Journal of Clinical Microbiology最新文献

{"title":"Photo Quiz: Asteroid bodies in a skin biopsy of a farmer.","authors":"Xiujiao Xia","doi":"10.1128/jcm.00478-25","DOIUrl":"10.1128/jcm.00478-25","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 7","pages":"e0047825"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144591366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improved HIV-1 RNA detection using whole blood versus plasma in antiretroviral-treated individuals.","authors":"Vivian I Avelino-Silva, Mars Stone, Leilani Montalvo, Clara Di Germanio, Sonia Bakkour, Marion C Lanteri, Eduard Grebe, Brian Custer, Xutao Deng, Renata Buccheri, Karen Harrington, Steven H Kleinman, Sandhya Vasan, Nittaya Phanuphak, Carlo Sacdalan, Siriwat Akapirat, Mark de Souza, Esper G Kallás, Sheila de Oliveira Garcia Mateos, Ester C Sabino, Philip J Norris, Michael P Busch","doi":"10.1128/jcm.01904-24","DOIUrl":"10.1128/jcm.01904-24","url":null,"abstract":"<p><p>Currently, nucleic acid testing (NAT) platforms detect HIV-1 in plasma. Using whole blood (WB) could improve HIV-1 detectability as cellular elements may also contain HIV-1 nucleic acids. We used well-characterized paired WB/plasma panels to evaluate HIV-1 RNA detection inhibition by WB, specificity, and enhanced HIV-1 RNA detectability by WB compared to plasma. Panels included: spiked samples; NAT-/serology-, NAT+/serology+, and NAT-/serology+ blood donor samples; samples from persons with HIV (PWH) who started antiretroviral treatment (ART) at chronic infection stages; and from PWH under ART since acute/early infection. We found one false-positive result on WB testing of 100 NAT-/serology- blood donors, and evidence of modest HIV-1 detection inhibition. Among NAT-/serology+ donors, HIV-1 RNA detectability in plasma and WB was similar (<i>P</i> = 0.64). Among 50 PWH starting ART at chronic infection stages, detectability was 24% in plasma and 92% in WB (<i>P</i> < 0.001). Among 345 PWH on ART since acute/early infection, detectability was 10% in plasma and 16% in WB (<i>P</i> = 0.013). HIV-1 RNA detectability in both plasma and WB was progressively lower for earlier Fiebig stages at ART initiation. WB increased HIV-1 detectability relative to plasma in PWH who initiated ART at all but the earliest infection stages. We failed to find enhanced HIV-1 RNA detectability by WB in NAT-/serology+ blood donors, who may include elite controllers. Enhancing HIV-1 nucleic acid detectability could improve infection ascertainment among PWH on ART with blunted serologic reactivity; investigation of breakthrough infection in PrEP users; and potentially for virus rebound monitoring in HIV-1 cure studies.</p><p><strong>Importance: </strong>Currently, tests to detect HIV genetic materials (RNA/DNA) are done using the liquid component of a blood sample (plasma). However, HIV may be present in blood cellular components, such as white cells and platelets. Here, we investigated if using whole blood (WB; liquid + cellular components) could improve HIV RNA detectability compared to plasma. WB increased HIV RNA detectability in persons with HIV under treatment, including those with early treatment initiation, but not among blood donors with positive HIV serology and undetectable HIV RNA in the donation screening. Enhancing HIV RNA/DNA detectability would support HIV diagnosis in cases with blunted serologic response, such as persons with early antiretroviral treatment initiation or pre-exposure prophylaxis users. It would also be useful for monitoring virus rebound in HIV cure studies and in blood donation screening, where high test sensitivity is required to guarantee the safety of the blood supply.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0190424"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144215990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accurate and reproducible whole-genome genotyping for bacterial genomic surveillance with Nanopore sequencing data.","authors":"K Prior, K Becker, C Brandt, A Cabal Rosel, J Dabernig-Heinz, C Kohler, M Lohde, W Ruppitsch, F Schuler, G E Wagner, A Mellmann","doi":"10.1128/jcm.00369-25","DOIUrl":"10.1128/jcm.00369-25","url":null,"abstract":"<p><p>Despite recent advances in error rate reduction, until recently, Oxford Nanopore Technologies (ONT) sequences lacked the accuracy required for fine-scale bacterial genomic analysis. Here, recent software improvements of ONT and the ONT-core-genome multilocus sequence typing (cgMLST)-Polisher within the SeqSphere⁺ software were evaluated. We used short-read (Illumina) and long-read ONT sequences of 80 multidrug-resistant organisms (MDROs) for