Journal of Clinical Microbiology最新文献

{"title":"Monocentric evaluation of the Novaplex dermatophyte multiplex qPCR assay in the diagnosis of dermatophytoses.","authors":"Florian Harel, Florence Robert-Gangneux, Jean-Pierre Gangneux, Hélène Guegan","doi":"10.1128/jcm.00894-24","DOIUrl":"10.1128/jcm.00894-24","url":null,"abstract":"<p><p>Superficial fungal infections caused by dermatophytes are a prevalent global health concern. Rapid and accurate diagnosis of these pathogens through molecular tools would offer a substantial advantage for early detection and effective treatment. The conventional fungal culture presents inherent limitations, including extended result delivery delay and variable sensitivity. This study aimed to evaluate the performance of the multiplex real-time PCR Novaplex dermatophyte assay (Seegene) in comparison to traditional mycological methods including direct examination and culture. A total of 312 nail, skin, and scalp samples collected from patients with suspected superficial fungal infections for mycological diagnosis were retrospectively subjected to the Novaplex dermatophyte assay. Overall, 170 (54.6%) and 186 (59.6%) samples tested positive for dermatophyte culture and dermatophyte PCR, respectively. The concordance between PCR and culture for dermatophyte detection was 87.2%. There were 158 culture-positive/PCR-positive samples, 12 culture-positive/PCR-negative samples, and 28 culture-negative/PCR-positive samples. The sensitivity of PCR against culture varied according to the dermatophyte target, ranging from 90.5% (<i>Trichophyton mentagrophytes/interdigitale/benhamiae</i>), 91.2% (<i>Trichophyton rubrum</i>), to 100% (<i>Microsporum</i> spp. and <i>Trichophyton tonsurans</i>). When considering the final diagnosis using composite criteria, the sensitivity and specificity for the diagnosis of dermatophytosis were 92.9% and 96.6% for PCR, 86.7% and 100% for culture, and 95.4% and 92.2% for direct examination and culture combined, respectively. The Seegene Novaplex dermatophyte assay is an easy-to-use automated one-step extraction-PCR system that offers satisfactory performance for routine diagnosis of dermatophytoses in clinical laboratories, particularly in non-specialized centers. However, it cannot fully replace conventional mycology due to its inability to detect mold infections and to identify dermatophytes at the species level.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0089424"},"PeriodicalIF":6.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142347642","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":"Defining the value of medical microbiology consultation.","authors":"Kyle G Rodino, Paul M Luethy, April N Abbott, Jeffrey M Bender, Allison R Eberly, Melissa Gitman, Amy Leber, Jennifer Dien Bard","doi":"10.1128/jcm.00359-24","DOIUrl":"10.1128/jcm.00359-24","url":null,"abstract":"<p><p>Medical microbiologists, defined as doctoral-level laboratory directors with subspecialty training in medical microbiology, lead the clinical laboratory operations through activities such as clinical consultations, oversight of diagnostic testing menu, institutional leadership, education, and scholastic activities. However, unlike their clinical colleagues, medical microbiologists are largely unable to bill for clinical consultations performed within the hospital and, therefore, unable to generate relative value units or a similar quantifiable metric. As hospital budgets tighten and justification of staffing becomes a necessity, this may present a challenge to the medical microbiologist attempting to prove their value to the organization. To aid in providing tangible data, the Personnel Standards and Workforce subcommittee of the American Society for Microbiology conducted a multi-center study across seven medical centers to document clinical consultations and their impact. Consults were generated equally from internal (laboratory-based) and external (hospital-based) parties, with the majority directly impacting patient management. Near universal acceptance of the medical microbiologist's recommendation highlights the worth derived from their expertise. External consults required more time commitment from the medical microbiologist than internal consults, although both presented ample opportunity for secondary value, including impact through stewardship, education, clinical guidance, and cost reduction. This study is a description of the content and impact of consultations that underscore the importance of the medical microbiologist as a key member of the healthcare team.