Journal of Clinical Microbiology最新文献

{"title":"Azole resistance screening in <i>Aspergillus fumigatus sensu stricto</i> using the azole-containing agar method (EUCAST E.Def 10.2): conidial suspension filtration and inoculum adjustment before inoculum preparation may not be needed.","authors":"Julia Serrano-Lobo, Elena Reigadas, Patricia Muñoz, Pilar Escribano, Jesús Guinea","doi":"10.1128/jcm.00369-24","DOIUrl":"10.1128/jcm.00369-24","url":null,"abstract":"<p><p>Azole resistance screening in <i>Aspergillus fumigatus sensu stricto</i> can be routinely carried out by using azole-containing agar plates (E.Def 10.2 procedure); however, conidial suspension filtering and inoculum adjustment before inoculum preparation are time-consuming. We evaluated whether skipping the filtration and inoculum adjustment steps negatively influenced the performance of the E.Def 10.2 procedure. <i>A. fumigatus sensu stricto</i> isolates (<i>n</i> = 98), previously classified as azole susceptible or azole resistant (E.Def 9.4 method), were studied. Azole-resistant isolates had either the wild-type <i>cyp51A</i> gene sequence (<i>n</i> = 1) or the following <i>cyp51A</i> gene substitutions: TR₃₄-L98H (<i>n</i> = 41), G54R (<i>n</i> = 5), TR₄₆-Y121F-T289A (<i>n</i> = 1), or G448S (<i>n</i> = 1). In-house azole-containing agar plates were prepared according to the EUCAST E.Def 10.2 procedure. Conidial suspensions obtained by adding distilled water (Tween 20 0.1%) were either filtered and the inocula adjusted to 0.5 McFarland or left unfiltered and unadjusted. Agreements between the agar screening methods using inocula prepared by each procedure were high for itraconazole (99%), voriconazole (100%), and posaconazole (94.9%). Sensitivity and specificity (considering the susceptibility category as per the microdilution E.Def 9.4 method as the gold standard) of E.Def 10.2 were 100% to rule in or rule out resistance when unfiltered and unadjusted suspensions were used; the resistance phenotype of isolates harboring the TR₃₄-L98H, G54R, or TR₄₆-Y121F-T289A substitutions was correctly detected. Unfiltered and unadjusted conidial suspensions do not negatively influence the performance of the E.Def 10.2 method when screening for azole resistance in <i>A. fumigatus sensu stricto</i>.</p><p><strong>Importance: </strong>Azole resistance screening in <i>Aspergillus fumigatus sensu stricto</i> can be routinely carried out by using azole-containing plates (E.Def 10.2 procedure); however, conidial suspension filtering and inoculum adjustment before inoculation of plates are time-consuming. We, here, showed that unfiltered and unadjusted conidial suspensions do not negatively influence the performance of the E.Def 10.2 method when screening for azole resistance in <i>A. fumigatus sensu stricto</i>.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11250424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141179788","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":"Overcoming analytical and preanalytical challenges associated with extragenital home collected STI specimens.","authors":"B E Hockman, M Qi, H Rotblatt, L Borenstein, R A Flynn, R A Muldrow, S Rajagopalan, D N Greene","doi":"10.1128/jcm.00311-24","DOIUrl":"10.1128/jcm.00311-24","url":null,"abstract":"<p><p>Home sample collection for sexually transmitted infection (STI) screening options can improve access to sexual healthcare across communities. For <i>Chlamydia trachomatis</i> (CT) and <i>Neisseria gonorrhoeae</i> (NG), genital infections have classically been the focus for remote collection options. However, infections may go undiagnosed if sampling is limited to urogenital sites because some individuals only participate in oral and/or anal intercourse. Here we evaluated samples for CT/NG detection after several pre-analytical collection challenges. A paired provider to self-collection validation was performed on rectal [<i>n</i> = 162; 22 + for CT and 9 + for NG by provider-collected (PC)] and throat (<i>N</i> = 158; 2 + for CT and 11 + for NG by provider-collected) swabs. The positive percent agreement for CT and NG ranged from 90.9% to 100%. The discrepancies were more often positive on self-collected (SC) (<i>n</i> = 9 SC+/PC-; <i>n</i> = 1 PC+/SC-; <i>n</i> = 1 PC+/SC Equiv.; <i>n</i> = 2 PC-/SC Equiv.). An empirical limit