benchmarking. Illumina reads were <i>de novo</i> assembled using SKESA. For ONT, Dorado Super Accurate (SUP) model v.4.3 or v.5.0 basecalled reads were assembled with Flye and then polished with Medaka v.1.12 m4.3 or Medaka v.2.0 bacterial methylation model. In addition, the ONT-cgMLST-Polisher was run over all assemblies. The \"ground truth\" (GT) hybrid assemblies were created using Hybracter v.0.10.0. Sixteen isolates from four species out of the original 80 isolates were sent to six laboratories for a ring trial. The 80 MDROs basecalled with SUP m4.3 had an average cgMLST allele distance (AD) to the GT of 4.94 with Medaka v.1.12 and 1.78 with Medaka v.2.0, respectively. After further polishing the Medaka v.2.0 data with the ONT-cgMLST-Polisher, the AD dropped to 0.09. Using data basecalled with SUP m5.0 with Medaka v.2.0 further reduced the AD significantly to 0.04. While the ring trial data basecalled with Dorado SUP m4.3 showed more variability and insufficient results for some samples, model 5.0 data resulted in average ADs of 0.36 and 0.17 without and with the ONT-cgMLST-Polisher, respectively. In conclusion, recent ONT Dorado and Medaka models combined with the ONT-cgMLST-Polisher improved ONT sequencing accuracy and made it sufficiently reproducible for genomic surveillance of bacteria.IMPORTANCEONT sequencing methodology is especially attractive for small and medium-sized laboratories due to its relatively low capital investment and price per sample consumable costs. However, until recently, it lacked accuracy and reproducibility for bacterial genomic genotyping. Here, we present an evaluation of the most recent ONT bioinformatic (basecalling and polishing of consensus) improvements and a new ONT-cgMLST-Polisher tool. We demonstrate that by applying those procedures, ONT whole-genome genotyping-based surveillance of bacteria is finally accurate and reproducible enough for routine application even in small laboratories.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0036925"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144284492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An urgent need for diagnostic tools to address global mpox public health emergencies.","authors":"Benjamin M Liu, Zhilong Yang","doi":"10.1128/jcm.01321-24","DOIUrl":"10.1128/jcm.01321-24","url":null,"abstract":"<p><p>Monkeypox virus (MPXV) is the causative agent of mpox, a zoonosis formerly known as monkeypox. MPXV can be divided into clades I and II, which are further divided into subclades Ia, Ib, IIa, and IIb. Since May 2022, subclade IIb MPXV has rapidly spread outside Africa to more than 100 countries due to increased human-to-human transmission. Clade I is a more virulent MPXV endemic in Central Africa with up to 10% mortality in humans. Clade I has recently evolved into a novel subclade Ib and caused outbreaks in non-endemic neighboring countries and other continents. In response to mpox, the World Health Organization has declared Public Health Emergencies of International Concern in July 2022 (subclade IIb) and August 2024 (subclade Ib). The emergence and spread of the more virulent subclade Ib MPXV has caused a significant global public health threat, particularly in low- and middle-income countries (LMICs). The evolution of MPXV has outpaced the development of novel diagnostic assays, hampering the global response. There is an urgent need for additional diagnostic tools for the detection and surveillance of MPXV, especially subclade Ib MPXV, in LMICs. Herein, we provide the current epidemiology of mpox, analyze the diagnostic gaps for mpox, and evaluate the potential of additional detection strategies to be added to the suite of mpox assays. This commentary not only sheds light on the currently available diagnostic tools for mpox but also highlights the urgent need for additional diagnostic tools in response to the new global mpox public health threats.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0132124"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144225623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and evaluation of a Pan-Mucorales Real-time PCR and a multiplex Real-time PCR for detection and identification of <i>Rhizopus arrhizus, Rhizopus microsporus</i>, and <i>Mucor</i> spp. in clinical specimens.","authors":"Helen M Tang, Sharon C-A Chen, Kerri Basile, Catriona L Halliday","doi":"10.1128/jcm.01937-24","DOIUrl":"10.1128/jcm.01937-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Mucormycosis is a life-threatening infection associated with high morbidity and mortality. Rapid and accurate diagnosis is essential for improving patient