International Journal of Medical Microbiology最新文献

{"title":"Helicobacter pylori CagT4SS proteins CagN and CagM bind DNA and CagN is involved in heptose-independent pro-inflammatory substrate translocation by the T4SS","authors":"Simon H. Bats ,&nbsp;Felix Metz ,&nbsp;Johanna Beilmann ,&nbsp;Christine Josenhans","doi":"10.1016/j.ijmm.2025.151661","DOIUrl":"10.1016/j.ijmm.2025.151661","url":null,"abstract":"<div><div>The Cag type 4 secretion system (CagT4SS) of <em>Helicobacter pylori</em> is encoded on the <em>cag</em> pathogenicity island (<em>cag</em>PAI) that is present in about 60 % of all strains. It translocates the effector protein CagA, DNA and small bacterial metabolites into human cells. The transport mechanisms of these substrates are not clear and may involve Cag proteins still in search of a function. CagN is a partially surface-exposed CagT4SS protein with a poorly described function. The <em>cagN</em> gene is present in all <em>cag</em>PAI-positive strains and thus likely to be of importance and indispensable for the functionality of the T4SS. CagM is an essential structural component located within the outer membrane core complex of the CagT4SS in the bacterial outer membrane. CagM has a close genomic association and interacts directly with CagN. In this study, we addressed two questions on the basis of prior findings of T4SS-dependent DNA transport and TLR9 activation by <em>H. pylori</em> in host cells. First, we analyzed the role of CagN and CagM in the binding of the presumed CagT4SS substrate DNA. Second, we attempted to elucidate a presumed functional role of CagN in heptose-independent T4SS substrate translocation which may lead to pro-inflammatory activation in human cells. Using electrophoretic mobility shift assays (EMSA) and thermal shift assays (TSA), we found that both CagM and CagN interact with dsDNA. They can also act as nucleases and cleave DNA. Since the transport of substrates through the CagT4SS is likely ATP-driven, we also determined whether CagM and CagN can process ATP, which tested positive for both proteins. Co-incubating <em>H. pylori</em> with human TIFA-k/o cells, which no longer respond to the bacterial translocated effector heptose, but can still be activated by DNA, we established a phenotype of loss of heptose-independent pro-inflammatory activity with <em>H. pylori cagN</em> mutants that could be reversed by complementation. Our results propose an important role for CagN and CagM to bind DNA which might impact or be involved in the transport of substrates such as DNA, through the CagT4SS.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"320 ","pages":"Article 151661"},"PeriodicalIF":4.5,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144489918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enteropathogenic Escherichia coli revisited – New insights into old EPEC isolates using whole genome sequencing","authors":"Alexander Kehl ,&nbsp;Lisa Bader ,&nbsp;Agnes C. Kaiping ,&nbsp;Bärbel Kieninger ,&nbsp;Jürgen Fritsch ,&nbsp;Alexander Mellmann ,&nbsp;Sabrina Mühlen","doi":"10.1016/j.ijmm.2025.151659","DOIUrl":"10.1016/j.ijmm.2025.151659","url":null,"abstract":"<div><div>Enteropathogenic <em>E. coli</em> (EPEC) cause severe diarrhoeal disease in children under the age of three in low- and middle-income countries. Upon ingestion of contaminated food or water, the bacteria colonise the small intestine. EPEC are grouped into typical and atypical isolates based on the presence or absence of the genes encoding the bundle-forming pilus (Bfp), with tEPEC (Bfp⁺) adhering to cells in microcolonies, whereas aEPEC show a more diffuse adherence phenotype. All EPEC express a type III secretion system (T3SS) encoded on the locus of enterocyte effacement (LEE) pathogenicity island, which is required for the translocation of effector proteins into the host cell, aiding bacterial adhesion and survival. Historically classified as EPEC by serogroups according to WHO guidelines, current practice identifies EPEC by PCR