of detection (LoD) lower than the manufacturer's claim (0.031 vs 2.5 IFU/mL for CT and 0.063 vs 124.8 CFU/ml for NG, respectively) was used to challenge additional variables. Common hand contaminants, including soap, hand sanitizer, lotion, and sunscreen were added to known positive (3× empirical LoD) or negative samples and did not influence detection. Samples at 2× and 10× the empirical LoD were challenged with extreme temperature cycling and extended room temperature storage. Detection was not affected by these conditions. These results indicate that remote self-collection is an appropriate method of sample acquisition for detecting extragenital CT/NG infections. Additionally, they provide a foundation towards meeting the regulatory standards for commercial testing of home collected extragenital samples.</p><p><strong>Importance: </strong>There is a clinical need for expanded extragenital bacterial sexually transmitted infection (STI) testing options, but the current regulatory landscape limits the wide-spread promotion and adoption of such services. Improved access, particularly for the LGBTQ+ community, can be achieved by validating testing for specimens that are self-collected at a remote location and arrive at the laboratory via a postal carrier or other intermediary route. Here we provide valuable data showing that self-collected samples for anal and oropharyngeal STI testing are equally or increasingly sensitive compared with those collected by a provider. We systematically consider the effects of storage time, exposure to temperature extremes, and the addition of common toiletries on results.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11250113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141248007","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":"Low utilization of epidemiological cutoff values to interpret <i>in vitro</i> antifungal susceptibility testing among clinical laboratory participants in two College of American Pathologists (CAP) proficiency testing programs.","authors":"Kaede V Sullivan, Thomas Long, Erica Hillesland, Daniel D Rhoads, Christina M Wojewoda, Sean X Zhang","doi":"10.1128/jcm.00421-24","DOIUrl":"10.1128/jcm.00421-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11250375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141450612","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":"CDC Trioplex diagnostic assay underperforms in detection of circulating Chikungunya West African genotype.","authors":"Mignane Ndiaye, Mouhamed Kane, Diamilatou Balde, Safietou Sankhé, Maimouna Mbanne, Seynabou Mbaye Souna Diop, Umar Ahmad, Gerald Mboowa, Samba Niang Sagne, Mamadou Cisse, Ndongo Dia, Amadou Alpha Sall, Ousmane Faye, Gamou Fall, Oumar Faye, Manfred Weidmann, Moussa Moïse Diagne, Idrissa Dieng","doi":"10.1128/jcm.00405-24","DOIUrl":"10.1128/jcm.00405-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11250485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141310822","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":"Generation of recombinant viruses directly from clinical specimens of COVID-19 patients.","authors":"Hirotaka Yamamoto, Tomokazu Tamura, Takaya Ichikawa, Yudai Taguchi, Kento Mori, Satoshi Oguri, Rigel Suzuki, Saori Suzuki, Takanori Teshima, Takasuke Fukuhara","doi":"10.1128/jcm.00042-24","DOIUrl":"10.1128/jcm.00042-24","url":null,"abstract":"<p><p>Rapid characterization of the causative agent(s) during a disease outbreak can aid in the implementation of effective control measures. However, isolation of the agent(s) from crude clinical samples can be challenging and time-consuming, hindering the establishment of countermeasures. In the present study, we used saliva specimens collected for the diagnosis of SARS-CoV-2-a good example of a practical target-and attempted to characterize the virus within the specimens without virus isolation. Thirty-four saliva samples from coronavirus disease 2019 patients were used to extract RNA and synthesize DNA amplicons by PCR. New primer sets were designed to generate DNA amplicons of the full-length spike (S) gene for subsequent use in a circular polymerase extension reaction (CPER), a simple method for deriving recombinant viral genomes. According to the S sequence, four clinical specimens were classified as BA. 1, BA.2, BA.5, and XBB.1 