Clinical Microbiology and Infection最新文献

{"title":"Evaluation of six generative large language models answering pre-analytical questions in medical microbiology.","authors":"Michelle Bressan, Eline Nadieh Meijer, Vladimira Hinic, Tilia Ellendorff, Jean-Philippe Goldman, Tannon Kew, Oliver Nolte, Gerold Schneider, Adrian Egli","doi":"10.1016/j.cmi.2026.09.035","DOIUrl":"https://doi.org/10.1016/j.cmi.2026.09.035","url":null,"abstract":"<p><strong>Objectives: </strong>Large language models (LLMs) have the potential to be integrated into diagnostics workflows, yet their reliability in pre-analytical diagnostic stewardship remains uncertain. We aimed to evaluate the performance of six LLMs answering common pre-analytical questions in the domain of medical microbiology. Next, we propose a blueprint to evaluate LLMs in medical microbiology.</p><p><strong>Methods: </strong>We compared general-purpose models from OpenAI (GPT-3.5, GPT-4) and Meta AI (Llama2-7B, Llama2-13B), alongside two domain-enhanced versions (customised GPT-4 agent and Llama2-7B Medical) in a hybrid evaluation framework. First, we quantified the response length (word count), then assessed the similarity between LLM-generated responses and expert-reviewed reference answers (BLEU/ROUGE scores, BERTScore). Finally, thirty-three medical professionals rated the accuracy and completeness of the LLM-generated responses on a 1-7-point scale.</p><p><strong>Results: </strong>Responses of OpenAI models showed greater similarity to the reference set and significantly outperformed Meta AI-based models in accuracy and completeness. The customized generative pre-trained transformer (GPT) matched performance of OpenAI's general-purpose models, while generating significantly shorter responses (p<0.001). Quality ratings varied markedly between professionals, as medical microbiologists and experienced infectious disease specialists assigned significantly lower scores compared to infectious disease trainees and medical students (p<0.001).</p><p><strong>Conclusions: </strong>We observed considerable variation in LLM performance and highlight differences in perceived response quality across professional groups, emphasizing the need for critical appraisal when consulting LLMs for pre-analytical guidance.</p>","PeriodicalId":10444,"journal":{"name":"Clinical Microbiology and Infection","volume":" ","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149179822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Circulating SARS-CoV-2 RNA detection in acute COVID-19 disease and post-COVID condition.","authors":"Roberta Rovito, Laura Terracciano, Giuseppe De Pinto, Claudia Acampora, Marta Limonta, Andrea Santoro, Valentina Sala, Matteo Augello, Camilla Tincati, Francesca Bravi, Giulia Carla Marchetti","doi":"10.1016/j.cmi.2026.08.045","DOIUrl":"10.1016/j.cmi.2026.08.045","url":null,"abstract":"<p><strong>Objectives: </strong>The study aimed to determine the clinical significance of circulating plasma SARS-CoV-2 RNA across acute COVID-19 and post-COVID condition (PCC) by investigating prevalence, determinants, and kinetics in a large longitudinal cohort, accounting for hospitalization and vaccination.</p><p><strong>Methods: </strong>We consecutively enrolled individuals with confirmed SARS-CoV-2 infection. Acute COVID-19 was classified as mild, severe, or critical per WHO criteria. PCC was assessed 3 months after symptom onset, and plasma SARS-CoV-2 RNA (RNAemia) was quantified during acute infection (T0) and at follow-up (T1) by RT-qPCR. Associations between RNAemia and acute disease severity or PCC were evaluated using multivariable logistic regression. RNAemia was analysed as tertiles, binary detectability, and continuous levels.</p><p><strong>Results: </strong>A total of 442 individuals with COVID-19 were included, of whom 195 (44.1%) had mild disease, 161 (36.4%) had severe illness, and 86 (19.5%) had critical illness. At a median of 3.2 (interquartile range, 2.7-3.9 months) months from symptom onset, 184 of 442 patients were followed up, and 144 of 184 (78.3%) reported at least one persistent symptom compatible with PCC, most commonly asthenia (22.9%), myalgic pain (26.4%), brain fog (19.4%), dyspnoea (31.3%), and cough (42.4%). RNAemia was detected in 67.4% of participants at baseline and in 53.6% at follow-up. RNAemia in the II-III tertiles or any detectable RNAemia was associated with critical COVID-19. Neither baseline nor follow-up RNAemia was associated with PCC, and results were unchanged in a sensitivity analysis excluding vaccinated individuals. RNAemia trajectories were not associated with PCC, PCC clusters, or upper respiratory tract viral clearance.