outcomes. Conventional diagnostic methods, such as histopathology and culture, are limited by low sensitivity and prolonged turnaround times, while commercial polymerase chain reaction (PCR) assays are costly and may lack specific genus or species targets. Here, we present a novel molecular diagnostic workflow to facilitate the rapid detection of Mucorales directly from clinical specimens. This workflow integrates two in-house &lt;i&gt;in vitro&lt;/i&gt; diagnostic PCR assays: a real-time, qualitative Pan-Mucorales PCR, followed by a real-time multiplex genus/species-specific PCR targeting &lt;i&gt;Rhizopus arrhizus&lt;/i&gt;, &lt;i&gt;Rhizopus microsporus&lt;/i&gt;, and &lt;i&gt;Mucor&lt;/i&gt; spp. Specificity of the assays was validated using cultured isolates of Mucorales, as well as non-Mucorales fungi and bacteria. The diagnostic performance was assessed across 166 clinical specimens (70 Mucorales-positive and 96 negative), confirmed by an in-house panfungal PCR and DNA sequencing protocol. Specimens studied included fresh and formalin-fixed paraffin-embedded tissues, fluid, bronchoalveolar lavage/washing fluid, fine needle aspirate, cerebrospinal fluid, and bone. The Pan-Mucorales PCR demonstrated 98.6% sensitivity and 100% specificity, while the multiplex genus/species-specific PCR assay yielded sensitivities of 93.8% for &lt;i&gt;R. arrhizus&lt;/i&gt;, 70.8% for &lt;i&gt;R. microsporus&lt;/i&gt;, and 75% for &lt;i&gt;Mucor&lt;/i&gt; spp., each with 100% specificity. Concordance with the panfungal PCR (&gt;99% for Pan-Mucorales PCR and &gt;89% for multiplex PCR) was high, supporting the robustness of the workflow. This diagnostic approach has the potential to significantly reduce turnaround times, labor and costs, while streamlining the diagnostic process through timely, precise diagnostics.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Mucorales fungi, identified collectively as a high-priority pathogen on the World Health Organization fungal priority pathogens list, are the causative agents of mucormycosis. Mortality is high (up to 80%), and early, accurate diagnosis is critical to enable timely initiation of targeted antifungal therapy and surgical debridement for source control to optimize patient outcomes. In our laboratory, as in many others, the current standard for the diagnosis of mucormycosis is histopathology and culture-based methods supplemented by panfungal PCR assay/DNA sequencing; however, this process may take 7 days, with considerable labor and cost implications. Here, we present two Mucorales-specific real-time PCR assays, which when used sequentially, reduce diagnostic turnaround time and costs to detect three common agents of mucormycosis-&lt;i&gt;Rhizopus microsporus&lt;/i&gt;, &lt;i&gt;Rhizopus arrhizus&lt;/i&gt;, and &lt;i&gt;Mucor&lt;/i&gt; species. This approach not only improves diagnostic efficiency and integration into workflow but can facilitate surveillance through accurate genus- and","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0193724"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144016790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preliminary performance of the VIDAS TB-IGRA as an aid in the diagnosis of individuals infected with <i>Mycobacterium tuberculosis</i>.","authors":"Potiandi Serge Diagbouga, Arthur Diakourga Djibougou, Camille Pease, Ariana Alcaide, Audrey Berthoux, Natalie Bruiners, Daniela Maria Cirillo, Ardjouma Combary, Nadine Falchero, Deborah Handler, Antoinette Kaboré, Alfred Lardizabal, Amanda Lopes, Marissa Loubet, Philippe Manivet, Clemence Margain, Valerie Meunier, Faiza Mougari, Alberta Onyuka, Sophie Rivoiron, Tani Sagna, Mathilde Sanvert, Léon Sawadogo, Jacques Simporé, Emmanuelle Cambau, Maria Laura Gennaro","doi":"10.1128/jcm.01641-24","DOIUrl":"10.1128/jcm.01641-24","url":null,"abstract":"<p><p>This preliminary study compares VIDAS TB-IGRA (bioMérieux, Marcy-l'Etoile, France) with the established QuantiFERON-TB Gold Plus (QFT-Plus) (Qiagen, Hilden, Germany) to evaluate diagnostic performance for the diagnosis of individuals infected with <i>Mycobacterium tuberculosis</i> complex (latent infection and disease). The study was multi-center and performed between 2 October 2019 and 4 February 2020. Participants were divided into tuberculosis (TB) disease, high-risk, and low-risk populations. The confirmed TB disease population included 104 patients. The high-risk population included 162 individuals with flagged risk factors on a questionnaire but without objective clinical confirmation of TB. The low-risk population included 117 healthy blood donors from the French National