Journal of Clinical Microbiology最新文献

{"title":"Comparison of the sensitivity and specificity of commercial anti-dengue virus IgG tests to identify persons eligible for dengue vaccination.","authors":"Freddy A Medina, Frances Vila, Laura E Adams, Jaime Cardona, Jessica Carrion, Elaine Lamirande, Luz N Acosta, Carlos M De León-Rodríguez, Manuela Beltran, Demian Grau, Vanessa Rivera-Amill, Angel Balmaseda, Eva Harris, Zachary J Madewell, Stephen H Waterman, Gabriela Paz-Bailey, Stephen Whitehead, Jorge L Muñoz-Jordán","doi":"10.1128/jcm.00593-24","DOIUrl":"10.1128/jcm.00593-24","url":null,"abstract":"<p><p>The Advisory Committee on Immunization Practices (ACIP) recommended that dengue pre-vaccination screening tests for Dengvaxia administration have at least 98% specificity and 75% sensitivity. This study evaluates the performance of commercial anti-DENV IgG tests to identify tests that could be used for pre-vaccination screening. First, for seven tests, we evaluated sensitivity and specificity in early convalescent dengue virus (DENV) infection, using 44 samples collected 7-30 days after symptom onset and confirmed by RT-PCR. Next, for the five best-performing tests and two additional tests (with and without an external test reader) that became available later, we evaluated performance to detect past dengue infection among a panel of 44 specimens collected in 2018-2019 from healthy 9- to 16-year-old children from Puerto Rico. Finally, a full-scale evaluation was done with the four best-performing tests using 400 specimens from the same population. We used virus focus reduction neutralization test and an in-house DENV IgG ELISA as reference standards. Of seven tests, five showed ≥75% sensitivity in detecting anti-DENV IgG in early convalescent specimens with low cross-reactivity to the Zika virus. For the detection of previous DENV infections, the tests with the highest performance were the Euroimmun NS1 IgG ELISA (sensitivity 84.5%, specificity 97.1%) and CTK Dengue IgG rapid test R0065C with the test reader (sensitivity 76.2% specificity 98.1%). There are IgG tests available that can be used to accurately classify individuals with previous DENV infection as eligible for dengue vaccination to support safe vaccine implementation.</p><p><strong>Importance: </strong>The Advisory Committee on Immunization Practices (ACIP) has set forth recommendations that dengue pre-vaccination screening tests must exhibit at least 98% specificity and 75% sensitivity. Our research rigorously assesses the performance of various commercial tests against these benchmarks using well-characterized specimens from Puerto Rico. The findings from our study are particularly relevant given FDA approval and ACIP recommendation of Sanofi Pasteur's Dengvaxia vaccine, highlighting the need for accurate pre-vaccination screening tools.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080485","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":"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":"https://doi.org/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":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adenovirus infections: new insights for the clinical laboratory.","authors":"Adriana E Kajon","doi":"10.1128/jcm.00836-22","DOIUrl":"https://doi.org/10.1128/jcm.00836-22","url":null,"abstract":"<p><p>Since their discovery in 1953, research on human adenoviruses (HAdVs) has had diverse foci, resulted in groundbreaking discoveries, such as gene splicing, and generated powerful oncolytic constructs and expression vectors for vaccine development and gene therapy. In contrast, virologists working in this field have made relatively little progress toward the prevention and treatment of the wide spectrum of HAdV-associated diseases. The understanding of species-specific features of viral pathogenesis, or of the mechanisms underlying the establishment of latency and reactivation, is still limited. This group of viruses currently comprises 7 species, 51 serotypes, and 116 unique genotypes. This complexity manifests with a challenging pathophenotypic diversity. Some types are highly virulent, and others do not seem to cause disease in immunocompetent hosts. The assessment of viral load in blood and respiratory specimens has well-acknowledged clinical utility, but the lack of virus typing capabilities easily implementable in clinical laboratories represents a lingering major limitation to the interpretation of positive tests. Some HAdV infections do have severe consequences for both immunocompetent and immunocompromised patients, and the understanding of why this is the case will require more research. Clinical isolates and collections of positive specimens can provide unique resources to investigate the molecular bases of viral virulence and fitness and also help gather information of spatial-temporal patterns of viral circulation in susceptible communities, but they are extremely scarce. Clinical laboratories are underutilized interfaces between patients and academic scientists and have, therefore, a high potential to become valuable collaborators in research moving forward.