Journal of Clinical Microbiology最新文献

{"title":"Specimen adequacy assay controls in nucleic acid amplification tests do not correlate with nasopharyngeal swab collection method","authors":"Katharine H. D. CrawfordMary Lynn BanieckiElizabeth G. DushinCassandra A. TierneyShunjie GuanLaurence L. StenslandAilyn C. Perez-OsorioAlexander L. Greninger1Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA2Pfizer, Inc., Cambridge, Massachusetts, USA3Pfizer, Inc., Groton, Connecticut, USA4Vaccine and Infectious Disease Division, Fred Hutchinson Research Center, Seattle, Washington, USARandall Hayden","doi":"10.1128/jcm.00975-24","DOIUrl":"https://doi.org/10.1128/jcm.00975-24","url":null,"abstract":"Journal of Clinical Microbiology, Ahead of Print. <br/>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"85 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identifying Candida auris transmission in a hospital outbreak investigation using whole-genome sequencing and SNP phylogenetic analysis","authors":"Brooks I. MitchellKendall KlingMaureen K. BolonShardul N. RathodMichael MalczynskiJavier RuizWanda PolancoKevin FritzSarah MaaliValentina StosorTeresa R. ZembowerChao Qi1Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA2Clinical Microbiology Laboratory, Northwestern Memorial Hospital, Chicago, Illinois, USA3Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA4Department of Healthcare Epidemiology and Infection Prevention, Northwestern Memorial Hospital, Chicago, Illinois, USAKimberly E. Hanson","doi":"10.1128/jcm.00680-24","DOIUrl":"https://doi.org/10.1128/jcm.00680-24","url":null,"abstract":"Journal of Clinical Microbiology, Ahead of Print. <br/>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"26 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A lipidomics-based method to eliminate negative urine culture in general population","authors":"Linda K. NarteyAbanoub MikhaelHelena PětrošováVictor YuenPamela KibseyMert PekcanRobert K. ErnstMichael X. ChenDavid R. Goodlett1Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada2Genome British Columbia proteomics center, University of Victoria, Victoria, British Columbia, Canada3Vancouver Island Health Authority, Vancouver, British Columbia, Canada4Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada5Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey6Department of Microbial Pathogenesis, University of Maryland, Baltimore, Maryland, USA7Division of Medical Sciences, University of Victoria, Victoria, British Columbia, CanadaPatricia J. Simner","doi":"10.1128/jcm.00819-24","DOIUrl":"https://doi.org/10.1128/jcm.00819-24","url":null,"abstract":"Journal of Clinical Microbiology, Ahead of Print. <br/>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"125 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of a dual antibody and antigen HCV immunoassay to standard of care algorithmic testing","authors":"Tina I. BuiAbigail P. BrownMeghan BrownSydney LawlessBrittany RoemmichNeil W. AndersonChristopher W. Farnsworth1Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, Saint Louis, Missouri, USA2Department of Pathology, University Hospitals Health System, Cleveland, Ohio, USARandall Hayden","doi":"10.1128/jcm.00832-24","DOIUrl":"https://doi.org/10.1128/jcm.00832-24","url":null,"abstract":"Journal of Clinical Microbiology, Ahead of Print. <br/>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"18 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predictive performance of urinalysis for urine culture results according to causative microorganisms: an integrated analysis with artificial intelligence","authors":"Min Hyuk ChoiDokyun KimHye Gyung BaeAe-Ran KimMikyeong LeeKyungwon LeeKyoung-Ryul LeeSeok Hoon Jeong1Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea2Seoul Clinical Laboratories, Yongin-si, South KoreaErin McElvania","doi":"10.1128/jcm.01175-24","DOIUrl":"https://doi.org/10.1128/jcm.01175-24","url":null,"abstract":"Journal of Clinical Microbiology, Ahead of Print. <br/>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"12 1","pages":"e0117524"},"PeriodicalIF":9.4,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142176574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Vaginitis and risk of sexually transmitted infections: results of a multi-center U.S. clinical study using STI nucleic acid amplification testing.","authors":"Jane R Schwebke, Paul Nyirjesy, Melissa Dsouza, Damon Getman","doi":"10.1128/jcm.00816-24","DOIUrl":"10.1128/jcm.00816-24","url":null,"abstract":"<p><p>Significant increases in rates of sexually transmitted infections (STIs) caused by <i>Trichomonas vaginalis</i> (TV), <i>Chlamydia trachomatis</i> (CT), <i>Neisseria gonorrhoeae</i> (NG), and <i>Mycoplasma genitalium</i> (MG) are occurring in the United States. We present results of a U.S. study examining the intersection of STIs and vaginitis. Among 1,051 women with diagnoses for the presence or