Blood Bank. Positive and negative percent agreement (PPA and NPA) were determined between the VIDAS TB-IGRA and QFT-Plus. In the TB disease population, sensitivity was measured against bacterial culture and PCR. The VIDAS TB-IGRA produced fewer indeterminate results than the QFT-Plus (1/104 vs 23/104) in the TB disease population and exhibited a sensitivity of 95.0% against bacterial culture. Furthermore, a 98.2% PPA was obtained in comparison to QFT-Plus. In the low-risk population, the VIDAS TB-IGRA demonstrated high specificity (94.9%) and a strong NPA (98.2%) compared to QFT-Plus. In the high-risk population, the VIDAS TB-IGRA exhibited a strong PPA (94.4%) with the QFT-Plus. A lower NPA was observed (85.2%) compared to QFT-Plus, which may be due to a higher sensitivity demonstrated in the TB disease population. The fully automated VIDAS TB-IGRA is a promising aid in the diagnosis of individuals infected with <i>Mycobacterium tuberculosis</i> (latent infection and active disease). It exhibits higher sensitivity while maintaining specificity and produces fewer indeterminate interpretations than QFT-Plus. Its easy-to-use, single-patient format may lead to increased TB testing to aid in the adequate diagnosis and management of the disease.IMPORTANCEThis study presents a comprehensive evaluation of the VIDAS TB-IGRA diagnostic test. This test is compared with the established QuantiFERON-TB Gold Plus to assess its effectiveness in diagnosing both latent and active tuberculosis (TB) infections. The study highlights the VIDAS TB-IGRA's higher sensitivity, fewer indeterminate results, and robust performance across different patient populations, including those with confirmed TB disease, high-risk, and low-risk groups. The findings suggest that the VIDAS TB-IGRA could enhance TB diagnosis and management, offering a fully automated, easy-to-use solution that reduces human error and result variability.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0164124"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153259/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of MALDI-TOF MS instruments and databases for the identification of uncommon yeasts, <i>Aspergillus</i> spp. and rare filamentous fungi.","authors":"Marion Dutkiewicz, Maéva Garros, Julie Bui, Véronique Charlier, Elodie Da Silva, Maryline Lemaire, Sarah Dellière, Anne-Cécile Normand, Renaud Piarroux, Samia Hamane, Théo Ghelfenstein-Ferreira, Alexandre Alanio","doi":"10.1128/jcm.01612-24","DOIUrl":"10.1128/jcm.01612-24","url":null,"abstract":"<p><p>Identification of uncommon fungi using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-MS) remains challenging. Its performance depends on the protein extraction method, instrument, algorithm, and database. This study compared two established mass spectrometers (VITEK MS [bioMérieux] and Microflex [Bruker]) to the new VITEK MS PRIME (bioMérieux) and four databases, including MSI-2, a non-commercial database constructed with spectra acquired with Bruker instruments. Isolates of <i>Aspergillus</i> species, rare molds, and uncommon yeasts, previously identified by sequencing, were analyzed. After a two-step protein extraction, MALDI-ToF-MS identification was performed, and spectra were submitted to <i>in vitro</i> diagnostic (IVD) (KB3.2 and KB3.3 [bioMérieux]), research use only (RUO) (FilFungi V5 [Bruker]) databases and MSI-2. A total of 169 isolates (61 <i>Aspergillus</i> spp., 72 rare molds, and 36 uncommon yeasts), representing 33 genera and 96 species, were included. Identification rates at species level for all fungi were similar between VITEK MS and VITEKMS PRIME (79% vs. 77%). The main difference lies in the rates of non-analyzable spectra, being 15% (26 strains) for VITEK MS PRIME versus only 3% (5 strains) for VITEK MS. For <i>Aspergillus</i> and rare molds, MSI-2 performed equally well on VITEK MS and Microflex (92% vs. 91%), indicating a spectra compatibility. For uncommon yeasts, all databases performed equally at the species level. For <i>Aspergillus</i> and rare molds, FilFungi V5 performed poorly (23% and 21%), while MSI-2 was best (77% and 82%) due to broader species coverage. Misidentifications mostly involved cryptic <i>Aspergillus</i> species. MALDI-ToF-MS is a powerful tool for identifying rare fungi. Improvements are needed in completing commercial databases and optimizing acquisition systems for fungal spectra.