therapy with ceftriaxone and azithromycin initially demonstrated efficacy, the rapid global rise in azithromycin resistance over the past five years threatens the efficacy of this regimen. Resistance mechanisms, including mutations in the 23S rRNA gene and overexpression of the MtrCDE efflux pump, are highly heterogeneous, complicating molecular diagnostic efforts. This review examines the evolving landscape of azithromycin resistance, highlighting key mechanisms of resistance, and recent epidemiological and genomic surveillance data. We discuss challenges in implementing molecular assays for routine resistance monitoring due to molecular heterogeneity in azithromycin resistance markers and emphasize the critical need for tailored approaches based on local genetic epidemiology. Enhanced surveillance and molecular diagnostics are essential to sustaining effective treatment strategies and combating gonococcal resistance.
Background Shigella causes severe bacterial diarrhea, especially in children in low- and middle-income countries. Rising antimicrobial resistance (AMR), including multidrug-resistant (MDR) and ESBL-producing strains, threatens empirical treatment, particularly cephalosporins. Methods We conducted a structured narrative review of PubMed, Scopus, Web of Science, ScienceDirect, and WHO GLASS. Included studies comprised randomized trials, cohorts, case series, and relevant in vitro studies. Quality was appraised using Joanna Briggs Institute checklists; findings were synthesized narratively. Results Third-generation cephalosporins (ceftriaxone, cefotaxime) remain highly effective for severe Shigella infections in hospitalized and pediatric patients when isolates are susceptible. Resistance varies regionally, with higher ESBL prevalence in East and South Asia. Resistance mechanisms include ESBLs, efflux pumps, PBP mutations, and altered membrane permeability. Susceptibility-guided therapy yields favorable outcomes, but ESBL/XDR strains cause treatment failures, longer hospital stays, and carbapenem use. Conclusion Cephalosporins are critical for severe shigellosis but are increasingly compromised by AMR. Structured surveillance, susceptibility-guided therapy, and stewardship are essential. Complementary strategies (vaccines, probiotics, phage therapy, novel antibiotics) are urgently needed.
Background Aerococcus urinae is an emerging uropathogen frequently misidentified as "other Gram-positive cocci", with limited data on its clinical characteristics and antimicrobial susceptibility, particularly in Japan. In this study, we investigated the clinical features and antimicrobial susceptibility of A. urinae isolates recovered from urine and blood cultures. Methods This retrospective study was conducted at a tertiary care hospital between January 2013 and August 2023. Aerococcus urinae isolates were identified using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Antimicrobial susceptibility was determined using a commercial broth microdilution system. Minimum inhibitory concentrations were interpreted according to the Clinical and Laboratory Standards Institute M45 criteria. For the primary analysis, only the first isolate per patient was included. Results Two hundred and sixty-eight patients (median age, 82 years; 124 [46.3%], male) were included in this study. Among these, 89 patients (33.2%) were diagnosed with urinary tract infection (UTI), whereas 179 (66.8%) were considered to be colonized. Three hundred thirty-nine A. urinae isolates (333 urine and 6 blood) were recovered from these patients. Aerococcus urinae was considered the primary pathogen in 8 patients (3.0%) and a possible pathogen in 81 (30.2%). Penicillin G, ceftriaxone, and levofloxacin susceptibility rates were 100%, 98.9%, and 76.8%, respectively. All patients with bacteremia exhibited complicated UTI and achieved clinical cure after antimicrobial therapy and source control. Conclusions Aerococcus urinae was more commonly identified as a possible rather than a primary urinary pathogen. The high susceptibility to β-lactam antibiotics supports their continued use as appropriate treatment options for suspected A. urinae UTI.
Objectives To determine the prevalence of intestinal colonization by extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) and carbapenem-resistant Enterobacterales (CRE) among patients admitted to the emergency department of a tertiary care hospital in Lima, Peru. Factors associated with colonization were also evaluated. Methods A cross-sectional study was conducted from December 2019 to March 2020. Patients were enrolled on one to two randomly selected days per week. A rectal or fecal swab was collected, and a standardized questionnaire was administered. Samples were cultured on chromogenic media (ChromAgar ESBL and ChromAgar mSuperCarba) and disc diffusion methods were used for confirmation of ESBL production and carbapenem resistance. The association of epidemiological and clinical factors with ESBL-E and CRE colonization was analyzed using bivariate generalized linear models with a Poisson distribution and robust variance. Results A total of 148 patients were sampled. The prevalence of ESBL-E and CRE colonization was 73.6% (109/148) and 8.1% (12/148), respectively. Hospitalization during the previous year (PR = 1.23, 95% CI: 1.02-1.49) was associated with ESBL-E colonization. Conclusions A high prevalence of ESBL-E intestinal colonization was found among patients with and without prior healthcare exposure admitted to the emergency department of a tertiary care hospital in Lima.
