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Azole resistance screening in Aspergillus fumigatus sensu stricto using the azole-containing agar method (EUCAST E.Def 10.2): conidial suspension filtration and inoculum adjustment before inoculum preparation may not be needed. 使用含唑琼脂法(EUCAST E.Def 10.2)对严格曲霉进行抗唑筛选:可能不需要在接种体制备前对分生孢子悬浮液进行过滤和接种体调整。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-05-31 DOI: 10.1128/jcm.00369-24
Julia Serrano-Lobo, Elena Reigadas, Patricia Muñoz, Pilar Escribano, Jesús Guinea

Azole resistance screening in Aspergillus fumigatus sensu stricto 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. A. fumigatus sensu stricto isolates (n = 98), previously classified as azole susceptible or azole resistant (E.Def 9.4 method), were studied. Azole-resistant isolates had either the wild-type cyp51A gene sequence (n = 1) or the following cyp51A gene substitutions: TR34-L98H (n = 41), G54R (n = 5), TR46-Y121F-T289A (n = 1), or G448S (n = 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 A. fumigatus sensu stricto.

Importance: Azole resistance screening in Aspergillus fumigatus sensu stricto 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 A. fumigatus sensu stricto.

使用含唑琼脂平板(E.Def 10.2 程序)可对严格曲霉进行常规的唑类抗性筛选;然而,接种体制备前的分生孢子悬浮液过滤和接种体调整非常耗时。我们评估了跳过过滤和接种体调整步骤是否会对 E.Def 10.2 程序的性能产生负面影响。我们研究了严格意义上的烟曲霉分离物(n = 98),这些分离物之前被归类为唑类敏感或唑类抗性(E.Def 9.4 方法)。抗唑分离物具有野生型 cyp51A 基因序列(n = 1)或以下 cyp51A 基因替换序列:TR34-L98H(n = 41)、G54R(n = 5)、TR46-Y121F-T289A(n = 1)或 G448S(n = 1)。室内含唑琼脂平板按照 EUCAST E.Def 10.2 程序制备。通过添加蒸馏水(吐温 20 0.1%)获得的分生孢子悬浮液要么经过过滤并将接种体调整至 0.5 McFarland,要么不经过过滤也不进行调整。对于伊曲康唑(99%)、伏立康唑(100%)和泊沙康唑(94.9%)来说,使用每种方法制备的接种体进行琼脂筛选方法之间的一致性很高。在使用未经过滤和调整的悬浮液时,E.Def 10.2 的灵敏度和特异性(以微量稀释 E.Def 9.4 方法的药敏性类别为金标准)均为 100%,可排除或排除耐药性;可正确检测出携带 TR34-L98H、G54R 或 TR46-Y121F-T289A 替换的分离物的耐药性表型。未经过滤和调整的分生孢子悬浮液不会对 E.Def 10.2 方法筛选严格曲霉菌的唑类抗性产生负面影响:使用含唑平板(E.Def 10.2 程序)可对严格曲霉进行唑类抗性筛选,但分生孢子悬浮液过滤和平板接种前的接种体调整非常耗时。我们在此表明,在筛选严格烟曲霉的唑抗性时,未经过滤和调整的分生孢子悬浮液不会对 E.Def 10.2 方法的性能产生负面影响。
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引用次数: 0
Overcoming analytical and preanalytical challenges associated with extragenital home collected STI specimens. 克服与生殖器外家庭采集性传播感染标本相关的分析和分析前难题。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-05 DOI: 10.1128/jcm.00311-24
B E Hockman, M Qi, H Rotblatt, L Borenstein, R A Flynn, R A Muldrow, S Rajagopalan, D N Greene

Home sample collection for sexually transmitted infection (STI) screening options can improve access to sexual healthcare across communities. For Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (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 [n = 162; 22 + for CT and 9 + for NG by provider-collected (PC)] and throat (N = 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) (n = 9 SC+/PC-; n = 1 PC+/SC-; n = 1 PC+/SC Equiv.; n = 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.

Importance: 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.