</p><p><strong>Importance: </strong>Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-MS) is key for fungal identification nowadays. We present here the largest comparison of MALDI-ToF-MS instruments and databases focusing on rare yeasts and molds identification, challenging the existing instruments and both commercial and academic databases. The strains were collected in Saint Louis Hospital (Paris) and identified using bar-code sequencing. We showed that commercial databases are efficient for the identification of the main fungal species tested, whereas the academic database outperforms them for the identification of cryptic species.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0161224"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153315/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Treatment and diagnostic challenges associated with the novel and rapidly emerging antifungal-resistant dermatophyte, <i>Trichophyton indotineae</i>.","authors":"Yasmeen Vincent Marbaniang, Daniela Leto, Huda Almohri, Mohammad Rubayet Hasan","doi":"10.1128/jcm.01407-24","DOIUrl":"10.1128/jcm.01407-24","url":null,"abstract":"<p><p><i>Trichophyton indotineae</i> is a recently discovered dermatophyte species that causes recalcitrant dermatophytosis. It was first reported from India and has quickly spread across the globe. The exact prevalence of <i>T. indotineae</i> remains unknown due to limited surveillance. It has reached epidemic proportions in the Indian subcontinent. In India, this new species has largely replaced other previously common dermatophytes. Reports from Western countries suggest most cases are imported, with some reports of local transmission. A recent report from the United Kingdom indicates that <i>T. indotineae</i> now accounts for 38% of dermatophyte isolates tested in their national referral laboratory. <i>T. indotineae</i> causes widespread, inflammatory dermatophytosis affecting large areas of the body. Dermatophytosis caused by <i>T. indotineae</i> is difficult to manage due to the limited availability of mycology laboratories capable of reliably identifying and performing antifungal susceptibility testing, and because of its resistance to commonly used antifungals. Culture and physiological characteristics cannot confirm identification to the species level, requiring species-level confirmation by molecular methods like internal transcribed spacer sequencing. It is important for clinicians and mycology laboratories to be aware of and consider the possibility of <i>T. indotineae</i> infection in patients with relevant demographic, clinical, and travel history. This would decrease delay in diagnosis, prevent inappropriate use of medications like steroids and ineffective antifungal agents, and provide opportunities to make recommendations for good hygiene practices to prevent transmission. In this mini review, we describe the emergence of <i>T. indotineae</i>, its diagnostic and treatment challenges, and the current state, and provide recommendations for future direction.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 6","pages":"e0140724"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144266390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The dark matter of bacterial genomic surveillance-antimicrobial resistance plasmid transmissions in the hospital setting.","authors":"Annika Sobkowiak, Vera Schwierzeck, Vincent van Almsick, Natalie Scherff, Franziska Schuler, Kyrylo Bessonov, James Robertson, Dag Harmsen, Alexander Mellmann","doi":"10.1128/jcm.00121-25","DOIUrl":"10.1128/jcm.00121-25","url":null,"abstract":"<p><p>Dissemination of antimicrobial resistance (AMR) is a growing global public health burden. The aim of this study was to characterize AMR plasmid transmissions within a tertiary care hospital and identify relevant AMR plasmid transmission pathways. During an 18-month observation period, 540 clinical gram-negative multidrug-resistant bacterial (MDRB) isolates were collected during routine hospital surveillance and subjected to Pacific Biosciences long-read whole genome sequencing. Potential clonal transmissions were determined based on core genome multilocus sequence typing (cgMLST), and plasmid transmissions were detected using a novel real-time applicable tool for plasmid transmission detection. Potential transmissions were validated using epidemiological data. Among the 471 eligible MDRB isolates, we detected 1,539 plasmids; 84.41% of these were circularized. We identified 38 potential clonal transmissions in 24 clusters based on cgMLST and 121 potential plasmid transmissions in 24 clusters containing genetically related AMR plasmids. Among the latter clusters, 10 contained different multilocus sequence types (involving 2-38 isolates, median: 3 isolates), and nine contained multiple species (2-18 isolates, median: 4). Epidemiological data confirmed 19 clonal transmissions (in seven clusters) and an additional 12 plasmid transmissions (within eight plasmid clusters). Among these, we identified seven cases of intra-host and five patient-to-patient plasmid transmissions. We demonstrate that intra-host and patient-to-patient transmissions of AMR plasmids can be identified by combining long-read sequencing with real-time applicable tools during routine molecular surveillance. In addition, our study highlights that more than a decade of bacterial genomic surveillance missed at least one-third of all AMR transmission events due to plasmids.