</p><p><strong>Importance: </strong>Medical microbiologists are invaluable to the clinical microbiology laboratory and the healthcare system as a whole. However, as medical microbiologists do not regularly generate relative value units, capturing and quantifying the value provided is challenging. As hospital budgets tighten, justification of staffing becomes a necessity. To aid in providing tangible data, the Personnel Standards and Workforce subcommittee of the American Society for Microbiology conducted a multi-center study across seven medical centers to document clinical consultations and their impact. To our knowledge, this is the first study to provide detailed evaluation of the consultative value provided by medical microbiologists.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0035924"},"PeriodicalIF":6.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141432001","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 an expanded antibiotic resistance gene panel on prediction of antimicrobial susceptibility results for Gram-negative bacteria in blood cultures.","authors":"Carmila Manuel, Richard Maynard, Synthia Simpkins, Michelle Haro, Romney Humphries","doi":"10.1128/jcm.01020-24","DOIUrl":"10.1128/jcm.01020-24","url":null,"abstract":"<p><p>The QIAstat-Dx BCID Panels (RUO) (\"QIAstat,\" QIAGEN, Hilden, Germany) for identification of 13 Gram-negative bacteria and 18 antimicrobial resistance (AMR) gene groups was evaluated. The study was conducted in two phases; in phase 1, analytical performance was evaluated against 154 challenge isolates against whole genome sequencing data. In this phase, sensitivity and specificity of organism identification calls were 153/154 (99.3%) and 1,748/1,749 (99.8%), respectively. For AMR genes, sensitivity was 434/435 (99.8%) and specificity was 2,334/2,337 (99.9%). One false-negative <i>bla</i>_IMP, one false-positive <i>bla</i>_CTX-M, and two false-positive aac-6'-lb detections were noted in this challenge set of organisms. In phase 2, 101 clinical blood culture isolates of Gram-negative rods were evaluated by the multiplexed PCR versus reference broth microdilution, for the ability of identification combined with AMR genes to predict final susceptibility results. Negative predictive values were 92.8% for ampicillin resistance (100% for <i>Escherichia coli</i>), 93.4% for ceftriaxone, 97.4% for ceftazidime, and 98.7% for cefepime. In constrast, negative predictive values for current standard of care (identification plus detection of <i>bla</i>_CTX-M) ranged from 56.5% to 88.8%. This study demonstrated additive value of additional beta-lactamase genes for bacteria isolated from blood cultures.</p><p><strong>Importance: </strong>Prediction of Gram-negative bacteria resistance through detection of resistance genes is complex. This study evaluated a novel, direct-from-blood or bacterial isolate multiplexed PCR for the detection of 17 resistance genes, and evaluated the prediction of antimicrobial susceptibility.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0102024"},"PeriodicalIF":6.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142288395","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":"Analytical and clinical validation of direct detection of antimicrobial resistance markers by plasma microbial cell-free DNA sequencing.","authors":"Fred C Christians, Jamilla Akhund-Zade, Kristin Jarman, Shivkumar Venkatasubrahmanyam, Nicholas Noll, Timothy A Blauwkamp, Sivan Bercovici, Aga Zielinska, Amy L Carr, Arryn Craney, Matthew Pike, John Joseph Farrell, Sanjeet Dadwal, James B Wood, Efrat Matkovich, Staci McAdams, Frederick S Nolte","doi":"10.1128/jcm.00425-24","DOIUrl":"10.1128/jcm.00425-24","url":null,"abstract":"<p><p>Sequencing of plasma microbial cell-free DNA (mcfDNA) has gained increased acceptance as a valuable adjunct to standard-of-care testing for diagnosis of infections throughout the body. Here, we report the analytical and clinical validation