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Evaluation of commercial, customized microdilution plates for Ureaplasma parvum, Ureaplasma urealyticum, and Mycoplasma hominis antimicrobial susceptibility testing and determination of antimicrobial resistance prevalence in France. 在法国,对用于副猪脲原体、尿解脲原体和人型支原体抗菌药物敏感性检测和确定抗菌药物耐药性流行率的商用定制微量稀释板进行评估。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-04 DOI: 10.1128/jcm.00226-24
Sabine Pereyre, Nadège Hénin, Amandine Dolzy, Jennifer Guiraud, Cécile Laurier-Nadalié, Marie Gardette, Cécile Bébéar

Antimicrobial susceptibility testing (AST) of human mycoplasmas using microdilution is time-consuming. In this study, we compared the performance of MICRONAUT-S plates (Biocentric-Bruker) designed for AST of Ureaplasma parvum, Ureaplasma urealyticum, and Mycoplasma hominis with the results using the Clinical & Laboratory Standards Institute (CLSI) reference method. Then, we investigated the prevalence and mechanisms of resistance to tetracyclines, fluoroquinolones, and macrolides in France in 2020 and 2021. The two methods were compared using 60 strains. For the resistance prevalence study, U. parvum-, U. urealyticum-, and M. hominis-positive clinical specimens were collected for 1 month each year in 22 French diagnostic laboratories. MICs were determined using the MICRONAUT-S plates. The tet(M) gene was screened using PCR, and fluoroquinolone resistance-associated mutations were screened using PCR and Sanger sequencing. Comparing the methods, 99.5% (679/680) MICs obtained using the MICRONAUT-S plates concurred with those obtained using the CLSI reference method. For 90 M. hominis isolates, the tetracycline, levofloxacin, and moxifloxacin resistance rates were 11.1%, 2.2%, and 2.2%, respectively, with no clindamycin resistance. For 248 U. parvum isolates, the levofloxacin and moxifloxacin resistance rates were 5.2% and 0.8%, respectively; they were 2.9% and 1.5% in 68 U. urealyticum isolates. Tetracycline resistance in U. urealyticum (11.8%) was significantly (P < 0.001) higher than in U. parvum (1.2%). No macrolide resistance was observed. Overall, the customized MICRONAUT-S plates are a reliable, convenient tool for AST of human mycoplasmas. Tetracycline and fluoroquinolone resistance remain limited in France. However, the prevalence of levofloxacin and moxifloxacin resistance has increased significantly in Ureaplasma spp. from 2010 to 2015 and requires monitoring.

Importance: Antimicrobial susceptibility testing of human urogenital mycoplasmas using the CLSI reference broth microdilution method is time-consuming and requires the laborious preparation of antimicrobial stock solutions. Here, we validated the use of reliable, convenient plates designed for antimicrobial susceptibility testing that allows the simultaneous determination of the MICs of eight antibiotics of interest. We then investigated the prevalence and mechanisms of resistance of each of these bacteria to tetracyclines, fluoroquinolones, and macrolides in France in 2020 and 2021. We showed that the prevalence of levofloxacin and moxifloxacin resistance has increased significantly in Ureaplasma spp. from 2010 to 2015 and requires ongoing monitoring.

