Clinical Microbiology and Infection

The emergence of vaccine covered serotypes causing invasive pneumococcal disease (IPD) is a serious concern worldwide. We investigated the unexpected rise of serotype 4 causing IPD primarily in non-vaccinated young adults after the COVID-19 pandemic that further spread to adults [≥] 65 years in recent years. For this purpose, we conducted a retrospective study of serotype 4 IPD cases (n=827) reported in Spain between 2009 and 2024. Whole-genome sequencing was performed to assess clonal lineag...

BackgroundThe epidemiology of suspected pediatric meningoencephalitis has shifted in the era of conjugate vaccines and multiplex PCR diagnostics, with viral pathogens now predominating over bacterial causes. Updated epidemiologic data are essential to adapt diagnostic and therapeutic algorithms to current clinical practice. MethodsThis retrospective single-center study included children and adolescents <18 years who underwent lumbar puncture with cerebrospinal fluid multiplex PCR for suspected ...

BackgroundHospital-acquired bacterial pneumonia (HABP) and ventilator-associated bacterial pneumonia (VABP), particularly those caused by multi-drug resistant organisms (MDROs), often require newer antibiotic treatment. The efficacy and safety of newer antibiotics compared to generic antibiotics in randomized controlled trials (RCTs) have not been evaluated before. MethodsIn this systematic review, we searched RCTs in the United States National Library of Medicine (PubMed), Cochrane Central Reg...

ObjectivesDiagnosis of community-acquired Legionnaires disease (CALD) relies on microbiological testing. Routine testing in hospitalised CAP patients has low positivity rates. We externally validated a Legionella prediction score, assessed its applicability in routine care, and explored potential updates. MethodsWe analysed data from 196 CALD patients from 20 Swiss hospitals and 196 Legionella-negative CAP controls matched by date of diagnosis ({+/-}14 days; August 2022-March 2024). We assessed...

This exploratory analysis of PAX LC, a Phase 2, 1:1 randomized, double-blind, superiority, placebo-controlled trial examined whether treatment with nirmatrelvir/ritonavir (NMV/r) versus placebo/ritonavir (PBO/r) in individuals with Long COVID could reveal immune features associated with symptom improvement. Eighty-two participants (n=45 PBO/r; n=37 NMV/r) provided blood samples at baseline (Day 0) and post-treatment (Day 28). Baseline demographic and immunological phenotypes were similar in the ...

BackgroundReliable identification of early predictors of adverse outcomes was essential during the pre-vaccination phase of the COVID-19 pandemic. Few studies have comprehensively integrated clinical presentation, laboratory parameters including arterial blood gas analysis, and chest computed tomography (CT) findings within a single well-characterized cohort, particularly in underrepresented regions of Brazil. MethodsThis retrospective cohort study included 482 consecutive adults (median age 61...

Withdrawal StatementThe authors have withdrawn this manuscript because it will undergo major modifications and revisions to improve accuracy and clarity. Therefore, the authors do not wish this work to be cited as a reference for the project. If you have any questions, please contact the corresponding author.

BackgroundRespiratory syncytial virus (RSV) is a major cause of lower respiratory tract infections in children, often leading to hospitalisation in infants. In low-resource settings where routine RSV diagnostics are unavailable, clinical overlap with bacterial pneumonia frequently results in unnecessary antibiotic use, contributing to antimicrobial resistance. ObjectiveTo evaluate the frequency and clinical determinants of antibiotic use among RSV-positive children under two years at a tertiary...

The COVID-19 pandemic led to significantly disrupted tuberculosis case detection and management. Additionally, overlapping symptoms, radiological findings and risk factors make differentiating tuberculosis and COVID-19 disease difficult. We conducted a prospective multicentre diagnostic accuracy study to determine sensitivity, specificity and operational characteristics of the Truenat MTB Ultima/COVID-19 assay, using a combined sputum plus nasopharyngeal swab specimen, in a single multiplex mol...

ImportanceRecent reports have highlighted an intense influenza activity related to the circulation of the influenza A(H3N2) subclade k variant. There is no data available on the impact of the emergence of H3N2 subclade k on the severity of the 2025-2026 epidemic or on the clinical phenotype of patients requiring admission to the intensive care unit (ICU). ObjectiveTo compare the clinical presentation, hospital mortality and virological characteristics of patients with laboratory-confirmed influ...