</p><p><strong>Conclusions: </strong>SARS-CoV-2 RNAemia was closely linked to acute COVID-19 severity but showed no association with PCC or PCC phenotype, which were assessed at 3 months from symptom onset in a cohort predominantly experiencing severe COVID-19 and hospitalization during acute infection. This dissociation may suggest that viral RNA in the peripheral blood is primarily involved in acute pathogenesis, whereas PCC likely arises from distinct biological mechanisms.</p>","PeriodicalId":10444,"journal":{"name":"Clinical Microbiology and Infection","volume":" ","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149165458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Yearly relative variations of bacteraemia and pneumonia incidence acquired in intensive care units at Lyon University Hospitals (2004-2024): a scatterplot visualization.","authors":"S Amour, E Kuczewski, P Vanhems","doi":"10.1016/j.cmi.2026.10.007","DOIUrl":"https://doi.org/10.1016/j.cmi.2026.10.007","url":null,"abstract":"","PeriodicalId":10444,"journal":{"name":"Clinical Microbiology and Infection","volume":" ","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149179855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Re: 'Systematic Three-Site Versus Classical Single-Site Screening for Chlamydia trachomatis and Neisseria gonorrhoeae Infections in Non-Sex Worker Women' by Prazuck et al.","authors":"Olivia Peuchant, Cécile Bébéar, Béatrice Berçot, Charles Cazanave","doi":"10.1016/j.cmi.2026.08.036","DOIUrl":"10.1016/j.cmi.2026.08.036","url":null,"abstract":"","PeriodicalId":10444,"journal":{"name":"Clinical Microbiology and Infection","volume":" ","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149168509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to \"Noninvasive diagnosis of pulmonary tuberculosis using face mask sampling: a prospective study in adults\" [Clin Microbiol Infection 32(4) (2026) 644-649].","authors":"Dariusz Woelk, Lennard Meiwes, Nelly Ciobanu, Valeriu Crudu, Anna-Marya Comanac, Stela Kulcitkaia, Anca Vasiliu, Anna Maria Mandalakas, Christoph Lange, Thomas Theo Brehm, Dumitru Chesov","doi":"10.1016/j.cmi.2026.10.009","DOIUrl":"10.1016/j.cmi.2026.10.009","url":null,"abstract":"","PeriodicalId":10444,"journal":{"name":"Clinical Microbiology and Infection","volume":" ","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149165121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanism and nomenclature of methicillin resistance in Staphylococcus aureus and implications for testing interpretation and management: a position statement on behalf of the Staphylococcus aureus working groups ISAC-SAWG and ESCMID-ESGS.","authors":"Kordo Saeed, Bibi C G C Mason-Slingerland, Michael Z David, Stefania Stefani, Marc Stegger, Margreet C Vos, Robert Leo Skov","doi":"10.1016/j.cmi.2026.09.030","DOIUrl":"10.1016/j.cmi.2026.09.030","url":null,"abstract":"<p><strong>Background: </strong>Beyond mec-mediated resistance, Staphylococcus aureus has developed complex resistance mechanisms against antistaphylococcal β-lactam antibiotics. The scientific community lacks a unified consensus on the nomenclature/clinical implications of these mechanisms.</p><p><strong>Objectives: </strong>This position statement by the members of Staphylococcus Working Groups of the International Society of Antimicrobial Chemotherapy and the European Society of Clinical Microbiology and Infectious Diseases propose a set of names for various types of methicillin/oxacillin reduced susceptibility/resistance in S. aureus.</p><p><strong>Content: </strong>The Working Groups propose the following categorization: (1) mec-mediated methicillin-resistant S. aureus: This is due to mec (mecA or mecB or mecC)-mediated resistance. They can exhibit heteroresistant expression to methicillin. (2) Methicillin-resistant S. aureus lacking mec: Isolates are cefoxitin and/or oxacillin-resistant but mec-negative, and do not show heteroresistance. They can be subdivided into (2a) hyperproduction of β-lactamase and (2b) modifications of natural penicillin-binding proteins. Importantly, these mechanisms cannot easily be differentiated in routine laboratories. If the resistance mechanism is not fully characterized, using the name methicillin-resistant lacking mec is suggested. Isolates with hyperproduction of β-lactamase show low-level resistance to oxacillin, but most isolates test susceptible to cefoxitin. When the mechanism is characterized, we propose that they should be named hyper- β-lactamase-producing S. aureus instead of the hitherto used term borderline oxacillin-resistant S. aureus. For isolates with reistance due to modifications of the penicillin-binding proteins 1-4 in S. aureus, it is proposed to continue to name these modified S. aureus. Modified S. aureus isolates in routine diagnostic laboratories most commonly present as cefoxitin-resistant. (3) Oxacillin-susceptible mec-positive S. aureus: Strains carry a mec gene but harbour mutations, deletions, or insertion rendering them phenotypically susceptible to oxacillin/cefoxitin.