absence of bacterial vaginosis (BV) and/or symptomatic vulvovaginal candidiasis (VVC), 195 (18.5%) had one or more STIs, including 101 (9.6%) with TV, 24 (2.3%) with CT, 9 (0.8%) with NG, and 93 (8.8%) with MG. STI prevalence in BV-positive women was 26.3% (136/518), significantly higher than STI prevalence of 12.5% (59/474) in BV-negative women (<i>P</i> < 0.0002). Unlike infections with CT or NG, solo infections of MG or TV were each significantly associated with a diagnosis of BV-positive/VVC-negative (OR 3.0751; 95% CI 1.5797-5.9858, <i>P</i> = 0.0113, and OR 2.873; 95% CI 1.5687-5.2619, <i>P</i> = 0.0017, respectively) and with mixed infections containing MG and TV (OR 3.4886; 95% CI 1.8901-6.439, <i>P</i> = 0.0042, and OR 3.1858; 95% CI 1.809-5.6103, <i>P</i> = 0.0014, respectively). TV and MG infection rates were higher in all Nugent score (NS) categories than CT and NG infection rates; however, both STIs had similar comparative prevalence ratios to CT in NS 6-10 vs NS 0-5 (CT: 3.06% vs 1.4%, 2.2-fold; MG: 10.7% vs 6.1%, 1.8-fold; TV: 14.5% vs 7.0%, 2.1-fold). NG prevalence was relatively invariant by the NS category. These results highlight the complexity of associations of STIs with two major causes of vaginitis and underscore the importance of STI testing in women seeking care for abnormal vaginal discharge and inflammation.</p><p><strong>Importance: </strong>This study reports high rates for sexually transmitted infections (STIs) in women seeking care for symptoms of vaginitis and bacterial vaginosis, revealing highly complex associations of STIs with two of the major causes of vaginal dysbiosis. These results underscore the importance of STI testing in women seeking care for abnormal vaginal discharge and inflammation.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0081624"},"PeriodicalIF":6.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11389145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975831","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 expired BD BACTEC blood culture vials.","authors":"Erik H Klontz, Lisa A Milien, David Lucier, Anand S Dighe, John A Branda, Sarah E Turbett","doi":"10.1128/jcm.01082-24","DOIUrl":"10.1128/jcm.01082-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0108224"},"PeriodicalIF":6.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11389134/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141855702","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":"Bridging the gap between molecular and genomic epidemiology in tuberculosis: inferring MIRU-VNTR patterns from genomic data.","authors":"Sergio Buenestado-Serrano, Miguel Martínez-Lirola, Anzaan Dippenaar, Amadeo Sanz-Pérez, José Antonio Garrido-Cárdenas, Ana Belén Esteban-García, Adriana Justine García-Toledo, Cristina Rodríguez-Grande, Marta Herranz-Martín, Sheri M Saleeb, Patricia Muñoz, Robin M Warren, Laura Pérez-Lago, Darío García de Viedma","doi":"10.1128/jcm.00741-24","DOIUrl":"10.1128/jcm.00741-24","url":null,"abstract":"<p><p>The transition from MIRU-VNTR-based epidemiology studies in tuberculosis (TB) to genomic epidemiology has transformed how we track transmission. However, short-read sequencing is poor at analyzing repetitive regions such as the MIRU-VNTR loci. This causes a gap between the new genomic data and the large amount of information stored in historical databases. Long-read sequencing could bridge this knowledge gap by allowing analysis of repetitive regions. However, the feasibility of extracting MIRU-VNTRs from long reads and linking them to historical data has not been evaluated. In our study, an <i>in silico</i> arm, consisting of inference of MIRU patterns from long-read sequences (using MIRUReader program), was compared with an experimental arm, involving standard amplification and fragment sizing. We analyzed overall performance on 39 isolates from South Africa and confirmed reproducibility in a sample enriched with 62 clustered cases from Spain. Finally, we ran 25 consecutive incident cases, demonstrating the feasibility of correctly assigning new clustered/orphan cases by linking data inferred from genomic analysis to MIRU-VNTR databases. Of the 3,024 loci analyzed, only 11 discrepancies (0.36%) were found between the two arms: three attributed to experimental error and eight to misassigned alleles from long-read sequencing. A second round of analysis of these discrepancies resulted in agreement between the experimental and <i>in silico</i> arms in all but one locus. Adjusting the MIRUReader program code allowed us to flag potential <i>in silico</i> misassignments due to suboptimal coverage or unfixed double alleles. Our study indicates that long-read sequencing could help address potential chronological and geographical gaps arising from the transition from molecular to genomic epidemiology of tuberculosis.