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142072985","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 retrospective observational study of mNGS test utilization to examine the role of diagnostic stewardship at two academic medical centers.","authors":"Ryan C Shean, Elizabeth Garrett, James Malleis, Joshua A Lieberman, Benjamin T Bradley","doi":"10.1128/jcm.00605-24","DOIUrl":"https://doi.org/10.1128/jcm.00605-24","url":null,"abstract":"<p><p>Given the cost and unclear clinical impact of metagenomic next-generation sequencing (mNGS), laboratory stewardship may improve utilization. This retrospective observational study examines mNGS results from two academic medical centers employing different stewardship approaches. Eighty mNGS orders [54 cerebrospinal fluid (CSF) and 26 plasma] were identified from 2019 to 2021 at the University of Washington (UW), which requires director-level approval for mNGS orders, and the University of Utah (Utah), which does not restrict ordering. The impact of mNGS results and the relationship to traditional microbiology orders were evaluated. Nineteen percent (10/54) of CSF and 65% (17/26) of plasma studies detected at least one organism. Compared to CSF results, plasma results more frequently identified clinically significant organisms (31% vs 7%) and pathogens not detected by traditional methods (12% vs 0%). Antibiotic management was more frequently impacted by plasma versus CSF results (31% vs 4%). These outcome measures were not statistically different between study sites. The number and cumulative cost of traditional microbiology tests at UW were greater than Utah for CSF mNGS testing (UW: 46 tests, $6,237; Utah: 26 tests, $2,812; <i>P</i> < 0.05) but similar for plasma mNGS (UW: 31 tests, $3,975; Utah: 21 tests, $2,715; <i>P</i> = 0.14). mNGS testing accounted for 30%-50% of the total microbiology costs. Improving the diagnostic performance of mNGS by stewardship remains challenging due to low positivity rates and difficulties assessing clinical impact. From a fiscal perspective, stewardship efforts should focus on reducing testing in low-yield populations given the high costs of mNGS relative to overall microbiology testing expenditures.</p><p><strong>Importance: </strong>Metagenomic next-generation sequencing (mNGS) stewardship practices remain poorly standardized. This study aims to provide actionable insights for institutions that seek to reduce the unnecessary usage of mNGS. Importantly, we highlight that clinical impact remains challenging to measure without standardized guidelines, and we provide an actual cost estimate of microbiology expenditures on individuals undergoing mNGS.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142004348","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 multicenter study on accuracy and reproducibility of nanopore sequencing-based genotyping of bacterial pathogens.","authors":"Johanna Dabernig-Heinz, Mara Lohde, Martin Hölzer, Adriana Cabal, Rick Conzemius, Christian Brandt, Matthias Kohl, Sven Halbedel, Patrick Hyden, Martin A Fischer, Ariane Pietzka, Beatriz Daza, Evgeny A Idelevich, Anna Stöger, Karsten Becker, Stephan Fuchs, Werner Ruppitsch, Ivo Steinmetz, Christian Kohler, Gabriel E Wagner","doi":"10.1128/jcm.00628-24","DOIUrl":"https://doi.org/10.1128/jcm.00628-24","url":null,"abstract":"<p><p>Nanopore sequencing has shown the potential to democratize genomic pathogen surveillance due to its ease of use and low entry cost. However, recent genotyping studies showed discrepant results compared to gold-standard short-read sequencing. Furthermore, although essential for widespread application, the reproducibility of nanopore-only genotyping remains largely unresolved. In our multicenter performance study involving five laboratories, four public health-relevant bacterial species were sequenced with the latest R10.4.1 flow cells and V14 chemistry. Core genome MLST analysis of over 500 data sets revealed highly strain-specific typing errors in all species in each laboratory. Investigation of the methylation-related errors revealed consistent DNA motifs at error-prone sites across participants at read level. Depending on the frequency of incorrect target reads, this either leads to correct or incorrect typing, whereby only minimal frequency deviations can randomly determine the final result. PCR preamplification, recent basecalling model updates and an optimized polishing strategy notably diminished the non-reproducible typing. Our study highlights the potential for new errors to appear with each newly sequenced strain and lays the foundation for computational approaches to reduce such typing errors. In conclusion, our multicenter study shows the necessity for a new validation concept for nanopore sequencing-based, standardized bacterial typing, where single nucleotide accuracy is critical.