</p><p><strong>Implications: </strong>The proposed changes clarify methicillin resistance nomenclature in S. aureus, removing current ambiguity from clinical communication and literature. As novel methicillin resistance mechanisms emerge in S. aureus, the definition must be updated accordingly.</p>","PeriodicalId":10444,"journal":{"name":"Clinical Microbiology and Infection","volume":" ","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149165048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hepatitis Delta in Spain: A Nationwide Prospective Characterization of Active Infection and Liver Disease Severity.","authors":"Ana Alberola, Adolfo de Salazar, Ana Fuentes, Raquel Carracedo, Teresa Cabezas, Isabel Viciana, Jaime Borrego, Francisco FrancoÁlvarez de Luna, Ana Belén Pérez, Sonia Algarate, Pablo A Fraile-Ribot, María Dolores Ocete, María Gil Fortuño, Marta Illescas-López, Magdalena Lara, María José Pena, Ana Rodríguez-Fernández, Alejandro González Praetorius, Belén Lorenzo, María Reyes Vidal-Acuña, Lucía Pérez-Rodríguez, Alberto Vázquez-Blanquiño, Miriam Blasco, Iker Falces-Romero, Beatriz Romero-Hernández, Roberto Alonso, Asunción Iborra, Ana Miqueleiz, Luis Elorduy, Carmen Gómez González, Paloma Liendo Arenzana, Yolanda Salicio, Antonio Aguilera, Federico García","doi":"10.1016/j.cmi.2026.09.037","DOIUrl":"https://doi.org/10.1016/j.cmi.2026.09.037","url":null,"abstract":"<p><strong>Objectives: </strong>Hepatitis delta virus (HDV) infection is associated with rapid progression to cirrhosis and liver-related complications. We aimed to characterize the clinical and virological profile of anti-HDV-positive individuals in Spain and identify factors associated with active infection and advanced fibrosis.</p><p><strong>Methods: </strong>This nationwide, multicentre, prospective observational study included adults with positive anti-HDV serology enrolled between April 2024 and March 2026 across 72 hospitals in 15 Spanish Autonomous Communities. Demographic, virological, laboratory and clinical data were collected in a centralized database. Multivariable logistic regression was used to identify factors independently associated with active HDV infection and advanced liver fibrosis.</p><p><strong>Results: </strong>Among 1,112 anti-HDV-positive individuals, 670/1,112 (60%) were male, median age was 54 years (IQR 43-61), and 457/926 (49%) were born in Spain. HIV co-infection and anti-HCV positivity were present in 189/944 (20%) and 217/1,112 (21%), respectively. HDV-RNA was detectable in 436/1,047 patients (42%), with a median viral load of 4.1 log IU/mL (IQR 2.9-5.1). Genotype 1 accounted for 108/121 (89%) genotyped infections. Advanced fibrosis was present in 222/536 (41%) evaluable patients and was more frequent in those with active infection than in non-viremic individuals (155/261, 59% versus 59/256, 23%; p<0.001). Active HDV infection was independently associated with younger age, hepatitis B virus (HBV) antiviral therapy, lower platelet count and lower albumin levels, whereas African origin was associated with lower odds of detectable HDV-RNA. Advanced fibrosis was independently associated with active HDV infection, HBV antiviral therapy and higher gamma-glutamyltransferase levels, while higher platelet count and haemoglobin levels were associated with lower odds of advanced fibrosis.</p><p><strong>Conclusions: </strong>Active HDV infection and advanced liver disease remain common in Spain. These findings support systematic HDV-RNA testing, standardized fibrosis assessment and close clinical follow-up of anti-HDV-positive individuals.</p>","PeriodicalId":10444,"journal":{"name":"Clinical Microbiology and Infection","volume":" ","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149164966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GAMRIC 2026 Proceedings: Translational R&D, Innovation, and Global Access.","authors":"Erika Asperges","doi":"10.1016/j.cmi.2026.10.003","DOIUrl":"https://doi.org/10.1016/j.cmi.2026.10.003","url":null,"abstract":"","PeriodicalId":10444,"journal":{"name":"Clinical Microbiology and Infection","volume":" ","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149164925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-invasive diagnosis of invasive aspergillosis in patients with haematological malignancies: a prospective diagnostic accuracy study.","authors":"Rutuja H Patil, Radim Dobiáš, Yuri Vanbiervliet, Robina Aerts, Katrien Lagrou, Johan Maertens, David A Stevens, Vladimír Havlíček","doi":"10.1016/j.cmi.2026.10.002","DOIUrl":"https://doi.org/10.1016/j.cmi.2026.10.002","url":null,"abstract":"<p><strong>Objectives: </strong>To evaluate a non-invasive panel integrating urinary triacetylfusarinine C normalised to creatinine (uTafC/Cr), serum galactomannan (sGM) and serum pentraxin-3 (sPtx3) for detection of invasive aspergillosis (IA) in patients with haematological malignancies.