使用微量稀释法对人类支原体进行抗菌药敏感性检测(AST)非常耗时。在这项研究中,我们比较了 MICRONAUT-S 菌落总数计数板(Biocentric-Bruker)与临床与实验室标准协会(CLSI)参考方法的性能。然后,我们调查了 2020 年和 2021 年法国四环素类、氟喹诺酮类和大环内酯类药物耐药性的流行情况和机制。我们使用 60 株菌株对两种方法进行了比较。在耐药性流行率研究中,22 个法国诊断实验室每年收集一个月的副猪脲菌、尿脲菌和人疟原虫阳性临床标本。使用 MICRONAUT-S 菌落总数计数板测定 MIC。使用 PCR 筛选 tet(M) 基因,使用 PCR 和 Sanger 测序筛选氟喹诺酮类药物耐药性相关突变。比较两种方法,使用 MICRONAUT-S 菌落总数计数板获得的 MIC 值与使用 CLSI 参考方法获得的 MIC 值一致率为 99.5%(679/680)。对于 90 株人乳头瘤病毒分离物,四环素、左氧氟沙星和莫西沙星耐药率分别为 11.1%、2.2% 和 2.2%,无克林霉素耐药。在 248 个 U. parvum 分离物中,对左氧氟沙星和莫西沙星的耐药率分别为 5.2% 和 0.8%;在 68 个 U. urealyticum 分离物中,对左氧氟沙星和莫西沙星的耐药率分别为 2.9% 和 1.5%。U. urealyticum(11.8%)对四环素的耐药性明显(P < 0.001)高于 U. parvum(1.2%)。未发现大环内酯类耐药性。总之,定制的 MICRONAUT-S 菌落总数计数板是一种可靠、方便的人类支原体检测工具。在法国,四环素和氟喹诺酮类药物的耐药性仍然有限。然而,从 2010 年到 2015 年,左氧氟沙星和莫西沙星耐药性在解脲支原体中的流行率显著上升,需要进行监测:使用 CLSI 参考肉汤微量稀释法对人类泌尿生殖道支原体进行抗菌药物敏感性检测非常耗时,而且需要费力地制备抗菌药物储备溶液。在这里,我们验证了可靠、方便的抗菌药敏感性检测板的使用方法,它可以同时测定八种相关抗生素的 MICs。然后,我们调查了 2020 年和 2021 年法国境内这些细菌对四环素类、氟喹诺酮类和大环内酯类药物的耐药性流行情况和机制。我们发现,从 2010 年到 2015 年,左氧氟沙星和莫西沙星耐药性在解脲脲原体中的流行率显著上升,需要持续监测。
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引用次数: 0
A simple and sensitive test for Candida auris colonization, surveillance, and infection control suitable for near patient use. 一种简单而灵敏的念珠菌定植、监测和感染控制检测方法,适合患者就近使用。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-18 DOI: 10.1128/jcm.00525-24
Sukalyani Banik, Burcu Ozay, Marisol Trejo, YanChun Zhu, Charan Kanna, Cynthia Santellan, Bennett Shaw, Sukantha Chandrasekaran, Sudha Chaturvedi, Lindy Vejar, Soumitesh Chakravorty, David Alland, Padmapriya Banada

Candida auris is a multidrug-resistant fungal pathogen with a propensity to colonize humans and persist on environmental surfaces. C. auris invasive fungal disease is being increasingly identified in acute and long-term care settings. We have developed a prototype cartridge-based C. auris surveillance assay (CaurisSurV cartridge; "research use only") that includes integrated sample processing and nucleic acid amplification to detect C. auris from surveillance skin swabs in the GeneXpert instrument and is designed for point-of-care use. The assay limit of detection (LoD) in the skin swab matrix was 10.5 and 14.8 CFU/mL for non-aggregative (AR0388) and aggregative (AR0382) strains of C. auris, respectively. All five known clades of C. auris were detected at 2-3-5× (31.5-52.5 CFU/mL) the LoD. The assay was validated using a total of 85 clinical swab samples banked at two different institutions (University of California Los Angeles, CA and Wadsworth Center, NY). Compared to culture, sensitivity was 96.8% (30/31) and 100% (10/10) in the UCLA and Wadsworth cohorts, respectively, providing a combined sensitivity of 97.5% (40/41), and compared to PCR, the combined sensitivity was 92% (46/50). Specificity was 100% with both clinical (C. auris negative matrix, N = 31) and analytical (non-C. auris strains, N = 32) samples. An additional blinded study with N = 60 samples from Wadsworth Center, NY yielded 97% (29/30) sensitivity and 100% (28/28) specificity. We have developed a completely integrated, sensitive, specific, and 58-min prototype test, which can be used for routine surveillance of C. auris and might help prevent colonization and outbreaks in acute and chronic healthcare settings.