for characteristic virulence genes <em>eae</em> (intimin) and <em>bfp</em>. Here, we analysed a collection of 41 older clinical isolates initially grouped as EPEC using whole genome sequencing (WGS) combined with phenotypic characterisation including biofilm formation, adherence type, and pedestal formation. This allowed us to correctly define isolate pathotypes in addition to determining the integration site of the LEE and identifying three potential new T3SS effectors. Uniting phenotypic characterisation with genetic information, we were able to identify the molecular mediators of observed phenotypes. This suggests that, while non-WGS-based isolate profiling is important to decide immediate treatment options, only detailed knowledge of the isolates can provide in-depth information on the potential disease development and severity.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"320 ","pages":"Article 151659"},"PeriodicalIF":4.5,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144307116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Occurrence of vanA/vanM-positive vancomycin-resistant Enterococcus faecium in hospital wastewater associated with clinical infections in Guangzhou, China: A genomic epidemiological study","authors":"Liling Zhang ,&nbsp;Minxuan Su ,&nbsp;Shaowei Meng ,&nbsp;Xuan Zhang ,&nbsp;Hao Wu ,&nbsp;Meina Wu ,&nbsp;Xiaojun Ao ,&nbsp;Xiaoyue Zhang ,&nbsp;Jiehao Lin ,&nbsp;Shijia Yu ,&nbsp;Yuqi Hong ,&nbsp;Xiucheng Zeng ,&nbsp;Shuyi Huang ,&nbsp;Yuxin Zhang ,&nbsp;Bangjie Yang ,&nbsp;Ni Zhang ,&nbsp;Yueting Jiang ,&nbsp;Lingqing Xu ,&nbsp;Zhongde Zhang ,&nbsp;Cha Chen ,&nbsp;Cong Shen","doi":"10.1016/j.ijmm.2025.151658","DOIUrl":"10.1016/j.ijmm.2025.151658","url":null,"abstract":"<div><h3>Background</h3><div>The emerging ST80 vancomycin-resistant <em>Enterococcus faecium</em> (VREfm) lineage, linked to the increases of clinical infections in China and Japan, raises concerns about environmental transmission. Hospital wastewater systems are recognized reservoirs for antimicrobial-resistant bacteria, but their role in disseminating ST80 VREfm remains unclear. This study investigates VREfm prevalence in hospital wastewater and genomic links between patients and hospital wastewater.</div></div><div><h3>Methods</h3><div>From December 2023 to May 2024, a total of 262 wastewater samples were collected from three hospitals in Guangzhou, China. VREfm was identified using vancomycin-supplemented media. Antimicrobial susceptibility was assessed using the broth dilution method. Ninety-five patient-derived VREfm genomes in the same hospitals were included. Whole-genome sequencing and bioinformatic analysis were performed to reveal genomic characterizations and genetic transmission links.</div></div><div><h3>Results</h3><div>VREfm was detected in 54.6 % (143/262) of samples. All isolates carried <em>vanA</em>, with 25.9 % (37/143) co-harboring <em>vanA</em> and <em>vanM</em>. The dominant ST80 lineage (43.4 %, n = 62) was linked to recent regional prevalence. A novel sequence type ST2460, belonging to CC17, emerged as the second most prevalent (27.2 %, n = 39). ST80 isolates exhibited enriched antimicrobial resistance genes, correlating with multidrug resistance phenotypes and high resistance rates. Genomic analysis revealed that 95.7 % (132/138) of ST80 isolates from wastewater and patients exhibited close genetic relatedness (median of SNP = 19, IQR: 14–23) and were linked within cross-source transmission networks, supported by the high similarity of a shared p23VRE019-like plasmid.</div></div><div><h3>Conclusions</h3><div>Hospital wastewater is a critical reservoir for high-risk VREfm clones, particularly the outbreak-associated ST80 lineage. The persistence of VREfm in effluents and evidence of cross-source transmission underscores the urgent need for enhanced environmental surveillance. Integrated strategies addressing environmental reservoirs are essential to combat the growing threat of VREfm.