of a novel application of mcfDNA sequencing, the non-invasive detection of seven common antimicrobial resistance (AMR) genetic markers in 18 important pathogens. The AMR markers include SCC<i>mec</i>, <i>mecA, mecC</i>, <i>vanA, vanB</i>, <i>bla</i>_CTX-M, and <i>bla</i>_KPC. The AMR markers were computationally linked to the pathogens detected. Analytical validation showed high reproducibility (100%), inclusivity (54 to 100%), and exclusivity (100%). Clinical accuracy was assessed with 114 unique plasma samples from patients at seven study sites with concordant culture results for target bacteria from a variety of specimen types and correlated with available phenotypic antimicrobial susceptibility test results and genotypic results. The positive percent agreement (PPA), negative percent agreement (NPA), and diagnostic yield (DY) were estimated for each AMR marker. DY was defined as the percentage of tests that yielded an actionable result of either detected or not detected. The results for the combination of SCC<i>mec</i> and <i>mecA</i> for staphylococci were PPA 19/20 (95.0%), NPA 21/22 (95.4%), DY 42/60 (70.0%); <i>vanA</i> for enterococci were PPA 3/3 (100%), NPA 2/2 (100%), DY 5/6 (83.3%); <i>bla</i>_CTX-M for gram-negative bacilli were PPA 5/6 (83.3%), NPA 29/29 (100%), DY 35/49 (71.4%); and <i>bla</i>_KPC for gram-negative bacilli were PPA 0/2 (0%), NPA: 23/23 (100%), DY 25/44 (56.8%). The addition of AMR capability to plasma mcfDNA sequencing should provide clinicians with an effective new culture-independent tool for optimization of therapy.</p><p><strong>Importance: </strong>This manuscript is ideally suited for the Innovative Diagnostic Methods sections as it reports the analytical and clinical validation of a novel application of plasma microbial cell-free DNA sequencing for direct detection of seven selected antimicrobial resistance markers in 18 target pathogens. Clearly, it has potential clinical utility in optimizing therapy and was incorporated into the Karius test workflow in September 2023. In addition, the workflow could readily be adapted to expand the number of target bacteria and antimicrobial resistance markers as needed.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0042524"},"PeriodicalIF":6.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080484","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":"Serosurveillance of <i>Coxiella burnetii</i> in feral swine populations of Hawai'i and Texas identifies overlap with human Q fever incidence.","authors":"Ian A McMillan, Michael H Norris, Samuel J Golon, Gregory A Franckowiak, James M Grinolds, Samuel M Goldstein, Darrin M Phelps, Michael J Bodenchuk, Bruce R Leland, Richard A Bowen, Vienna R Brown, Bradley R Borlee","doi":"10.1128/jcm.00780-24","DOIUrl":"10.1128/jcm.00780-24","url":null,"abstract":"<p><p>Feral swine are invasive in the United States and a reservoir for infectious diseases. The increase in feral swine population and the geographic range are a concern for the spread of zoonotic diseases to humans and livestock. Feral swine could contribute to the spread of <i>Coxiella burnetii,</i> the causative agent of human Q fever. In this study, we characterized the seroprevalence of <i>C. burnetii</i> in feral swine populations of Hawai'i and Texas, which have low and high rates of human Q fever, respectively. Seropositivity rates were as high as 0.19% and 6.03% in Hawai'i and Texas, respectively, indicating that feral swine cannot be ruled out as a potential reservoir for disease transmission and spread. In Texas, we identified the overlap between seropositivity of feral swine and human Q fever incidence. These results indicate that there is a potentially low but detectable risk of <i>C. burnetii</i> exposure associated with feral swine populations in Hawai'i and Texas.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0078024"},"PeriodicalIF":6.