Importance: This study has the potential to offer a better solution to healthcare providers at hospitals and long-term care facilities in their ongoing efforts for effective and timely control of Candida auris infection and hence quicker response for any potential future outbreaks.

念珠菌是一种具有多种耐药性的真菌病原体,具有在人体定植和在环境表面持久存在的倾向。在急诊和长期护理环境中发现的念珠菌侵袭性真菌病越来越多。我们已开发出一种基于盒式检测器的C. auris监测原型(CaurisSurV盒式检测器;"仅供研究使用"),该检测器集成了样本处理和核酸扩增功能,可在GeneXpert仪器中检测监测皮肤拭子中的C. auris,专为护理点使用而设计。皮肤拭子基质中的非聚集菌株(AR0388)和聚集菌株(AR0382)的检测限(LoD)分别为 10.5 CFU/mL 和 14.8 CFU/mL。在 LoD 为 2-3-5 倍(31.5-52.5 CFU/mL)时,可检测到所有五个已知的弓形虫支系。该检测方法通过两个不同机构(加州大学洛杉矶分校和纽约州沃兹沃思中心)的 85 份临床拭子样本库进行了验证。与培养相比,加州大学洛杉矶分校和沃兹沃思中心的灵敏度分别为 96.8%(30/31)和 100%(10/10),综合灵敏度为 97.5%(40/41);与 PCR 相比,综合灵敏度为 92%(46/50)。对临床样本(阴性阴沟球菌基质,N = 31)和分析样本(非阴沟球菌菌株,N = 32)的特异性均为 100%。对纽约州沃兹沃思中心的 N = 60 份样本进行的另一项盲法研究显示,灵敏度为 97%(29/30),特异性为 100%(28/28)。我们开发出了一种完全集成、灵敏、特异且只需 58 分钟的原型检测方法,可用于对阿氏杆菌的常规监测,并有助于预防急性和慢性医疗机构中的定植和疫情爆发:本研究有可能为医院和长期护理机构的医护人员提供更好的解决方案,帮助他们及时有效地控制念珠菌感染,从而更快地应对未来可能爆发的疫情。
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引用次数: 0
Improved Blue Carba test and Carba NP test for detection and classification of major Class A and B carbapenemases, including dual producers, among Gram-negative bacilli. 用于检测和分类革兰氏阴性杆菌中主要的 A 类和 B 类碳青霉烯酶(包括双重生产者)的改进型蓝色卡巴检测法和卡巴 NP 检测法。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-21 DOI: 10.1128/jcm.01255-23
Lucía Maccari, Paola Ceriana, Hugo Norberto Granchetti, Antonella Viviana Pezzaniti, Celeste Lucero, Melina Rapoport, Alejandra Menocal, Alejandra Corso, Fernando Pasteran
<p><p>Prompt and precise identification of carbapenemase-producing organisms is crucial for guiding clinical antibiotic treatments and limiting transmission. Here, we propose modifying the Blue Carba test (BCT) and Carba NP-direct (CNPd) to identify molecular carbapenemase classes, including dual carbapenemase strains, by adding specific Class A and Class B inhibitors. We tested 171 carbapenemase-producing Gram-negative bacilli strains-21 in Class A (KPC, NMC, SME), 58 in Class B (IMP, VIM, NDM, SPM), and 92 with dual carbapenemase production (KPC+NDM, KPC+IMP, KPC+VIM), all previously positive with BCT or CNPd. We also included 13 carbapenemase non-producers. β-lactamases were previously characterized by PCR. The improved BCT/CNPd methods detect imipenem hydrolysis from an imipenem-cilastatin solution, using pH indicators and Class A (avibactam) and/or Class B (EDTA) inhibitors. Results were interpreted visually based on color changes. CNPd achieved 99.4% sensitivity and 100% specificity in categorizing carbapenemases, while BCT had 91.8% sensitivity and 100% specificity. Performance varied by carbapenemase classes: both tests classified all Class A-producing strains. For Class B, the CNP test identified 57/58 strains (98.3%), whereas the BCT test, 45/58 strains (77.6%), with non-fermenters posing the greatest detection challenge. For Classes A plus B dual producers, both tests performed exceptionally well, with only one indeterminate strain for the BCT. The statistical comparison showed both methods had similar times to a positive result, with differences based on the carbapenemase class or bacterial group involved. This improved assay rapidly distinguishes major Class A or Class B carbapenemase producers among Gram-negative bacilli, including dual-class combinations, in less than 2 hours.