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"319 ","pages":"Article 151658"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144184651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From crisis to routine – Standardization of SARS-CoV-2 genome detection by enhanced EQA schemes in a scientific pandemic network","authors":"Martin Kammel ,&nbsp;Hans-Peter Grunert ,&nbsp;Anika Zimmermann ,&nbsp;Annemarie Martin ,&nbsp;Vanessa Lindig ,&nbsp;Samuel Samuleit ,&nbsp;Ulf Dühring ,&nbsp;Mechthild Adams-Bagusche ,&nbsp;Dirk Sander ,&nbsp;Hannah Zeichhardt ,&nbsp;Christian Drosten ,&nbsp;Victor M. Corman ,&nbsp;Sandra Ciesek ,&nbsp;Holger F. Rabenau ,&nbsp;Martin Obermeier ,&nbsp;Robert Ehret ,&nbsp;Rolf Kaiser ,&nbsp;Jim Huggett ,&nbsp;Denise O'Sullivan ,&nbsp;Peter M. Vallone ,&nbsp;Heinz Zeichhardt","doi":"10.1016/j.ijmm.2025.151656","DOIUrl":"10.1016/j.ijmm.2025.151656","url":null,"abstract":"<div><div>In the beginning of 2020, the outbreak of the COVID-19 pandemic led to a crisis in which diagnostic methods for the genome detection of SARS-CoV-2 were urgently needed. Based on the very early publication of the basic principles for a diagnostic test for the genome detection of SARS-CoV-2, the first noncommercial laboratory-developed tests (LDTs) and commercial tests were introduced. As there was considerable uncertainty about the reliability and performance of different tests and different laboratories, INSTAND established external quality assessment (EQA) schemes for the detection of SARS-CoV-2 starting in April 2020. In close partnership in a scientific network, the EQA schemes were enhanced, especially the April, June and November 2020 terms. The enhancement included: (i) immediate provision of suitable virus including variants of concern at the beginning of the pandemic outbreak, (ii) short frequency of EQA schemes, (iii) concentration dependency of the testing and sensitivity check, achieved by using SARS-CoV-2-positive samples from a 10-fold dilution series of the same starting material, (iv) specificity check of the testing, achieved by using SARS-CoV-2-negative samples containing human coronaviruses or MERS CoV, (v) revealed samples for orientation on test performance during an ongoing or at the start of an EQA scheme using a pre-quantified SARS-CoV-2-positive EQA sample with a low viral RNA load of only 1 570 copies/mL assigned by digital PCR (dPCR) in June 2020 and (vi) quantified reference materials based on the experiences of the first two EQA schemes with dPCR-assigned values in copies/mL beginning in November 2020 for self-evaluation of the applied test system. This manuscript summarizes the results of a total of 13 EQA schemes for the detection of SARS-CoV-2 between April 2020 and June 2023 in which a total of 1 413 laboratories from 49 countries participated. The qualitative results for the detection of SARS-CoV-2-positive samples were between 95.8 % and 99.7 % correct positive, excluding extremely low concentration samples. For all SARS-CoV-2-negative EQA samples, the qualitative success rates ranged from 95.1 % to 99.4 % correct negative results. The widely varying values for the cycle threshold (Ct)/crossing point (Cq) reported for the different target genes and test systems were striking. A few laboratories reported quantitative results in copies/mL for several VOCs with an acceptable rate of over 93 % correct positive results in the majority of cases. The description of the enhanced EQA schemes for SARS-CoV-2 detection in terms of timing and scope can serve as a blueprint for the rapid development of a quality assessment of diagnostics for an emerging pathogen.