International Journal of Medical Microbiology最新文献

{"title":"Genomic insights into Klebsiella pneumoniae: Virulence, resistance, and transmission in South and Southeast Asia","authors":"Woranich Hinthong ,&nbsp;Jody Phelan ,&nbsp;Arif Hussain ,&nbsp;Razib Mazumder ,&nbsp;Azra ,&nbsp;Ihtisham Ul Haq ,&nbsp;Ihsan Ullah ,&nbsp;Thomas Roberts ,&nbsp;Naphatcha Thawong ,&nbsp;Nina Billows ,&nbsp;Susana Campino ,&nbsp;Taj Ali Khan ,&nbsp;Dinesh Mondal ,&nbsp;Taane G. Clark","doi":"10.1016/j.ijmm.2025.151666","DOIUrl":"10.1016/j.ijmm.2025.151666","url":null,"abstract":"<div><h3>Background</h3><div><em>Klebsiella pneumoniae</em> has long posed a significant challenge in clinical settings worldwide, particularly due to its carbapenemase production and multidrug-resistant (MDR) characteristics. While extensive genomic studies of <em>K. pneumoniae</em> have been conducted globally, research in Asia, particularly South Asia, remains limited.</div></div><div><h3>Objectives</h3><div>This study aims to address and compare the genomic characteristics of <em>K. pneumoniae</em> isolates from South Asia and Southeast Asia, including virulence, antimicrobial resistance (AMR), plasmids, and mobile genetic elements (MGE) profiles, as well as potential transmission dynamics.</div></div><div><h3>Methods</h3><div>A total of 463 <em>K. pneumoniae</em> genomes were included from collected samples and public databases. All genomes underwent comprehensive analysis, including pan-genome profiling, multi-locus sequence typing (MLST), annotation of virulence factors, AMR genes, plasmids, and MGEs, as well as SNP distance–based analysis to infer transmission dynamics, using established bioinformatic tools.</div></div><div><h3>Results</h3><div><em>K. pneumoniae</em> isolates exhibited diverse virulence determinants. Hypervirulent isolates were primarily associated with ST23 and ST86, and commonly harbour <em>aerobactin</em>, <em>salmochelin</em>, and <em>rmpA</em>. The majority of isolates were predicted to be MDR, with those from Southeast Asia showing a higher relative abundance of AMR genes associated with the antibiotic classes examined in this study. Among all isolates, the predominant carbapenemase-associated gene was <em>bla</em>_{<em>NDM-1</em>}. <em>Col440I_1</em> was the most prevalent plasmid replicon, although it did not co-occur with any AMR genes. Association between the IncFII_1_pKP9 plasmid replicon and resistance genes <em>sul-5, bla</em>_{<em>CTX-M</em>}, and <em>bla</em>_<em>TEM</em> was found. <em>ISSen9</em> was the dominant MGE, frequently co-occurring with the plasmid replicons <em>IncFIB(K)_1_Kpn3</em> and <em>IncFII_1_pKP91</em>. Transmission analysis indicated that the highest isolate similarity occurred within MLST and country. However, clustering based on plasmid replicon profiles revealed that some clusters comprised isolates from multiple countries.</div></div><div><h3>Conclusion</h3><div>This study provides a comprehensive analysis of the genomic characteristics and transmission patterns of <em>K. pneumoniae</em> in South and Southeast Asia, contributing to our understanding of its virulence and resistance mechanisms. These findings further suggest that plasmid replicons may play a critical role in shaping transmission dynamics and provide valuable insights to inform future AMR surveillance and control strategies.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"320 ","pages":"Article 151666"},"PeriodicalIF":4.5,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144680051","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":"Biofilm-associated Achromobacter xylosoxidans prosthetic valve infective endocarditis","authors":"Lisa-Marie Wackernagel ,&nbsp;Judith Kikhney ,&nbsp;Tassilo Kruis ,&nbsp;Peter Menzel ,&nbsp;Matthias Schneider-Reigbert ,&nbsp;Herko Grubitzsch ,&nbsp;Julia Gogolok ,&nbsp;Leif Erik Sander ,&nbsp;Florian Kurth ,&nbsp;Annette Moter ,&nbsp;Tilman Lingscheid","doi":"10.1016/j.ijmm.2025.151664","DOIUrl":"10.1016/j.ijmm.2025.151664","url":null,"abstract":"<div><h3>Background</h3><div>Infective endocarditis (IE) caused by Gram-negative bacteria is a rare but increasingly recognized emerging infectious disease. <em>Achromobacter xylosoxidans</em>, a Gram-negative non-fermenting opportunistic bacterium, has rarely been associated with IE and its biofilm potential <em>in vivo</em> is unknown.</div></div><div><h3>Methods</h3><div>Specimens from a patient with <em>A. xylosoxidans</em> IE were obtained during cardiac surgery. Fluorescence in situ hybridization was used for visualization of microorganisms within heart valve tissues in combination with 16S rRNA gene PCR and sequencing (FISHseq) for correlation with prior blood culture isolates and to establish a definite diagnosis. The infected prosthetic valve had been implanted six months before. Following implantation, the patient developed relapsing bacteremia with <em>A. xylosoxidans</em> over three months, despite repeated adequate antibiotic treatment.</div></div><div><h3>Results</h3><div>Conventional microbiological analysis of the explanted valve yielded no bacterial growth and prior imaging by repeated positron emission tomography and transesophageal echocardiography did not reveal evidence of infective endocarditis. FISHseq detected <em>A. xylosoxidans</em> in the heart valve samples and demonstrated numerous microorganisms, including FISH-positive, metabolically active bacteria, within in-vivo-grown biofilms. The genomic profile of <em>A. xylosoxidans</em> LB-23–519–25 confirmed the presence of resistance genes commonly found in this intrinsically multidrug-resistant species, which, together with biofilm formation, explains the observed therapeutic failure.