and were used for the <i>de novo</i> generation of recombinant viruses carrying the entire S gene. Additionally, chimeric viruses carrying the gene encoding GFP were generated to evaluate viral propagation using a plate reader. We successfully used the RNA purified directly from clinical saliva samples to generate chimeric viruses carrying the entire S gene by our updated CPER method. The chimeric viruses exhibited robust replication in cell cultures with similar properties. Using the recombinant GFP viruses, we also successfully characterized the efficacy of the licensed antiviral AZD7442. Our proof-of-concept demonstrates the novel utility of CPER to allow rapid characterization of viruses from clinical specimens.</p><p><strong>Importance: </strong>Characterization of the causative agent(s) for infectious diseases helps in implementing effective control measurements, especially in outbreaks. However, the isolation of the agent(s) from clinical specimens is often challenging and time-consuming. In this study, saliva samples from coronavirus disease 2019 patients were directly subjected to purifying viral RNA, synthesizing DNA amplicons for sequencing, and generating recombinant viruses. Utilizing an updated circular polymerase extension reaction method, we successfully generated chimeric SARS-CoV-2 viruses with sufficient <i>in vitro</i> replication capacity and antigenicity. Thus, the recombinant viruses generated in this study were applicable for evaluating the antivirals. Collectively, our developed method facilitates rapid characterization of specimens circulating in hosts, aiding in the establishment of control measurements. Additionally, this approach offers an advanced strategy for controlling other (re-)emerging viral infectious diseases.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11250110/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141317464","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: False-negative <i>Pneumocystis</i> PCR.","authors":"Jacob Rattin, Kelly Marigney, Cyndee Miranda, A Valeria Arrossi, Anisha Misra, Hannah Wang","doi":"10.1128/jcm.00094-24","DOIUrl":"10.1128/jcm.00094-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11250520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141620045","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 BD Phoenix and disk diffusion to broth microdilution for determining cefepime susceptibility among carbapenem-resistant Enterobacterales.","authors":"Aliaa Fouad, Patricia J Simner, David P Nicolau, Tomefa E Asempa","doi":"10.1128/jcm.01520-23","DOIUrl":"10.1128/jcm.01520-23","url":null,"abstract":"<p><p>There are increasing reports of carbapenem-resistant Enterobacterales (CRE) that test as cefepime-susceptible (S) or susceptible-dose dependent (SDD). However, there are no data to compare the cefepime testing performance of BD Phoenix automated susceptibility system (BD Phoenix) and disk diffusion (DD) relative to reference broth microdilution (BMD) against carbapenemase-producing (CP<i>_bla</i>_KPC-CRE) and non-producing (non-CP CRE) isolates. Cefepime susceptibility results were interpreted according to CLSI M100Ed32. Essential agreement (EA), categorical agreement (CA), minor errors (miEs), major errors (MEs), and very major errors (VMEs) were calculated for BD Phoenix (NMIC-306 Gram-negative panel) and DD relative to BMD. Correlates were also analyzed by the error rate-bounded method. EA and CA for CP<i>_bla</i>_KPC-CRE isolates (<i>n</i> = 64) were <90% with BD Phoenix while among non-CP CRE isolates (<i>n</i> = 58), EA and CA were 96.6%, and 79.3%, respectively. CA was <90% with DD for both cohorts. No ME or VME was observed for either isolate cohort; however, miEs were >10% for CP<i>_bla</i>_KPC-CRE and non-CP CRE with BD Phoenix and DD tests. For error rate-bounded method, miEs were <40% for I_High + 1 to I_Low - 1 ranges for CP<i>_bla</i>_KPC-CRE and non-CP CRE with BD Phoenix. Regarding disk diffusion, miEs were unacceptable for all MIC ranges among CP<i>_bla</i>_KPC-CRE. For non-CP CRE isolates, only I_High + 1 to I_Low - 1 range was acceptable at 37.2%. Using this challenge set of genotypic-phenotypic discordant CRE, the BD Phoenix MICs and DD susceptibility results trended higher (toward SDD and resistant phenotypes) relative to reference BMD results yielding lower CA. These results were more prominent among CP<i>_bla</i>_KPC-CRE than non-CP CRE.