</p><p><strong>Importance: </strong>Rapid and accurate identification of carbapenemase-producing organisms is of vital importance in guiding appropriate clinical antibiotic treatments and curbing their transmission. The emergence of negative bacilli carrying multiple carbapenemase combinations during and after the severe acute respiratory syndrome coronavirus 2 pandemic has posed a challenge to the conventional biochemical tests typically used to determine the specific carbapenemase type in the isolated strains. Several initiatives have aimed to enhance colorimetric methods, enabling them to independently identify the presence of Class A or Class B carbapenemases. Notably, no previous efforts have been made to distinguish both classes simultaneously. Additionally, these modifications have struggled to differentiate between carriers of multiple carbapenemases, a common occurrence in many Latin American countries. In this study, we introduced specific Class A and Class B carbapenemase inhibitors into the Blue Carba test (BCT) and Carba NP-direct (CNP) colorimetric assays to identify the type of carbapenemase, even in cases of multiple carbapenemase producers wit
及时、准确地识别产碳青霉烯酶生物对于指导临床抗生素治疗和限制传播至关重要。在此,我们建议修改蓝色卡巴试验(BCT)和卡巴NP-直接试验(CNPd),通过添加特异性A类和B类抑制剂来鉴定分子碳青霉烯酶类别,包括双重碳青霉烯酶菌株。我们检测了 171 株产碳青霉烯酶的革兰氏阴性杆菌,其中 21 株属于 A 类(KPC、NMC、SME),58 株属于 B 类(IMP、VIM、NDM、SPM),92 株产双重碳青霉烯酶(KPC+NDM、KPC+IMP、KPC+VIM),所有这些菌株之前都用 BCT 或 CNPd 检测呈阳性。我们还纳入了 13 种不产生碳青霉烯酶的细菌。β-内酰胺酶之前已通过 PCR 鉴定。改进的 BCT/CNPd 方法使用 pH 指示剂和 A 类(阿维巴坦)和/或 B 类(乙二胺四乙酸)抑制剂检测亚胺培南-西司他丁溶液中的亚胺培南水解作用。检测结果根据颜色变化直观判读。CNPd 对碳青霉烯酶分类的灵敏度为 99.4%,特异性为 100%,而 BCT 的灵敏度为 91.8%,特异性为 100%。碳青霉烯酶类别不同,检测结果也不同:两种检测方法都能对所有 A 类产菌菌株进行分类。对于 B 类,CNP 检测可识别 57/58 株菌株(98.3%),而 BCT 检测可识别 45/58 株菌株(77.6%),其中非发酵菌株的检测难度最大。对于 A 类和 B 类双重生产者,两种检测方法的表现都非常出色,BCT 检测方法仅检测出一株不确定菌株。统计比较显示,两种方法得出阳性结果的时间相近,但因涉及的碳青霉烯酶类别或细菌群而有所不同。这种改进后的检测方法能在不到 2 小时的时间内快速区分革兰氏阴性杆菌中主要的 A 类或 B 类碳青霉烯酶生产者,包括双类组合:重要意义:快速、准确地鉴定碳青霉烯酶产生菌对指导适当的临床抗生素治疗和遏制其传播至关重要。在严重急性呼吸系统综合征冠状病毒 2 大流行期间和之后,出现了携带多种碳青霉烯酶组合的阴性杆菌,这给通常用于确定分离菌株中特定碳青霉烯酶类型的传统生化检验带来了挑战。有几项计划旨在改进比色法,使其能够独立识别 A 类或 B 类碳青霉烯酶的存在。值得注意的是,此前还没有人尝试过同时区分这两种类型。此外,这些改良方法也很难区分多种碳青霉烯酶的携带者,而这在许多拉美国家都很常见。在这项研究中,我们将特定的 A 类和 B 类碳青霉烯酶抑制剂引入蓝色卡巴试验(BCT)和卡巴 NP-直接(CNP)比色测定法中,以确定碳青霉烯酶的类型,即使在这些类别中存在多种碳青霉烯酶生产者的情况下也是如此。这些更新后的检测方法具有极高的灵敏度和特异性(≥ 90%),而且所有检测都能在 2 小时内快速完成,通常只需 45 分钟即可完成。这些对 BCT 和 CNP 检测方法的内部改进为确定主要碳青霉烯酶类别提供了一种快速、直接和经济有效的方法。它们可以作为分子生物学或免疫层析技术的可行替代方法,在整个过程中充当初始诊断步骤。