BackgroundNeutralising antibody titres are widely used as key immunogenicity endpoints in Ebola virus (EBOV) vaccine and monoclonal antibody clinical trials. However, direct comparison of results across studies remains challenging due to the use of heterogeneous neutralisation platforms, ranging from pseudotyped viruses to live EBOV assays. These limitations restrict assay standardisation, validation, scalability, and compliance with good clinical laboratory practice (GCLP), particularly in outb...

ObjectivesPneumococcal surveillance typically focuses on invasive disease (IPD), collecting limited clinical data. We used a longitudinal adult cohort of IPD and non-invasive pneumococcal disease (non-IPD) patients in three hospitals between 2006-22, to describe clinical disease, including site of infection, and serotype distribution. MethodsThe demographics of IPD and non-IPD were compared and survival analysis performed. Features of IPD in different sites were compared and serotype distributi...

In Tijuana General Hospital, Mexico, pleural empyema (PE) was monitored through passive surveillance (2000 - 2005), active surveillance with PCR (2005 - 2018), and again through passive surveillance (2022 - 2024). The implementation of active surveillance combined with molecular diagnostics markedly improved pathogen detection and enabled assessment of the 7-valent (PCV7, 2005 - 2012) and 13-valent (PCV13, 2012 - 2018) pneumococcal conjugate vaccines. This strategy yielded precise insights into ...

BackgroundPreoperative biliary stenting alters biliary colonization and may reduce the effectiveness of perioperative antibiotic prophylaxis in pancreatoduodenectomy. Although broader-spectrum regimens have been associated with improved infectious outcomes, their microbiological adequacy in routine clinical practice remains poorly defined. We therefore evaluated the real-world adequacy of a prolonged ampicillin-sulbactam protocol, its association with infectious outcomes and survival, and the po...

BackgroundMpox-related ophthalmic disease (MPOXROD) ranges from mild conjunctivitis to sight-threatening keratitis, however, data based on systematic ophthalmological assessment are scarce. We aimed to characterise the prevalence, features, and temporal evolution of MPOXROD during a clade Ib mpox outbreak. MethodsWe conducted MBOTE-EYE, a prospective ophthalmological sub-study, nested within a clinical characterisation cohort in Kamituga, South-Kivu, Democratic Republic of the Congo. All hospit...

A multivariant total subclass analysis has been performed for a control cohort (n=15) and a long COVID patient cohort (n=15) measuring the IgG1, IgG2, IgG3, IgG4 and IgE response to the following 14 variants of SARS-CoV-2: Wuhan, Alpha, Delta, BA.1, BA.2, BA.5, EG.5.1, XBB.1.5, BA.2.75, CH.1.1, BA.2.12.1, BQ.1.1, JN.1, and KP.3. Significant differences (p < 0.05 and p < 0.005) between concentrations of IgG subclasses by variant were found in 24% of variants and in mean-normalised distributions. ...

Background and objectiveRespiratory Syncytial Virus (RSV) can cause severe illness in adults, leading to respiratory and non-respiratory complications, functional decline, hospitalisation, and death. This study describes French patients aged [&ge;]50 years hospitalised with RSV (2015-2022) and their care pathways, including hospitalisation and outpatient healthcare use and costs. MethodsData were extracted from the French National Health Data System (SNDS). Patients were classified into four ri...

ObjectivesTo quantify how urine sample type and polymicrobial context impact antimicrobial resistance (AMR) in urinary tract infections (UTIs), using routine diagnostics at scale. MethodsIn this retrospective, single-centre study, we analysed 188,687 urine cultures from the Institute of Medical Microbiology, University of Zurich, Switzerland (January 2015 to May 2023). We compared midstream urine (MU), indwelling catheter (IDC), and intermittent catheter (IMC) samples. Samples were classified a...

To evaluate the impact of sex on acute SARS-CoV-2 infection, 668 participants from the ACTIV-2/A5401 study were followed over a 28-day period. A primary analysis was performed on the 469 participants who had quantifiable viral loads at baseline. Male and female participants had comparable nasal SARS-CoV-2 RNA levels at study entry and throughout follow-up. However, sex-specific differences in viral shedding emerged when stratified by duration of symptoms. In the first three days from symptom ons...

BackgroundSub-Saharan Africa has a high burden of disease due to antimicrobial resistance that is thought to be driven by a combination of sub-optimal antibiotic use and frequent exposures to AMR in different One Health compartments. We evaluated a community-based, co-created intervention bundle to improve antibiotic use and hygiene practices, targeting all community-level healthcare providers and communities. MethodsIn a cluster-randomised, controlled trial in 44 villages, we measured the inte...