</p><p><strong>Importance: </strong>The transition from molecular epidemiology in tuberculosis (TB), based on the analysis of repetitive regions (VNTR-based genotyping), to genomic epidemiology transforms in the precision with which we track transmission. However, short-read sequencing, the most common method for performing genomic analysis, is poor at analyzing repetitive regions. This means that we face a gap between the new genomic data and the large amount of information stored in historical databases, which is also an obstacle to cross-national surveillance involving settings where only molecular data are available. Long-read sequencing could help bridge this knowledge gap by allowing analysis of repetitive regions. Our study demonstrates that MIRU-VNTR patterns can be successfully inferred from long-read sequences, allowing the correct assignment of new cases as clustered/orphan by linking new data extracted from genomic analysis to historical MIRU-VNTR databases. Our data may provide a starting point for bridging the knowledge gap between the molecular and genomic eras in tuberculosis epidemiology.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0074124"},"PeriodicalIF":6.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11389143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141971224","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 detection of mycobacteria in CF and tissue samples grown in mycobacteria growth indicator tube incubated at 30°C compared to conventional growth conditions of liquid and solid media.","authors":"J Kehrmann, A L Stumpf, A Dragaqina, J Buer","doi":"10.1128/jcm.00683-24","DOIUrl":"10.1128/jcm.00683-24","url":null,"abstract":"<p><p>This study evaluates the growth of mycobacteria in samples from cystic fibrosis (CF) patients and tissue samples using the mycobacteria growth indicator tube (MGIT) incubated at 30°C in comparison to conventional MGIT cultures incubated at 37°C in a BACTEC MGIT 960 device and solid media incubated at 36°C and 30°C. A total of 1,549 samples were analyzed, of which 202 mycobacterial isolates were cultured from 197 positive specimens, including five mixed cultures. The highest detection rate was achieved from MGIT at 30°C, with 84.2% of mycobacterial isolates (170 of 202), which was significantly higher than any other culture condition (<i>P</i> < 0.0001 for any condition). MGIT at 37°C yielded 61.4% (124 of 202) of the recovered isolates, whereas Löwenstein Jensen (LJ) and Stonebrink at 36°C, and LJ and Stonebrink at 30°C retrieved 47.0% (95), 49.5% (100), 50.0% (101), and 53.0% (107) of the isolates, respectively. Of the 53 isolates that were grown exclusively under one culture condition, the highest number of isolates (36) was recovered from MGIT incubated at 30°C. MGIT at 37°C recovered eight of the 53 isolates, whereas LJ incubated at 30°C and Stonebrink incubated at 30°C and 36°C recovered five, three, and one isolate, respectively. No isolates were grown exclusively from LJ incubated at 36°C. In CF patients and tissue samples, MGIT cultivated at 30°C for 8 weeks increases the performance of mycobacterial culture.</p><p><strong>Importance: </strong>Our study shows that the addition of mycobacteria growth indicator tube (MGIT) liquid culture incubated at 30°C improves the detection of mycobacteria from CF and tissue samples. MGIT incubated at 30°C recovered significantly more mycobacterial isolates than MGIT incubated at 37°C and significantly more isolates than either Lowenstein Jensen or Stonebrink solid media incubated at either 36°C or 30°C. Of 202 mycobacterial isolates recovered from 1,549 specimens, 170 were recovered from MGIT incubated at 30°C, followed by MGIT incubated at 37°C with 124 isolates and solid media culture conditions that recovered between 95 and 107 mycobacterial isolates. All conventional culture conditions combined without MGIT incubated at 30°C recovered 166 isolates. MGIT incubated at 30°C recovered the highest number of isolates detected exclusively by a single culture condition and recovered mycobacterial isolates of highly relevant mycobacterial species, including <i>Mycobacterium abscessus</i> and <i>Mycobacterium tuberculosis</i>.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0068324"},"PeriodicalIF":6.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11389136/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141971225","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 Brief Case: Tricky Trichosporon asahii in the urinary tract","authors":"Michaela J. EickhoffRebekah E. Dumm1Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USAAlexander J. McAdam","doi":"10.1128/jcm.00557-24","DOIUrl":"https://doi.org/10.1128/jcm.00557-24","url":null,"abstract":"Journal of Clinical Microbiology, Volume 62, Issue 9, September 2024. <br/>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"8 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142176622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}