{"title":"Improved Blue Carba test and Carba NP test for detection and classification of major Class A and B carbapenemases, including dual producers, among Gram-negative bacilli.","authors":"Lucía Maccari, Paola Ceriana, Hugo Norberto Granchetti, Antonella Viviana Pezzaniti, Celeste Lucero, Melina Rapoport, Alejandra Menocal, Alejandra Corso, Fernando Pasteran","doi":"10.1128/jcm.01255-23","DOIUrl":"10.1128/jcm.01255-23","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Prompt and precise identification of carbapenemase-producing organisms is crucial for guiding clinical antibiotic treatments and limiting transmission. Here, we propose modifying the Blue Carba test (BCT) and Carba NP-direct (CNPd) to identify molecular carbapenemase classes, including dual carbapenemase strains, by adding specific Class A and Class B inhibitors. We tested 171 carbapenemase-producing Gram-negative bacilli strains-21 in Class A (KPC, NMC, SME), 58 in Class B (IMP, VIM, NDM, SPM), and 92 with dual carbapenemase production (KPC+NDM, KPC+IMP, KPC+VIM), all previously positive with BCT or CNPd. We also included 13 carbapenemase non-producers. β-lactamases were previously characterized by PCR. The improved BCT/CNPd methods detect imipenem hydrolysis from an imipenem-cilastatin solution, using pH indicators and Class A (avibactam) and/or Class B (EDTA) inhibitors. Results were interpreted visually based on color changes. CNPd achieved 99.4% sensitivity and 100% specificity in categorizing carbapenemases, while BCT had 91.8% sensitivity and 100% specificity. Performance varied by carbapenemase classes: both tests classified all Class A-producing strains. For Class B, the CNP test identified 57/58 strains (98.3%), whereas the BCT test, 45/58 strains (77.6%), with non-fermenters posing the greatest detection challenge. For Classes A plus B dual producers, both tests performed exceptionally well, with only one indeterminate strain for the BCT. The statistical comparison showed both methods had similar times to a positive result, with differences based on the carbapenemase class or bacterial group involved. This improved assay rapidly distinguishes major Class A or Class B carbapenemase producers among Gram-negative bacilli, including dual-class combinations, in less than 2 hours.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Rapid and accurate identification of carbapenemase-producing organisms is of vital importance in guiding appropriate clinical antibiotic treatments and curbing their transmission. The emergence of negative bacilli carrying multiple carbapenemase combinations during and after the severe acute respiratory syndrome coronavirus 2 pandemic has posed a challenge to the conventional biochemical tests typically used to determine the specific carbapenemase type in the isolated strains. Several initiatives have aimed to enhance colorimetric methods, enabling them to independently identify the presence of Class A or Class B carbapenemases. Notably, no previous efforts have been made to distinguish both classes simultaneously. Additionally, these modifications have struggled to differentiate between carriers of multiple carbapenemases, a common occurrence in many Latin American countries. In this study, we introduced specific Class A and Class B carbapenemase inhibitors into the Blue Carba test (BCT) and Carba NP-direct (CNP) colorimetric assays to identify the type of carbapenemase, even in cases of multiple carbapenemase producers wit","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0125523"},"PeriodicalIF":6.