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"319 ","pages":"Article 151656"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144221261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of outer membrane vesicles of Aggregatibacter actinomycetemcomitans serotypes a, b and c and their interactions with human neutrophils","authors":"Yanyan Fu ,&nbsp;Anke Trautwein-Schult ,&nbsp;Sjouke Piersma ,&nbsp;Chang Sun ,&nbsp;Johanna Westra ,&nbsp;Anne de Jong ,&nbsp;Dörte Becher ,&nbsp;Jan Maarten van Dijl","doi":"10.1016/j.ijmm.2025.151655","DOIUrl":"10.1016/j.ijmm.2025.151655","url":null,"abstract":"<div><div><em>Aggregatibacter actinomycetemcomitans (Aa)</em> is a Gram-negative oral pathogen associated with periodontitis and systemic diseases. Seven serotypes of <em>Aa</em> are known, with serotypes a, b and c being most prevalent worldwide. Interestingly, serotype a, b and c isolates present differences in virulence. This focuses interest on their secreted virulence factors. Gram-negative bacteria evolved a specific protein secretion mechanism, based on the release of outer membrane vesicles (OMVs) with a protein cargo. The present study was therefore aimed at investigating whether differences in the protein cargo of OMVs could be associated with the differential virulence of <em>Aa</em> serotypes a, b or c. Accordingly, the different OMV proteomes were defined by mass spectrometry and infection assays were performed with human neutrophils that represent the main innate defense against oral pathogens like <em>Aa</em>. Subsequently, we correlated the OMV proteome data with the observed OMV-neutrophil interactions. A total of 276 OMV-associated proteins was identified, including 53 known virulence factors. Interestingly, OMVs from <em>Aa</em> isolates with different serotypes displayed similar protein cargo, but the relative quantities differed. OMVs of serotype a isolates were exceptional in carrying CRISPR proteins with a potential role in virulence. Intriguingly, <em>Aa</em> OMVs mostly coated the neutrophil surface, triggering formation of neutrophil extracellular traps (NETs). Conversely, the NETs captured <em>Aa</em> OMVs. Since the observed OMV-neutrophil interplay will occur at a distance from the OMV-producing bacteria, we postulate that it allows the bacteria to evade capture and elimination by neutrophils.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"319 ","pages":"Article 151655"},"PeriodicalIF":4.5,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144134901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing potential misidentification of Staphylococcus argenteus as Staphylococcus aureus in clinical routine samples: A retrospective study","authors":"Farah Alhussein ,&nbsp;Dennis Held ,&nbsp;Ahmad Mohamed Mostafa Abdrabou ,&nbsp;Judith Fürstenberg ,&nbsp;Ricarda Michels ,&nbsp;Jamie Alex Maurer ,&nbsp;Stefan Wagenpfeil ,&nbsp;Sören L. Becker ,&nbsp;Cihan Papan","doi":"10.1016/j.ijmm.2025.151657","DOIUrl":"10.1016/j.ijmm.2025.151657","url":null,"abstract":"<div><div><em>Staphylococcus argenteus</em> is a recently described member of the <em>Staphylococcus aureus</em> complex. Thus far, its frequency in clinical samples has been rarely described. Following an update of the commercially available matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) database (Bruker Daltonics) for pathogen identification, isolates from our <em>S. aureus</em> biobank were reanalysed for the detection of potentially misdiagnosed <em>S. argenteus</em> isolates. Additionally, we assessed whether phenotypical characteristics can be used to differentiate between <em>S. aureus</em> and <em>S. argenteus</em> in routine microbiological diagnostics. Among 505 investigated isolates, no <em>S</em>. <em>argenteus</em> or another member of the <em>S</em>. <em>aureus</em> complex were found. Furthermore, the morphological difference could not reliably distinguish between <em>S. aureus</em> and <em>S. argenteus</em>, as the latter was significantly more often missed by the staff in our study. Continuous surveillance of <em>S. argenteus</em> is essential to more accurately understand its epidemiology.