Objectives The aim of this study was to estimate the prevalence of carbapenem-resistant Enterobacterales (CRE) and characterize the distribution of carbapenemase genes among Enterobacterales isolates in the medical microbiology laboratory of Prince Mohammed Bin Nasser Hospital, Jazan, Saudi Arabia. Methods The current cross-sectional study was conducted in a secondary-care center in Jazan, Saudi Arabia, and included consecutive Enterobacterales isolates from clinical specimens of hospitalized patients from June 2023 to April 2024. Demographic data and clinically relevant information were retrieved from electronic medical records. The statistical analyses were performed using the software R and IBM SPSS Statistics. Results A total of 260 Enterobacterales isolates were studied; of these, 26 (10%) fulfilled the criteria for CRE. In the subpopulation of CRE, Klebsiella pneumoniae was the most common (81%), followed by Enterobacter cloacae complex (11%), Escherichia coli (4%), and Klebsiella oxytoca (4%). The most common resistant CRE gene was NDM (58%), followed by a combination of OXA48 and NDM (23%), and then OXA48 (19%). Statistically significant associations existed for admission to a critical care unit, the presence of a central line, and the use of a urinary catheter with the isolation of CRE. Conclusion In this hospital-based cohort, CRE were commonly found among Enterobacterales isolates, mainly K. pneumoniae, and were predominantly driven by the NDM and OXA-48-type carbapenemases. Associations between CRE isolation and exposure to critical care and invasive devices suggest strengthened surveillance, device-related infection-prevention measures, and antimicrobial stewardship should be emphasized in this setting, with a focus on high-risk inpatients.
Objectives: Clostridium butyricum is an anaerobic gram-positive bacillus widely used as a probiotic preparation in Japan. Although generally considered safe, C. butyricum has rarely been isolated from blood cultures, particularly in immunocompromised or medically complex patients. We aimed to describe the clinical characteristics, microbiological findings, treatment, and outcomes of patients with C. butyricum isolated from blood cultures at a single academic hospital and to summarize published cases. Methods: We retrospectively reviewed 16 patients with C. butyricum isolated from blood cultures at University of Tsukuba Hospital between 2015 and 2025. Clinical characteristics, microbiological findings, antimicrobial treatment, and outcomes were evaluated. Preserved institutional isolates were identified using mass spectrometry and polymerase chain reaction–based ribotyping. We also summarized 31 published cases descriptively. Results: Sixteen institutional cases were identified. The most common clinical characteristic was central venous catheter use (75.0%). In many cases, C. butyricum was isolated from a single anaerobic blood culture bottle. All preserved institutional isolates were confirmed as C. butyricum and showed type B ribotyping patterns; however, strain-level attribution was not possible. All patients received β-lactam antibiotics, and three patients (18.8%) died. The 31 published cases were heterogeneous in age, clinical context, and microbiological identification methods. Conclusions: C. butyricum is rarely isolated from blood cultures but may warrant clinical assessment in medically complex patients. A possible association with probiotic exposure requires further investigation using genomic methods.
Background Plasmids are the principal vehicles of horizontal antimicrobial resistance (AMR) gene transfer, yet risk analyses rarely combine gene content, mobility, and network topology. We asked whether explainable machine learning over these dimensions can stratify plasmid dissemination risk, and tested rigorously where it succeeds and fails. Methods From 72,556 PLSDB 2025 plasmids we integrated 251,138 AMRFinderPlus gene records with CARD v3 ontology and MOBsuite typing, built a co-resistance network, and derived a composite PlasmidRisk score from five features. Three classifiers were evaluated by five-fold cross-validation; external validation used WHO and ECDC 2024 to 2025 carbapenemase designations as a feature-independent reference. We added length- and host-adjusted burden models, phylum-normalized enrichment, and feature-category ablation. Results AMR genes occurred in 41.0% of plasmids across 85 drug classes. The network (29,758 nodes) was heterogeneous rather than scale-free. Internal cross-validation AUCs exceeded 0.999, but because labels derived from the scored features this reflects internal consistency, not generalization. The feature-independent external AUC was modest (0.607): strong for the metallo-beta-lactamases blaNDM, blaVIM, and blaIMP (0.72 to 0.73) but at or below chance for blaKPC and blaOXA-48 (0.45 to 0.51). The conjugative burden advantage did not survive adjustment for length and host phylum (adjusted incidence rate ratio 0.93), with length dominant. Conclusions PlasmidRiskNet offers a useful pre-screening layer for MBL-bearing plasmids but not for the compact serine-carbapenemase backbones (blaKPC, blaOXA-48), which require replicon typing. Honest external and confounder-adjusted evaluation, not internal metrics, defines its class-specific surveillance value.