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11250402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141432002","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
Performance evaluation of the Panbio COVID-19/Flu A&B Panel for detection of SARS-CoV-2, influenza A, and influenza B antigens using mid-turbinate nasal swabs. Panbio COVID-19/Flu A&B Panel 的性能评估:使用鼻中拭子检测 SARS-CoV-2、甲型流感和乙型流感抗原。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-18 DOI: 10.1128/jcm.00207-24
Shao-Hua Yu, Keun-Ju Kim, Chien-Chang Lee, Yanely Pineiro Puebla, Gelza Mae A Zabat, Hong-Mo Shih, Po-Ren Hsueh

The Panbio COVID-19/Flu A&B Panel (Abbott) is an in vitro diagnostic rapid test designed for the qualitative detection of nucleocapsid proteins SARS-CoV-2 and nucleoprotein influenza A and B antigens in nasal mid-turbinate (NMT) swab specimens from symptomatic individuals meeting COVID-19 and influenza clinical and/or epidemiological criteria. This study, the largest global one to date using fresh samples, aimed to assess the diagnostic sensitivity and specificity of the Panbio COVID-19/Flu A&B Panel in freshly collected NMT swab specimens from individuals suspected of respiratory viral infection consistent with COVID-19 and/or influenza within the first 5 days of symptom onset compared with results obtained with the cobas SARS-CoV-2 and influenza A/B qualitative assay (cobas 6800/8800 systems), which were tested using nasopharyngeal swab samples. A total of 512 evaluable subjects were enrolled in the COVID-19 cohort across 18 sites, and 1,148 evaluable subjects were enrolled in the influenza cohort across 22 sites in the Asia-Pacific, Europe, and the USA. The Panbio COVID-19/Flu A&B Panel demonstrated a sensitivity of 80.4% and a specificity of 99.7% for COVID-19. For influenza A, the sensitivity and specificity rates were 80.6% and 99.3%, respectively. Likewise, for influenza B, the sensitivity and specificity rates were 80.8% and 99.4%, respectively. In conclusion, the Panbio COVID-19/Flu A&B Panel emerges as a suitable rapid test for detecting COVID-19 and influenza in symptomatic subjects across diverse global populations, exhibiting high sensitivity. The assay achieved a sensitivity of 94.4% in samples with Ct ≤24 for COVID-19 and 92.6% in samples with Ct ≤30 for influenza A and B.

Importance: The Panbio COVID-19/Flu A&B Panel is a suitable rapid test for detecting COVID-19 and influenza in symptomatic subjects across diverse global populations, exhibiting high sensitivity. The assay achieved a sensitivity of 94.0% in samples with Ct ≤24 for COVID-19 and 92.6% in samples with Ct ≤30 for influenza A and B.