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"319 ","pages":"Article 151657"},"PeriodicalIF":4.5,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144166756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DDX17 promotes DENV-2 replication via interaction with viral dsRNA and G3BP1","authors":"Peijun Han ,&nbsp;Wei Ye ,&nbsp;Hongwei Ma ,&nbsp;Yangchao Dong ,&nbsp;Xin Lv ,&nbsp;He Liu ,&nbsp;Linfeng Cheng ,&nbsp;Liang Zhang ,&nbsp;Sumin Li ,&nbsp;Yingfeng Lei ,&nbsp;Fanglin Zhang","doi":"10.1016/j.ijmm.2025.151654","DOIUrl":"10.1016/j.ijmm.2025.151654","url":null,"abstract":"<div><div>Dengue virus (DENV) is one of the major arboviruses that pose a serious threat to global human health. However, there is currently no specific antiviral drug available for the treatment of DENV infection. DDX17, a member of the DExD/H-box helicase family, has been implicated in the replication processes of various viruses. Our research group discovered that during the early stages of dengue virus replication, DDX17 promotes viral replication and suppresses the activity of the IFN promoter. Furthermore, DDX17 binds to viral dsRNA and interacts with G3BP1, a component of stress granules (SGs), to inhibit SG formation, thereby enhancing viral replication. By elucidating the role of DDX17 in the early stages of dengue virus replication, our findings provide valuable insights into host-pathogen interactions during DENV infection, offering potential therapeutic perspectives.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"319 ","pages":"Article 151654"},"PeriodicalIF":4.5,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144071836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Carbon source utilization in hybrid Shiga toxin-producing and uropathogenic Escherichia coli indicates uropathogenic origin","authors":"Imke Johanna Temme,&nbsp;Petya Berger,&nbsp;Ulrich Dobrindt,&nbsp;Alexander Mellmann","doi":"10.1016/j.ijmm.2025.151653","DOIUrl":"10.1016/j.ijmm.2025.151653","url":null,"abstract":"<div><div>To investigate the adaptation of hybrid <em>Escherichia coli</em> to the intestinal and extraintestinal milieu, we compared our model hybrid Shiga toxin-producing (STEC) and uropathogenic (UPEC) <em>E. coli</em> O2:H6 strains with non-pathogenic <em>E. coli</em> and canonical UPEC and STEC strains in a carbon source utilization assay testing 95 common carbon sources under aerobic and anaerobic conditions. Comparison of anaerobic to aerobic growth showed a 2-fold decrease and 2.5-fold increase in the growth capacity and lag phase, respectively. While the UPEC and STEC/UPEC hybrids retained the utilization of several organic acids, amino acids, and peptides, the STEC and non-pathogenic strains relied almost exclusively on the utilization of sugar compounds under anaerobic conditions. Cluster analysis indicated a higher degree of difference and separation between all strains under aerobic conditions. The UPEC, hybrids, and STEC strain B2F1 showed high similarities in aerobic carbon utilization following growth patterns observed in previous phenotype assays. Additionally, we observed known UPEC virulence traits, such as the aerobic utilization of D-serine in our model STEC/UPEC hybrids. Combined, these findings suggest that the intestinal STEC/UPEC O2:H6 isolates originated from a UPEC background and acquired the ability to cause intestinal disease with the addition of Shiga toxin as a virulence factor.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"319 ","pages":"Article 151653"},"PeriodicalIF":4.5,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143874457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics of clinical hybrid Escherichia coli strains in Norway","authors":"Misti D. Finton ,&nbsp;Roger Meisal ,&nbsp;Davide Porcellato ,&nbsp;Lin T. Brandal ,&nbsp;Bjørn-Arne Lindstedt","doi":"10.1016/j.ijmm.2025.151651","DOIUrl":"10.1016/j.ijmm.2025.151651","url":null,"abstract":"<div><div>The global rise of hybrid <em>Escherichia coli</em> (<em>E. coli</em>) is a major public health concern, as enhanced virulence from multiple pathotypes complicates the traditional <em>E. coli</em> classification system and challenges clinical diagnostics. Hybrid strains are particularly concerning as they can infect both