</p><p><strong>Methods: </strong>Prospectively collected urine and serum from 148 clinical episodes in 138 high-risk patients with haematological malignancies (Leuven, 2018-2021) were analysed in a diagnostic accuracy study (37 proven/probable IA episodes from 37 patients; 111 control episodes from 104 patients). Median sampling days relative to the diagnostic reference day (day 0) were +1 for urine uTafC/Cr, 0 for sGM and +2 for sPtx3. uTafC/Cr was quantified by liquid chromatography-mass spectrometry (LC-MS); sGM and sPtx3 by enzyme immunoassays. Prespecified cut-offs were used for sGM and uTafC/Cr; sPtx3 positivity was receiver operating characteristic-derived. Analytical TafC stability and the relative analytical sensitivity of LC-MS and MALDI-MS were assessed in validation experiments.</p><p><strong>Results: </strong>sGM and uTafC/Cr showed no false positives in available control episodes (sGM, 0/98; uTafC/Cr, 0/111) and each detected 51.4% of IA episodes (19/37). sPtx3 alone showed sensitivity of 70.3% (26/37) and specificity of 58.3% (21/36). Adding sPtx3 to the uTafC/Cr or sGM pair increased case detection to 83.8% (31/37), with lower specificity in the complete-case control episode subset (57.6%; 19/33 control episodes). In a ±72 h paired-window analysis, bronchoalveolar lavage fluid (BALF) mycology, defined as BALF GM, Aspergillus PCR and/or fungal culture, was positive in 19/23 tested IA episodes (82.6%; 95% CI, 62.9-93.0%). TafC was stable at 4 °C, and LC-MS was more sensitive than MALDI-MS.</p><p><strong>Conclusions: </strong>uTafC/Cr or sGM provides an Aspergillus-focused non-invasive adjunct to BALF-based testing; sPtx3 increased case detection but had limited specificity and requires prospective validation.</p>","PeriodicalId":10444,"journal":{"name":"Clinical Microbiology and Infection","volume":" ","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149165352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reassessing host genetic susceptibility to tick-borne encephalitis: evidence from a systematic review and meta-analysis.","authors":"Piyush Gampawar, Daniel Ruzek, Benno Kohlmaier, Markus Seidel, Werner Zenz","doi":"10.1016/j.cmi.2026.10.004","DOIUrl":"https://doi.org/10.1016/j.cmi.2026.10.004","url":null,"abstract":"<p><strong>Background: </strong>Host genetic factors have been proposed to influence susceptibility to tick-borne encephalitis (TBE), but findings from candidate-gene association studies have been inconsistent.</p><p><strong>Objective: </strong>To evaluate evidence for common genetic variants associated with TBE susceptibility and severity by synthesising candidate-gene and genome-wide association study (GWAS) data.</p><p><strong>Methods: </strong>Data source: PubMed and Web of Science were searched for studies published between January 2005 and December 2025 following PRISMA 2020 guidelines.</p><p><strong>Study eligibility criteria: </strong>Case-control studies of laboratory-confirmed TBE reporting genotype or allele frequencies sufficient to estimate effect sizes.</p><p><strong>Participants: </strong>The review included 16 candidate-gene studies and one European consortium GWAS, comprising 3,759 patients with TBE (1,521 mild; 1,454 severe) and 11,771 controls from nine countries. Assessment of risk of bias: Methodological quality was assessed using the Q-Genie tool.</p><p><strong>Methods: </strong>of data synthesis: Random-effects meta-analyses were performed for variants investigated in ≥4 datasets. Heterogeneity, publication bias, subgroup analyses, and minimum detectable odds ratios (MDORs) were assessed.</p><p><strong>Results: </strong>Four variants met the criteria for quantitative synthesis. No significant associations with TBE susceptibility were observed for CCR5 rs333 (OR = 1.12, 95% CI = 0.98-1.29), TLR3 rs3775291 (OR = 0.87, 95% CI = 0.68-1.10), IL10 rs1800872 (OR = 0.97, 95% CI = 0.88-1.08), or CD209 rs2287886 (OR = 0.96, 95% CI = 0.80-1.15). Analyses of severe disease yielded similarly null results. MDOR analyses indicated adequate power to detect moderate genetic effects (OR≈1.12-1.18), indicating that any true effects are likely to be small.</p><p><strong>Conclusions: </strong>This study provides the most comprehensive synthesis of TBE genetic association studies to date and demonstrates that the most extensively investigated genetic variants are unlikely to serve as clinically useful predictors of TBE susceptibility or severity, supporting genome-wide discovery, rare variant analyses, and integrative approaches to identify biologically relevant host determinants of TBE.</p>","PeriodicalId":10444,"journal":{"name":"Clinical Microbiology and Infection","volume":" ","pages":""},"PeriodicalIF":8.7,"publicationDate":"2026-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149166909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}