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142072986","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":"Performance of MALDI-TOF MS, real-time PCR, antigen detection, and automated biochemical testing for the identification of <i>Burkholderia pseudomallei</i>.","authors":"Stuart Campbell, Brooke Taylor, Dimitrios Menouhos, Jann Hennessy, Mark Mayo, Robert Baird, Bart J Currie, Ella M Meumann","doi":"10.1128/jcm.00961-24","DOIUrl":"10.1128/jcm.00961-24","url":null,"abstract":"<p><p><i>Burkholderia pseudomallei</i> is the causative agent of melioidosis, a disease highly endemic to Southeast Asia and northern Australia, though the area of endemicity is expanding. Cases may occur in returning travelers or, rarely, from imported contaminated products. Identification of <i>B. pseudomallei</i> is challenging for laboratories that do not see this organism frequently, and misidentifications by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and automated biochemical testing have been reported. The <i>in vitro</i> diagnostic database for use with the Vitek MS has recently been updated to include <i>B. pseudomallei</i> and we aimed to validate the performance for identification in comparison to automated biochemical testing with the Vitek 2 GN card, quantitative real-time polymerase chain reaction (qPCR) targeting the type III secretion system, and capsular polysaccharide antigen detection using a lateral flow immunoassay (LFA). We tested a \"derivation\" cohort including geographically diverse <i>B. pseudomallei</i> and a range of closely related <i>Burkholderia</i> species, and a prospective \"validation\" cohort of <i>B. pseudomallei</i> and <i>B. cepacia</i> complex clinical isolates. MALDI-TOF MS had a sensitivity of 1.0 and specificity of 1.0 for the identification and differentiation of <i>B. pseudomallei</i> from related <i>Burkholderia</i> species when a certainty cutoff of 99.9% was used. In contrast, automated biochemical testing for <i>B. pseudomallei</i> identification had a sensitivity of 0.83 and specificity of 0.88. Both qPCR and LFA correctly identified all <i>B. pseudomallei</i> isolates with no false positives. Due to the high level of accuracy, we have now incorporated MALDI-TOF MS into our laboratory's <i>B. pseudomallei</i> identification workflow.IMPORTANCE<i>Burkholderia pseudomallei</i> causes melioidosis, a disease associated with high morbidity and mortality that disproportionately affects rural areas in Southeast Asia and northern Australia. The known area of endemicity is expanding and now includes the continental United States. Laboratory identification can be challenging which may result in missed or delayed diagnoses and poor patient outcomes. In this study, we compared mass spectrometry using an updated spectral database with multiple other methods for <i>B. pseudomallei</i> identification and found mass spectrometry highly accurate. We have therefore incorporated this fast and cost-effective method into our laboratory's workflow for <i>B. pseudomallei</i> identification.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0096124"},"PeriodicalIF":6.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132880","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":"Valid and accepted novel bacterial taxa isolated from non-domestic animals and taxonomic revisions published in 2023.","authors":"Erik Munson, Claire R Burbick, Sara D Lawhon, Trinity Krueger, Elena Ruiz-Reyes","doi":"10.1128/jcm.01042-24","DOIUrl":"10.1128/jcm.01042-24","url":null,"abstract":"<p><p>Continued investigation into the bacteria associated with non-domestic animals provides important information for recognizing normal flora, assessing the health status of these unique species of animals, and identifying new or emerging pathogens of concern. In this summary of novel taxa and taxonomic revisions, considerable additions have been made toward understanding fecal and mucosal flora in multiple wild animal species. In addition, novel pathogenic bacteria are discussed, including multiple <i>Chlamydia</i> spp. causing disease in a hawk and crocodile, two <i>Corynebacterium</i> spp. causing oral lesions in penguins and a lesser-known genus, <i>Mergibacter</i> within Family <i>Pasteurellaceae</i>, causing disease in multiple wild bird species. Finally, a few revisions to bacteria isolated from normal non-domestic animal body sites are mentioned.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0104224"},"PeriodicalIF":6.