intestinal and extraintestinal sites, complicating treatment and increasing the risk of severe disease. This study analyzed virulence-associated genes (VAGs) in 13 <em>E. coli</em> isolates from fecal samples of patients with symptoms of gastrointestinal (GI) infection in Norwegian hospitals and clinics. Whole genome sequencing (WGS) was conducted using Oxford Nanopore’s MinION and Illumina’s MiSeq platforms. Eleven strains harbored molecular diagnostic markers of atypical enteropathogenic <em>E. coli</em> (aEPEC), enteroinvasive <em>E. coli</em> (EIEC), Shiga toxin-producing <em>E. coli</em> (STEC), enterotoxigenic <em>E. coli</em> (ETEC), or typical enteropathogenic <em>E. coli</em> (tEPEC). Two of those isolates were identified as triple intestinal hybrids with molecular diagnostic markers for aEPEC, EIEC, and STEC. Notably, two isolates lacked any IPEC-specific molecular diagnostic markers, yet were suspected of causing the patient’s GI infection. Furthermore, genes associated with extraintestinal pathogenic <em>E. coli</em> (ExPEC)—including adhesins, toxins, protectins, siderophores, iron acquisition systems, and invasins—were identified in all the isolates. Thus, most of the isolates were classified as hybrid aEPEC/ExPEC, STEC/ExPEC, tEPEC/ExPEC, or aEPEC/EIEC/STEC/ExPEC. These findings emphasize the genomic plasticity of <em>E. coli</em> and highlight the need to revise the classification system for enteric pathogens.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"318 ","pages":"Article 151651"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143578573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Validation of ML-algorithms for the prediction of positive urine cultures from flow cytometry routine data in patients with suspected bacteriuria","authors":"Alexander Brenner ,&nbsp;Jutta Esser ,&nbsp;Franziska Schuler ,&nbsp;Julian Varghese ,&nbsp;Frieder Schaumburg","doi":"10.1016/j.ijmm.2025.151652","DOIUrl":"10.1016/j.ijmm.2025.151652","url":null,"abstract":"<div><div>Urine samples are frequently analyzed in microbiology laboratories, but a large proportion of them are culture-negative. The aim of this study was to test whether positive urine cultures can be predicted from routine flow cytometric data. Urine samples (n = 1325) were used for a train dataset (n = 1032) and three independent test datasets (n = 93–100 samples) that were collected three months apart. Predictors from flow cytometry were total counts per µl of bacteria, erythrocytes, yeast-like cells, hyaline casts, crystals, leukocytes, squamous epithelial cells, non-hyaline casts and non-squamous epithelial cells in addition to age, sex and type of urine sample. Labels were positive culture and detection of clinically relevant uropathogens. Three classifiers (decision tree, random forest classifier, CatBoost) were 5-fold cross-validated on the train dataset to select an optimized model with ≥ 95 % sensitivity. The optimized model was trained on the complete train dataset and evaluated on the three independent test sets. In total, 72.5 % (960/1325) samples were culture positive with a predominance of <em>Escherichia coli</em> (n = 295). CatBoost outperformed the other classifiers in terms of balanced accuracy (train data) and was selected as the classifier for predictions. With optimised hyperparameters, the balanced accuracy was 62–74 % for the prediction of a positive culture (test data) and had a sensitivity that was stable over a period of six months (94–96 %, negative predictive value [NPV]: 67–77 %, positive predictive value [PPV]: 78–81 %). For the prediction of uropathogens, the balanced accuracy was 57–63 % with a stable sensitivity (95–100 %, NPV: 83–100 %, PPV: 48–59 %). In conclusion, the ML algorithms showed high sensitivity for detecting positive urine cultures.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"318 ","pages":"Article 151652"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143549155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}