通过家庭样本采集进行性传播感染(STI)筛查可改善社区内性保健的可及性。对于沙眼衣原体(CT)和淋病奈瑟菌(NG)而言,生殖器感染一直是远程采集方案的重点。然而,如果采样仅限于泌尿生殖器部位,感染可能会得不到诊断,因为有些人只参与口交和/或肛交。在此,我们对经过几次分析前采集挑战后的 CT/NG 检测样本进行了评估。对直肠拭子(n = 162;22 + 为 CT,9 + 为 NG,由提供者采集 (PC))和咽喉拭子(n = 158;2 + 为 CT,11 + 为 NG,由提供者采集)进行了提供者与自我采集配对验证。CT 和 NG 的阳性一致率从 90.9% 到 100% 不等。自采(SC)拭子的阳性率较高(n = 9 SC+/PC-;n = 1 PC+/SC-;n = 1 PC+/SC Equiv.;n = 2 PC-/SC Equiv.)。使用低于制造商声称的经验检测限(LoD)(CT 为 0.031 vs 2.5 IFU/ml,NG 为 0.063 vs 124.8 CFU/ml)来检测其他变量。将肥皂、洗手液、乳液和防晒霜等常见手部污染物添加到已知阳性(3 倍经验 LoD)或阴性样本中,不会影响检测结果。2 倍和 10 倍经验负荷值的样品都经过了极端温度循环和长时间室温储存的考验。检测不受这些条件的影响。这些结果表明,远程自采集是检测生殖器外 CT/NG 感染的一种合适的样本采集方法。此外,这些结果还为达到对家庭采集的生殖器外样本进行商业检测的监管标准奠定了基础:临床上需要更多的生殖器外细菌性传播感染(STI)检测选择,但目前的监管环境限制了此类服务的广泛推广和采用。通过对在偏远地区自取并通过邮递员或其他中介途径送达实验室的标本进行检测验证,可以提高检测的可及性,尤其是对 LGBTQ+ 群体而言。我们在此提供的宝贵数据显示,与医疗服务提供者采集的样本相比,自采样本进行肛门和口咽性传播感染检测的灵敏度相同或更高。我们系统地考虑了储存时间、暴露于极端温度以及添加常用洗浴用品对结果的影响。
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引用次数: 0
Low utilization of epidemiological cutoff values to interpret in vitro antifungal susceptibility testing among clinical laboratory participants in two College of American Pathologists (CAP) proficiency testing programs. 两个美国病理学家学会 (CAP) 能力测试项目的临床实验室参与者在解释体外抗真菌药敏试验时对流行病学临界值的利用率较低。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-26 DOI: 10.1128/jcm.00421-24
Kaede V Sullivan, Thomas Long, Erica Hillesland, Daniel D Rhoads, Christina M Wojewoda, Sean X Zhang
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引用次数: 0
CDC Trioplex diagnostic assay underperforms in detection of circulating Chikungunya West African genotype. 疾病预防控制中心的 Trioplex 诊断测定在检测循环基孔肯雅病西非基因型方面表现不佳。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-13 DOI: 10.1128/jcm.00405-24
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
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引用次数: 0
Generation of recombinant viruses directly from clinical specimens of COVID-19 patients. 直接从 COVID-19 患者的临床标本中生成重组病毒。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-14 DOI: 10.1128/jcm.00042-24
Hirotaka Yamamoto, Tomokazu Tamura, Takaya Ichikawa, Yudai Taguchi, Kento Mori, Satoshi Oguri, Rigel Suzuki, Saori Suzuki, Takanori Teshima, Takasuke Fukuhara

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 de novo 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.

Importance: 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 in vitro 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.