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142347644","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":"Outbreak-associated <i>Salmonella</i> Baildon found in wastewater demonstrates how sewage monitoring can supplement traditional disease surveillance.","authors":"Nkuchia M M'ikanatha, Zoe S Goldblum, Nicholas Cesari, Erin M Nawrocki, Yezhi Fu, Jasna Kovac, Edward G Dudley","doi":"10.1128/jcm.00825-24","DOIUrl":"10.1128/jcm.00825-24","url":null,"abstract":"<p><p>Non-typhoidal <i>Salmonella</i> is a common cause of gastroenteritis worldwide, but current non-typhoidal <i>Salmonella</i> surveillance is suboptimal. Here, we evaluated the utility of wastewater monitoring to enhance traditional surveillance for this foodborne pathogen. In June 2022, we tested raw sewage collected twice a week from two treatment plants in central Pennsylvania for non-typhoidal <i>Salmonella</i> and characterized isolates using whole-genome sequencing. We recovered 43 <i>Salmonella</i> isolates from wastewater samples, differentiated by genomic analysis into seven serovars: 16 Panama (37.2%), 9 Senftenberg (20.9%), 8 Baildon (18.6%), and 3 or fewer of four other serovars. We assessed genetic relatedness and epidemiologic links between these wastewater isolates with those from patients with salmonellosis. All <i>S</i>. Baildon isolates from wastewater were genetically similar to those associated with a known contemporaneous salmonellosis outbreak. <i>S</i>. Baildon from wastewater and 42 outbreak-related isolates in the national outbreak detection database had the same core genome multilocus sequence typing, and outbreak code differed by zero or one single polynucleotide polymorphism. One of the 42 outbreak-related isolates was obtained from a patient residing in the wastewater sample collection catchment area, which serves approximately 17000 people. <i>S</i>. Baildon is a rare serovar (reported in <1% cases nationally, over five years). Our study underscores the value of monitoring sewage from a defined population to supplement traditional surveillance methods for the evidence of <i>Salmonella</i> infections and to determine the extent of outbreaks.IMPORTANCEDuring the COVID-19 pandemic, monitoring for SARS-CoV-2 in wastewater was highly effective in identifying the variants of concern earlier than clinical surveillance methods. Here, we show that monitoring domestic sewage can also augment traditional reporting of foodborne illnesses to public health authorities. Our study detected multiple <i>Salmonella enterica</i> serovars in samples from two wastewater treatment plants in central Pennsylvania. Using whole-genome sequencing, we demonstrated that the isolates of variant <i>S</i>. Baildon clustered with those from a foodborne salmonellosis outbreak that occurred in a similar time frame. Cases were primarily from Pennsylvania, and one individual lived within the wastewater treatment catchment area. This study highlights the effectiveness of domestic sewage testing as a proactive public health strategy to track and respond to infectious disease outbreaks.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0082524"},"PeriodicalIF":6.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481576/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142288321","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":"Nationwide upsurge in invasive disease in the context of longitudinal surveillance of carriage and invasive <i>Streptococcus pyogenes</i> 2009-2023, the Netherlands: a molecular epidemiological study.","authors":"Lidewij W Rümke, Matthew A Davies, Stefan M T Vestjens, Boas C L van der Putten, Wendy C M Bril-Keijzers, Marlies A van Houten, Nynke Y Rots, Alienke J Wijmenga-Monsuur, Arie van der Ende, Brechje de Gier, Bart J M Vlaminckx, Nina M van Sorge","doi":"10.1128/jcm.00766-24","DOIUrl":"10.1128/jcm.00766-24","url":null,"abstract":"<p><p>Since 2022, many countries have reported an upsurge in invasive group A streptococcal (iGAS) infections. We explored whether changes in <i>Streptococcus pyogenes</i> carriage rates or emergence of strains with potentially altered virulence, such as <i>emm</i>1 variants M1_UK and M1_DK, contributed to the 2022/2023 surge in the Netherlands. We determined <i>emm</i> (sub)type distribution for 2,698 invasive and 351 <i>S</i>. <i>pyogenes</i> carriage isolates collected between January 2009 and March 2023. Genetic evolution of <i>emm</i>1 