Background: Mosquito-borne chikungunya virus (CHIKV) causes acute febrile illness with potentially persisting polyarthralgia, and its global resurgence in international travelers poses a risk of importation into non-endemic regions. Methods: We describe a cluster of ten travelers returning from the Seychelles to Berlin, Germany, between December 2025 and April 2026, diagnosed with acute CHIKV infection at an outpatient travel clinic. The diagnosis was confirmed by either reverse transcription polymerase chain reaction (RT-qPCR) or serological detection of Immunoglobulin M (IgM). Samples with a sufficient viral load were additionally sequenced. Results: Symptomatic patients (six male/four female; age range 27–64 years) presented 1–54 days after symptom onset; most reported fever and arthralgia at disease onset. CHIKV infection was confirmed by PCR in five of seven tested patients and by IgM serology in seven patients, including three PCR-positive cases who were initially seronegative early in infection. No dengue infections were detected. All patients were unvaccinated against CHIKV, and only one had sought pre-travel medical advice. Epidemiological assessment suggested multiple probable exposure sites within the Seychelles. Genomic sequencing was successfully performed in two samples. Conclusions: This cluster reflects ongoing CHIKV activity in the Seychelles and underscores the risk of international spread to Europe. Early diagnostic testing, particularly PCR during the acute phase, is essential to detect potential viremic patients. Improved pre-travel counseling, vaccination uptake, and clinician awareness are needed to reduce missed diagnoses and mitigate the risk of autochthonous transmission in regions with established Aedes mosquito populations.
Background:Respiratory tract infections are a major cause of pediatric hospitalization. Post-COVID-19 pandemic, atypical surges and disrupted respiratory pathogen circulation underscore the need for continuous surveillance. Methods:We retrospectively analyzed respiratory pathogen detection among hospitalized children aged 28 days to 18 years at the largest quaternary hospital in Malaysia from January 2018 to May 2023. The study period was classified into pre-pandemic (2018-2019), pandemic (2020-2021), and post-pandemic (2022-2023) phases. Respiratory pathogens were identified using the FilmArray BioFire® Respiratory Panel 2.1. Results:Among 20,556 hospitalized children, 7707 (37.5%) underwent BioFire® testing. Overall pathogen positivity remained similar during the pre-pandemic and pandemic periods (50.4% and 50.9%, respectively) and increased to 86.2% post-pandemic. Single-pathogen infections increased from 46.4% to 43.1% to 64.6%, while co-infections rose from 4.0% to 7.9% to 21.6%, respectively. Human rhinovirus/enterovirus and respiratory syncytial virus were consistently detected, whereas adenovirus and influenza viruses increased significantly post-pandemic. Influenza A and B re-emerged after minimal detection during the pandemic, returning to pre-pandemic detection rates. Monthly positivity varied substantially before and during the pandemic but remained consistently high post-pandemic, peaking at 94.4%. Despite increased pathogen detection, pediatric intensive care unit admissions remained low across all periods. Conclusion:Substantial post-pandemic increases in respiratory pathogen positivity, co-infections, and pathogen diversity were observed among hospitalized children despite stable pediatric intensive care unit admission rates. These findings likely reflect respiratory pathogen re-emergence following relaxation of non-pharmaceutical interventions, altered exposure patterns, and increased BioFire® testing after the COVID-19 pandemic.
Beyond its socio-economic impact, COVID-19 has been associated with respiratory, gastrointestinal, neurological and neuropsychiatric symptoms across many countries, including in Senegal. While the SARS-CoV-2 virus primarily targets the respiratory and cardiovascular systems, if not detected and treated early, it can invade the nervous system and lead to severe neurological complications. This study focuses on the molecular and serological characterization of the SARS-CoV-2 strains associated with encephalitis manifestations of the disease. The presence of the virus in the central nervous system was confirmed by RT-PCR and sequencing and also serological techniques. Genetic analysis identified Delta (B.1.617.2-like) and Eta (B.1.525-like) variants in encephalitis patients. In silico analysis revealed three mutations (p.Pro4619Leu, p.Ala103Pro and p.Thr40Ile) predicted to affect protein function, generating hypotheses regarding their possible involvement in neurological manifestations. Among 11 patients with SARS-CoV-2-associated encephalitis, 30% had SARS-CoV-2 IgG antibodies in their serum, and 20% had them in cerebrospinal fluid (CSF). As part of the surveillance system for infectious encephalitis in Senegal (ENSENE), our data provided evidence of SARS-CoV-2 involvement in the epidemiology of viral encephalitis during the COVID-19 pandemic. Similar approaches should be promoted in future studies to investigate the biological significance of these mutations and improve the diagnosis and management of neurological manifestations associated with SARS-CoV-2 infection.