</p><p><strong>Importance: </strong>Antimicrobial resistance (AMR) poses a significant threat to human health. Most AMR determinants are encoded extra-chromosomally on plasmids. Although current infection control strategies primarily focus on clonal transmission of multidrug-resistant bacteria, until today, AMR plasmid transmission routes are neither understood nor analyzed in the hospital setting. In our study, we simultaneously determined both clonal, that is, based on chromosomes, and AMR plasmid transmissions during routine molecular surveillance by combining long-read sequencing with a novel real-time applicable software tool and validated all potential transmission events with epidemiological data. Our analysis determined not only the yet unknown plasmid transmissions within healthcare facilities or within the community but also resulted, in addition to the clonal transmissions, in at least a third more transmissions due to AMR plasmids.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0012125"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144002930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of MicroScan and VITEK 2 systems for susceptibility testing of Enterobacterales with updated breakpoints.","authors":"Sandra S Richter, Elizabeth L Dominguez, Aaron A Hupp, Matt Griffis, Shawn H MacVane","doi":"10.1128/jcm.00048-25","DOIUrl":"10.1128/jcm.00048-25","url":null,"abstract":"<p><p>We compared the performance of two commercial antimicrobial susceptibility testing (AST) systems for contemporary Enterobacterales strains using broth microdilution (BMD) as the reference standard with 2022 Clinical and Laboratory Standards Institute or current FDA breakpoints applied. Enterobacterales clinical isolates with BMD results were tested in parallel using VITEK 2 AST test cards (N802, XN15, bioMérieux, Hazelwood, MO, USA) and MicroScan NM56 AST panels (Beckman Coulter, Sacramento, CA, USA). The 200 isolates (57 <i>Escherichia coli</i>, 55 <i>Klebsiella pneumoniae</i>, 21 <i>Enterobacter cloacae</i> complex, 18 <i>Serratia marcescens</i>, 12 <i>Proteus mirabilis</i>, 10 <i>Citrobacter koseri</i>, 9 <i>Citrobacter freundii</i>, 8 <i>Klebsiella oxytoca</i>, 5 <i>Klebsiella aerogenes</i>, 3 <i>Providencia stuartii</i>, and 2 <i>Morganella morganii</i>) included 25% extended-spectrum beta-lactamase (ESBL), 23% carbapenem-resistant Enterobacterales (CRE), and 4.5% AmpC resistance phenotypes. For the 28 antimicrobial agents tested, essential agreement (EA, MIC within ±1 doubling dilution), categorical agreement (CA, same categorical interpretation: susceptible, intermediate, susceptible dose dependent, and resistant), and error rates were calculated using BMD as the reference standard. Time to results (TTR) was determined for each instrument for all 200 isolates. Hands-on time was assessed by timing two technologists each setting up six batches of five isolates on each system. Accuracy was similar between systems with an overall CA > 94% and EA ≥ 96%. The CA was ≥90% for most agents tested on both systems (exceptions were ampicillin-sulbactam, cefoxitin, minocycline, and nitrofurantoin). The MicroScan with Prompt inoculum preparation required less hands-on setup time than VITEK (1.29 vs 1.83 min/isolate). The median instrument TTR was less for VITEK (11.7 vs 18 hours, <i>P</i> < 0.001), yielding an overall faster turnaround time.IMPORTANCEThere are limited data directly comparing the performance of commercial antimicrobial susceptibility testing systems for contemporary bacterial strains using the Clinical and Laboratory Standards Institute broth microdilution method as the reference standard and applying updated breakpoints. These data will hopefully encourage labs to perform the necessary verification or validation studies needed to implement current breakpoints and ensure antimicrobial resistance is detected.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0004825"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144063866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}