Panbio COVID-19/Flu A&B Panel(雅培)是一种体外诊断快速检测试剂盒,设计用于定性检测符合COVID-19和流感临床和/或流行病学标准的有症状者鼻中拭子(NMT)标本中的核壳蛋白SARS-CoV-2和核蛋白甲型和乙型流感抗原。该研究是迄今为止使用新鲜样本进行的规模最大的全球性研究,旨在评估 Panbio COVID-19/Flu A&B Panel 在新鲜采集的鼻中拭子标本中的诊断灵敏度和特异性,这些标本来自症状出现后 5 天内疑似感染 COVID-19 和/或流感的呼吸道病毒感染者,与使用鼻咽拭子标本进行检测的 cobas SARS-CoV-2 和甲型/乙型流感定性检测(cobas 6800/8800 系统)的结果进行比较。COVID-19队列共招募了512名可评估受试者,分布在18个研究机构;流感队列共招募了1148名可评估受试者,分布在亚太地区、欧洲和美国的22个研究机构。Panbio COVID-19/Flu A&B Panel对COVID-19的灵敏度为80.4%,特异性为99.7%。对甲型流感的灵敏度和特异性分别为 80.6% 和 99.3%。同样,对于乙型流感,灵敏度和特异性分别为 80.8% 和 99.4%。总之,Panbio COVID-19/Flu A&B Panel 是一种适用于检测全球不同人群中有症状者的 COVID-19 和流感的快速检测方法,具有很高的灵敏度。在COVID-19检测Ct≤24的样本中,该检测方法的灵敏度达到94.4%;在甲型和乙型流感检测Ct≤30的样本中,该检测方法的灵敏度达到92.6%:Panbio COVID-19/Flu A&B Panel是一种适用于检测全球不同人群中有症状者的COVID-19和流感的快速检测方法,具有很高的灵敏度。在COVID-19检测Ct≤24的样本中,该检测方法的灵敏度达到94.0%;在甲型和乙型流感检测Ct≤30的样本中,该检测方法的灵敏度达到92.6%。
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引用次数: 0
Genomic evolution of ST228 SCCmec-I MRSA 10 years after a major nosocomial outbreak. ST228 SCCmec-I MRSA 的基因组进化是在一次严重的院内疫情爆发 10 年后发生的。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-27 DOI: 10.1128/jcm.00203-24
Florian Mauffrey, Claire Bertelli, Gilbert Greub, Laurence Senn, Dominique S Blanc

In this study, we investigated the genomic changes in a major methicillin-resistant Staphylococcus aureus (MRSA) clone following a significant outbreak at a hospital. Whole-genome sequencing of MRSA isolates was utilized to explore the genomic evolution of post-outbreak MRSA strains. The epidemicity of the clone declined over time, coinciding with the introduction of multimodal infection control measures. A genome-wide association study (GWAS) identified multiple genes significantly associated with either high or low epidemic success, indicating alterations in mobilome, virulence, and defense mechanisms. Random Forest models pinpointed a gene related to fibrinogen binding as the most influential predictor of epidemicity. The decline of the MRSA clone may be attributed to various factors, including the implementation of new infection control measures, single nucleotide polymorphisms accumulation, and the genetic drift of a given clone. This research underscores the complex dynamics of MRSA clones, emphasizing the multifactorial nature of their evolution. The decline in epidemicity seems linked to alterations in the clone's genetic profile, with a probable shift towards decreased virulence and adaptation to long-term carriage. Understanding the genomic basis for the decline of epidemic clones is crucial to develop effective strategies for their surveillance and management, as well as to gain insights into the evolutionary dynamics of pathogen genomes.