was analyzed by whole-genome sequencing of 497 <i>emm</i>1 isolates. The nationwide iGAS upsurge coincided with a sharp increase of <i>emm</i>1.0 from 18% (18/100) of invasive isolates in Q1 2022 to 58% (388/670) in Q1 2023 (Fisher's exact test, <i>P</i> < 0.0001). M1_UK became dominant among invasive <i>emm</i>1 isolates in 2016 and further expanded from 72% in Q1 2022 to 96% in Q1 2023. Phylogenetic comparison revealed evolution and clonal expansion of four new M1_UK clades in 2022/2023. DNase Spd1 and superantigen SpeC were acquired in 9% (46/497) of <i>emm</i>1 isolates. <i>S. pyogenes</i> carriage rates and <i>emm</i>1 proportions in carriage isolates remained stable during this surge, and the expansion of M1_UK in iGAS was not reflected in carriage isolates. During the 2022/2023 iGAS surge in the Netherlands, expansion of four new M1_UK clades was observed among invasive isolates, but not carriage isolates, suggesting increased virulence and fitness of M1_UK compared to contemporary M1 strains. The emergence of more virulent clades has important implications for public health strategies such as antibiotic prophylaxis for close contacts of iGAS patients.IMPORTANCEThis study describes the molecular epidemiology of invasive group A streptococcal (iGAS) infections in the Netherlands based on >3,000 <i>Streptococcus pyogenes</i> isolates from both asymptomatic carriers and iGAS patients collected before, during, and after the COVID-19 pandemic period (2009-2023) and is the first to assess whether changes in carriage rates or carried <i>emm</i> types contributed to the alarming post-COVID-19 upsurge in iGAS infections. We show that the 2022/2023 iGAS surge coincided with a sharp increase of <i>emm</i>1, particularly the toxicogenic M1_UK variant, in invasive isolates, but not in carriage isolates. These findings suggest that increased virulence and fitness of M1_UK likely contributes to an increased dissemination between hosts. The emergence of a more virulent and fit lineage has important implications for iGAS control interventions such as antibiotic prophylaxis for close contacts of iGAS patients and calls for a reappraisal of iGAS control interventions and guidelines.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0076624"},"PeriodicalIF":6.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080486","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 foundation for the microbiology laboratory's essential role in diagnostic stewardship: an ASM Laboratory Practices Subcommittee report.","authors":"Rebekah E Dumm, Elizabeth M Marlowe, Logan Patterson, Paige M K Larkin, Rosemary C She, Laura M Filkins","doi":"10.1128/jcm.00960-24","DOIUrl":"10.1128/jcm.00960-24","url":null,"abstract":"<p><p>Diagnostic stewardship (DxS) has gained traction in recent years as a cross-disciplinary method to improve the quality of patient care while appropriately managing resources within the healthcare system. Clinical microbiology laboratorians have been highly engaged in DxS efforts to guide best practices with conventional microbiology tests and more recently with molecular infectious disease diagnostics. Laboratories can experience resistance to their role in DxS, especially when the clinical benefits, motivations for interventions, and underlying regulatory requirements are not clearly conveyed to stakeholders. Clinical laboratories must not only ensure ethical practices but also meet obligatory requirements to steward tests responsibly. In this review, we aim to support clinical microbiology laboratorians by providing the background and resources that demonstrate the laboratory's essential role in DxS. The heart of this review is to collate regulatory and accreditation requirements that, in essence, mandate DxS practices as a long-standing, core element of high-quality laboratory testing to deliver the best possible patient care. While examples of the clinical impact of DxS are plentiful in the literature, here, we focus on the operational and regulatory justification for the laboratory's role in stewardship activities.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0096024"},"PeriodicalIF":6.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142347643","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}