在疾病爆发期间迅速确定病原体的特征有助于实施有效的控制措施。然而,从粗糙的临床样本中分离病原体既具有挑战性又耗费时间,从而阻碍了对策的制定。在本研究中,我们使用了为诊断 SARS-CoV-2 而采集的唾液样本--这是一个实用目标的很好例子--并尝试在不分离病毒的情况下确定样本中病毒的特征。我们利用 34 份来自 2019 年冠状病毒病患者的唾液样本提取 RNA,并通过 PCR 合成 DNA 扩增子。设计了新的引物组来生成全长尖峰(S)基因的DNA扩增子,以便随后用于循环聚合酶延伸反应(CPER),这是一种获得重组病毒基因组的简单方法。根据 S 序列,四个临床样本被分为 BA.1、BA.2、BA.3、BA.4 和 BA.5。1、BA.2、BA.5 和 XBB.1,并用于从头生成携带整个 S 基因的重组病毒。此外,我们还生成了携带 GFP 编码基因的嵌合病毒,以使用平板阅读器评估病毒繁殖情况。我们成功地利用直接从临床唾液样本中纯化的 RNA,通过更新的 CPER 方法生成了携带整个 S 基因的嵌合病毒。嵌合病毒在细胞培养物中表现出强大的复制能力,并具有相似的特性。利用重组 GFP 病毒,我们还成功鉴定了特许抗病毒药物 AZD7442 的疗效。我们的概念验证证明了 CPER 在快速鉴定临床标本病毒特征方面的新用途:重要意义:确定传染病病原体的特征有助于实施有效的控制措施,尤其是在疫情爆发时。然而,从临床标本中分离病原体往往具有挑战性且耗时较长。在本研究中,2019 年冠状病毒病患者的唾液样本被直接用于纯化病毒 RNA、合成用于测序的 DNA 扩增子以及生成重组病毒。利用最新的环形聚合酶延伸反应方法,我们成功生成了具有足够体外复制能力和抗原性的嵌合型SARS-CoV-2病毒。因此,本研究生成的重组病毒可用于评估抗病毒药物。总之,我们开发的方法有助于快速鉴定宿主体内循环的标本,帮助建立控制测量。此外,这种方法还为控制其他(重新)出现的病毒性传染病提供了一种先进的策略。
{"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}
引用次数: 0
The Brief Case: False-negative Pneumocystis PCR. 简要案例:肺孢子虫 PCR 假阴性。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 DOI: 10.1128/jcm.00094-24
Jacob Rattin, Kelly Marigney, Cyndee Miranda, A Valeria Arrossi, Anisha Misra, Hannah Wang
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引用次数: 0
Comparison of BD Phoenix and disk diffusion to broth microdilution for determining cefepime susceptibility among carbapenem-resistant Enterobacterales. 在确定耐碳青霉烯类肠杆菌对头孢吡肟的敏感性时,比较 BD Phoenix 和磁盘扩散法与肉汤微量稀释法。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-06-12 Epub Date: 2024-05-07 DOI: 10.1128/jcm.01520-23
Aliaa Fouad, Patricia J Simner, David P Nicolau, Tomefa E Asempa

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 (CPblaKPC-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 CPblaKPC-CRE isolates (n = 64) were <90% with BD Phoenix while among non-CP CRE isolates (n = 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 CPblaKPC-CRE and non-CP CRE with BD Phoenix and DD tests. For error rate-bounded method, miEs were <40% for IHigh + 1 to ILow - 1 ranges for CPblaKPC-CRE and non-CP CRE with BD Phoenix. Regarding disk diffusion, miEs were unacceptable for all MIC ranges among CPblaKPC-CRE. For non-CP CRE isolates, only IHigh + 1 to ILow - 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 CPblaKPC-CRE than non-CP CRE.

越来越多的报告显示,耐碳青霉烯类肠杆菌(CRE)的检测结果为头孢吡肟敏感(S)或易感剂量依赖(SDD)。然而,目前还没有数据比较 BD Phoenix 自动药敏系统(BD Phoenix)和磁盘扩散(DD)相对于肉汤微量稀释(BMD)对碳青霉烯酶产生型(CPblaKPC-CRE)和非产生型(非 CP CRE)分离物的头孢吡肟检测性能。头孢吡肟药敏结果根据 CLSI M100Ed32 进行解释。计算了 BD Phoenix(NMIC-306 革兰氏阴性菌检测板)和 DD 相对于 BMD 的基本一致度 (EA)、分类一致度 (CA)、微小误差 (miEs)、主要误差 (MEs) 和非常主要误差 (VMEs)。还用误差率限值法分析了相关系数。CPblaKPC-CRE 分离物(n = 64)的 EA 和 CA 分别为 96.6% 和 79.3%(n = 58)。在 BD Phoenix 和 DD 试验中,CPblaKPC-CRE 和非 CP CRE 的 CA 为 10%。在误差率限制法中,CPblaKPC-CRE 和使用 BD Phoenix 的非CP CRE 的 miE 为 High + 1 到 ILow - 1 范围。在盘扩散法中,CPblaKPC-CRE 的所有 MIC 范围的 miE 都是不可接受的。对于非 CP CRE 分离物,只有 IHigh + 1 到 ILow - 1 范围的 miE 为 37.2%。利用这组基因型-表型不一致的 CRE 挑战,BD Phoenix MICs 和 DD 药敏结果趋于更高(趋向 SDD 和耐药表型),而参考 BMD 结果的 CA 值较低。这些结果在 CPblaKPC-CRE 中比非 CP CRE 中更为突出。
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引用次数: 0
Proceedings of the Clinical Microbiology Open 2023: discussions about pandemic preparedness. 2023 年临床微生物学开放会议记录:关于大流行病准备工作的讨论。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-06-12 Epub Date: 2024-05-22 DOI: 10.1128/jcm.00144-24
Eleanor A Powell, Alexander L Greninger, Elizabeth M Marlowe, Samia N Naccache, Christopher D Doern