</div></div><div><h3>Conclusion</h3><div>Valve culture and imaging failed to identify this case of Gram-negative bacteria IE correctly, but diagnosis of definite IE was eventually established via FISHseq according to the 2023 Duke-ISCVID Criteria. The biofilm-forming potential of <em>A. xylosoxidans</em> and its implications for the efficacy of antimicrobial therapy should be considered in future patients.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"320 ","pages":"Article 151664"},"PeriodicalIF":4.5,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144694357","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":"Drug resistance of Mycobacterium tuberculosis in West Java, Indonesia","authors":"Ariel Pradipta ,&nbsp;David Virya Chen ,&nbsp;Ihsan Fauzan ,&nbsp;Adhityo Wicaksono ,&nbsp;Basti Andriyoko ,&nbsp;Rifky Waluyajati Rachman ,&nbsp;Gusti Ayu Prani Pradani ,&nbsp;Azzania Fibriani ,&nbsp;Anuraj H. Shankar","doi":"10.1016/j.ijmm.2025.151665","DOIUrl":"10.1016/j.ijmm.2025.151665","url":null,"abstract":"<div><div>Tuberculosis (TB) is currently one of the leading causes of infectious disease deaths globally, and Indonesia ranks 2nd in annual TB cases, below only India. Accurate TB diagnosis and detection of multidrug-resistant TB (MDR-TB) in real-world settings are crucial for prompt treatment and surveillance. We therefore compared multiple methods for TB detection and drug resistance profiling, including a cartridge-based nucleic acid amplification test (CBNAAT), line probe assay (LPA), and phenotypic drug susceptibility testing (pDST) with targeted long-read next generation sequencing (tNGS) and whole genome sequencing (WGS) on 133 patients in West Java, Indonesia. WGS enabled comprehensive phylogenetic analyses and insights into TB evolution and drug resistance patterns, but its low read counts limit practicality for clinical use. Comparatively, tNGS demonstrated superior sensitivity and specificity, effectively identifying resistance profiles across multiple first-line and second-line drugs with rapid turnaround times. Notably, when compared to LPA, tNGS showed positive percent agreement (PPA) values of 100 % for rifampicin, isoniazid and ethionamide, and an overall agreement of 94 % across multiple drugs. In comparison with CBNAAT, the tNGS PPA for rifampicin remained high at 91 %. The results show that long-read tNGS technology offers a robust tool for enhanced TB treatment and surveillance, ensuring both timely detection and enabling effective tracing through in-depth genetic analysis. The findings significantly contribute to the development of strategies for TB control and management, especially in regions with a high burden of TB cases.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"320 ","pages":"Article 151665"},"PeriodicalIF":4.5,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144703727","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":"Nanopore-targeted sequencing: A new and effective technique for the diagnosis of non-tuberculous mycobacteria pulmonary disease","authors":"Li-ping Cheng ,&nbsp;Li Wang ,&nbsp;Yun-fei Wang ,&nbsp;Jin-hui Yang ,&nbsp;Jie Cao ,&nbsp;Xiao-na Shen ,&nbsp;Zhi-bin Liu ,&nbsp;Wei Wei ,&nbsp;Wei Sha ,&nbsp;Qin Sun","doi":"10.1016/j.ijmm.2025.151663","DOIUrl":"10.1016/j.ijmm.2025.151663","url":null,"abstract":"<div><div>Non-tuberculous mycobacteria pulmonary disease (NTM-PD) has become a significant public health issue threatening human health in recent years. Traditional mycobacterial culture is complex, time-consuming, and unable to identify NTM at the species level. Nanopore-targeted sequencing (NTS) is a novel molecular detection technology that integrates the high sensitivity of targeted multiplex PCR with the high specificity of third-generation long-read sequencing. NTS has significant advantages in diagnosing, precise differentiation of mixed infection pathogens and antibiotic resistance genes in infectious diseases. The present study compared the diagnostic performance of NTS with fluorescence-stained smears and BACTEC 960 culture in NTM-PD. In respiratory specimens from suspected NTM-PD individuals, NTS exhibited a sensitivity of 88.2 %, significantly higher than culture (74.0 %) and smears (37.8 %) (both P &lt; 0.05). The AUC for NTS was 0.893, surpassing that of culture (0.869) and smears (0.605). The sensitivity varied among respiratory specimens: bronchoalveolar lavage fluid (BALF) 90.1 %, sputum 78.6 %, and lung puncture fluid 50.0 %. The NTS sensitivity and specificity for predicting resistance to amikacin and clarithromycin were 42.9 %, 35.5 % and 98.8 %, 98.3 %, respectively. Compared to culture and smears, NTS demonstrated higher sensitivity, with slightly lower specificity than culture. However, its predictive value for drug-resistant mycobacteria is limited. BALF specimens exhibit maximal sensitivity among different respiratory samples. Taken together, NTS is a novel, rapid, and efficient molecular diagnostic method for NTM-PD.</div></div>","PeriodicalId":50312,"journal":{"name":"International Journal of Medical Microbiology","volume":"320 ","pages":"Article 151663"},"PeriodicalIF":4.5,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144623323","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":"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}