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140858137","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":"Proceedings of the Clinical Microbiology Open 2023: discussions about pandemic preparedness.","authors":"Eleanor A Powell, Alexander L Greninger, Elizabeth M Marlowe, Samia N Naccache, Christopher D Doern","doi":"10.1128/jcm.00144-24","DOIUrl":"10.1128/jcm.00144-24","url":null,"abstract":"<p><p>The 4th Clinical Microbiology Open (CMO) took place in Carlsbad, California, on 10 and 11 February 2023. This event facilitated discussion between clinical and public health laboratory directors, government agencies, and industry representatives from the companies that make up ASM's Corporate Council. While many topics were discussed, much of the discussion focused on pandemic preparedness. There were four major questions addressed: (i) When is the perfect the enemy of good in pandemic testing? (ii) What other types of pathogens might cause another pandemic and how would this affect laboratory response? (iii) What research is needed to better understand the effectiveness of the pandemic response? (iv) What have we learned about the utility of self and at-home testing in future pandemics? This review serves as a summary of these discussions.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237618/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141076138","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: Yeast, chlamydospores, and hyphae-a case of disseminated mucormycosis.","authors":"Nicole E Putnam, Khadija Tayabali, Justine R Yu, Isabel Decolin, Anna F Lau, William Twaddell, Katya Prakash, J Kristie Johnson","doi":"10.1128/jcm.01638-23","DOIUrl":"10.1128/jcm.01638-23","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237672/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141306086","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":"Core genome multilocus sequence typing (cgMLST) applicable to the monophyletic <i>Klebsiella oxytoca</i> species complex.","authors":"Johanna Dabernig-Heinz, Gabriel E Wagner, Karola Prior, Michaela Lipp, Sabine Kienesberger, Werner Ruppitsch, Torunn G Rønning, Dag Harmsen, Ivo Steinmetz, Eva Leitner","doi":"10.1128/jcm.01725-23","DOIUrl":"10.1128/jcm.01725-23","url":null,"abstract":"<p><p>The environmental bacterium <i>Klebsiella oxytoca</i> displays an alarming increase of antibiotic-resistant strains that frequently cause outbreaks in intensive care units. Due to its prevalence in the environment and opportunistic presence in humans, molecular surveillance (including resistance marker screening) and high-resolution cluster analysis are of high relevance. Furthermore, <i>K. oxytoca</i> previously described in studies is rather a species complex (KoSC) than a single species comprising at least six closely related species that are not easily differentiated by standard typing methods. To reach a discriminatory power high enough to identify and resolve clusters within these species, whole genome sequencing is necessary. The resolution is achievable with core genome multilocus sequence typing (cgMLST) extending typing of a few housekeeping genes to thousands of core genome genes. CgMLST is highly standardized and provides a nomenclature enabling cross laboratory reproducibility and data exchange for routine diagnostics. Here, we established a cgMLST scheme not only capable of resolving the KoSC species but also producing reliable and consistent results for published outbreaks. Our cgMLST scheme consists of 2,536 core genome and 2,693 accessory genome targets, with a percentage of good cgMLST targets of 98.31% in 880 KoSC genomes downloaded from the National Center for Biotechnology Information (NCBI). We also validated resistance markers against known resistance gene patterns and successfully linked genetic results to phenotypically confirmed toxic strains carrying the <i>til</i> gene cluster. In conclusion, our novel cgMLST enables highly reproducible typing of four different clinically relevant species of the KoSC and thus facilitates molecular surveillance and cluster investigations.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141081610","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}