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.

第四届临床微生物学公开赛(CMO)于 2023 年 2 月 10 日和 11 日在加利福尼亚州的卡尔斯巴德举行。这次活动促进了临床和公共卫生实验室主任、政府机构和来自 ASM 公司理事会成员公司的行业代表之间的讨论。虽然讨论的话题很多,但大部分讨论都集中在大流行病的防范上。主要讨论了四个问题:(i) 在大流行病检测中,什么时候完美是好的敌人?(ii) 哪些其他类型的病原体可能导致另一次大流行,这将如何影响实验室的应对措施? (iii) 需要开展哪些研究,以更好地了解大流行应对措施的有效性? (iv) 我们对未来大流行中自我检测和家庭检测的效用有哪些了解?本综述是这些讨论的总结。
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引用次数: 0
The Brief Case: Yeast, chlamydospores, and hyphae-a case of disseminated mucormycosis. 病例简介:酵母菌、衣孢子和菌丝--一例播散性粘孢子虫病。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-06-12 DOI: 10.1128/jcm.01638-23
Nicole E Putnam, Khadija Tayabali, Justine R Yu, Isabel Decolin, Anna F Lau, William Twaddell, Katya Prakash, J Kristie Johnson
{"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}
引用次数: 0
Core genome multilocus sequence typing (cgMLST) applicable to the monophyletic Klebsiella oxytoca species complex. 核心基因组多焦点序列分型(cgMLST)适用于单系氧合克雷伯菌种群。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-06-12 Epub Date: 2024-05-23 DOI: 10.1128/jcm.01725-23
Johanna Dabernig-Heinz, Gabriel E Wagner, Karola Prior, Michaela Lipp, Sabine Kienesberger, Werner Ruppitsch, Torunn G Rønning, Dag Harmsen, Ivo Steinmetz, Eva Leitner

The environmental bacterium Klebsiella oxytoca 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, K. oxytoca 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 til 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.

环境细菌克雷伯氏菌(Klebsiella oxytoca)中抗生素耐药菌株的增加速度令人震惊,经常在重症监护室中引起疫情爆发。由于其在环境中的普遍存在以及在人类中的机会性存在,分子监测(包括耐药性标记筛选)和高分辨率聚类分析具有高度相关性。此外,以前研究中描述的 K. oxytoca 是一个物种复合体(KoSC),而不是由至少六个近缘物种组成的单一物种,这些物种不易用标准分型方法区分。为了达到足够高的鉴别力来识别和解决这些物种内的群集问题,有必要进行全基因组测序。核心基因组多焦点序列分型(cgMLST)可将少数看家基因的分型扩展到数千个核心基因组基因,从而达到分辨的目的。CgMLST 标准化程度很高,并提供了一种命名法,可实现跨实验室的可重复性和常规诊断的数据交换。在这里,我们建立了一个 cgMLST 方案,该方案不仅能分辨 KoSC 的种类,还能为已公布的疫情提供可靠、一致的结果。我们的 cgMLST 方案包括 2,536 个核心基因组和 2,693 个附属基因组目标,在从美国国家生物技术信息中心(NCBI)下载的 880 个 KoSC 基因组中,良好的 cgMLST 目标占 98.31%。我们还根据已知的抗性基因模式对抗性标记进行了验证,并成功地将遗传结果与表型确认的携带 til 基因簇的有毒菌株联系起来。总之,我们的新型 cgMLST 能够对四种不同的临床相关 KoSC 进行高重复性分型,从而促进分子监测和集群调查。
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Journal of Clinical Microbiology
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