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142000060","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":"Erratum for Leber, \"Maternal and congenital human cytomegalovirus infection: laboratory testing for detection and diagnosis\".","authors":"Amy L Leber","doi":"10.1128/jcm.01164-24","DOIUrl":"https://doi.org/10.1128/jcm.01164-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142000061","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":"Evaluation of a point-of-care rapid HIV antibody test with insights into acute HIV symptomatology in a population with low prevalence.","authors":"Tina I Bui, Christopher W Farnsworth, Neil W Anderson","doi":"10.1128/jcm.00620-24","DOIUrl":"https://doi.org/10.1128/jcm.00620-24","url":null,"abstract":"<p><p>Many emergency departments (ED) use rapid human immunodeficiency virus (HIV) antibody tests as screening tools, despite limited sensitivity for detecting acute HIV infections. In a 4-year retrospective analysis of 1,192 patients, we evaluated the performance of a third-generation rapid HIV antibody assay tested at point-of-care (POC, Chembio Sure Check HIV 1/2) against in-lab fourth-generation screening (Abbott Architect Ag/Ab Combo). Compared to complete algorithmic testing, the POC test demonstrated a 92.5% sensitivity (95% CI = 84.6-96.5), 98.1% specificity (95% CI = 97.1-98.8), 99.5% negative predictive value (NPV; 95% CI = 98.8-99.8), and a 77.9% positive predictive value (PPV; 95% CI = 68.6-85.1). Notably, the POC test failed to detect 100% (3/3) of acute HIV infections (defined as Fiebig stage 2) and 3.8% (2/52) established HIV infections, where viral loads were 5.9, 6.7, and >7 log₁₀ copies/mL. Symptoms such as fever, nausea/vomiting, malaise, headache, and photophobia were significantly associated with acute HIV infections diagnosed in the ED. The rapid HIV antibody test demonstrated high sensitivity, specificity, and NPV in our study population, reaffirming its effectiveness as a valuable screening tool. However, the low PPV and 100% failure to detect acute HIV infections underscore the importance of prioritizing in-lab fourth-generation HIV antigen/antibody combination immunoassays in cases of suspected acute HIV infection to ensure a timely and accurate diagnosis.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141988099","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":"https://doi.org/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":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Practical updates in clinical antiviral resistance testing.","authors":"Hannah Wang","doi":"10.1128/jcm.00728-23","DOIUrl":"10.1128/jcm.00728-23","url":null,"abstract":"<p><p>The laboratory diagnosis of antiviral resistance is a quickly changing field due to new drug availability, the sunsetting of older drugs, the development of novel technologies, rapid viral evolution, and the financial/logistic pressures of the clinical laboratory. This mini-review summarizes the current state of clinically available antiviral resistance testing in the United States in 2024, covering the most commonly used test methods, mechanisms, and clinical indications for herpes simplex virus, cytomegalovirus, human immunodeficiency virus, influenza, hepatitis B virus, and hepatitis C virus drug resistance testing. Common themes include the move away from phenotypic to genotypic methods for first-line clinical testing, as well as uncertainty surrounding the clinical meaningfulness of minority variant detection as next-generation sequencing methods have become more commonplace.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11323466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759063","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":"IgM tests for detecting <i>Treponema pallidum</i> infection in newborns: time to establish a reference comparator.","authors":"Lao-Tzu Allan-Blitz, Diana Villarreal, Jeffrey D Klausner","doi":"10.1128/jcm.00551-24","DOIUrl":"10.1128/jcm.00551-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11323539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141579835","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}