在本研究中,我们调查了一家医院重大疫情爆发后主要耐甲氧西林金黄色葡萄球菌(MRSA)克隆的基因组变化。我们利用 MRSA 分离物的全基因组测序来探索疫情爆发后 MRSA 菌株的基因组进化。随着多模式感染控制措施的引入,该克隆的流行率逐渐下降。全基因组关联研究(GWAS)发现了多个与流行成功率高或低显著相关的基因,这表明动员组、毒力和防御机制发生了改变。随机森林模型确定了一个与纤维蛋白原结合相关的基因是最有影响力的流行预测因子。MRSA克隆的减少可归因于多种因素,包括新感染控制措施的实施、单核苷酸多态性的积累以及特定克隆的基因漂移。这项研究凸显了 MRSA 克隆的复杂动态,强调了其进化的多因素性质。流行性的下降似乎与克隆基因图谱的改变有关,可能向毒力下降和适应长期携带转变。了解流行性克隆下降的基因组基础对于制定有效的监控和管理策略以及深入了解病原体基因组的进化动态至关重要。
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引用次数: 0
Comparison of three colloidal gold immunoassays and GeneXpert Carba-R for the detection of Klebsiella pneumoniae blaKPC-2 variants. 三种胶体金免疫测定和 GeneXpert Carba-R 检测肺炎克雷伯氏菌 blaKPC-2 变体的比较。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-05-29 DOI: 10.1128/jcm.00154-24
Jinghao Zhang, Jieli Xu, Siquan Shen, Li Ding, Weiwei Yang, Chengkang Tang, Qingyu Shi, Hu Zhao, Yan Guo, Renru Han, Fupin Hu

The increasing use of ceftazidime-avibactam has led to the emergence of a wide range of ceftazidime-avibactam-resistant blaKPC-2 variants. Particularly, the conventional carbapenemase phenotypic assay exhibited a high false-negative rate for KPC-2 variants. In this study, three colloidal gold immunoassays, including the Gold Mountainriver CGI test, Dynamiker CGI test and NG-Test CARBA5, and GeneXpert Carba-R, were used to detect the presence of KPC-2 carbapenemase and its various variants in 42 Klebsiella pneumoniae strains. These strains covered blaKPC-2 (13/42) and 16 other blaKPC-2 variants including blaKPC-12 (1/42), blaKPC-23 (1/42), blaKPC-25 (1/42), blaKPC-33 (6/42), blaKPC-35 (1/42), blaKPC-44 (1/42), blaKPC-71 (1/42), blaKPC-76 (8/42), blaKPC-78 (1/42), blaKPC-79 (1/42), blaKPC-100 (1/42), blaKPC-127 (1/42), blaKPC-128 (1/42), blaKPC-144 (1/42), blaKPC-157 (2/42), and blaKPC-180 (1/42). For KPC-2 strains, all four assays showed 100% negative percentage agreement (NPA) and 100% positive percentage agreement (PPA) with sequencing results. For all 16 KPC-2 variants, GeneXpert Carba-R showed 100% NPA and 100% PPA, and the three colloidal gold immunoassays showed 100% NPA, while the PPAs of the Gold Mountainriver CGI test, Dynamiker CGI test, and NG-Test CARBA5 were 87.5%, 87.5%, and 68.8%, respectively. We also found a correlation between the mutation site in the amino acid of the variants and false-negative results by colloidal gold immunoassays. In conclusion, the GeneXpert Carba-R has been proven to be a reliable method in detecting KPC-2 and its variants, and the colloidal gold immunoassay tests offer a practical and cost-effective approach for their detection. For the sample with a negative result by a colloidal gold immunoassay test but not matching the drug-resistant phenotype, it is recommended to retest using another type of kit or the GeneXpert Carba-R assay, which can significantly improve the accuracy of detection.

随着头孢他啶-阿维菌素使用量的增加,出现了多种耐头孢他啶-阿维菌素的 blaKPC-2 变体。特别是,传统的碳青霉烯酶表型检测对 KPC-2 变体的假阴性率很高。本研究采用了三种胶体金免疫测定方法,包括 Gold Mountainriver CGI 测试、Dynamiker CGI 测试和 NG-Test CARBA5 以及 GeneXpert Carba-R,检测 42 株肺炎克雷伯菌中是否存在 KPC-2 碳青霉烯酶及其各种变体。blaKPC-71 (1/42)、blaKPC-76 (8/42)、blaKPC-78 (1/42)、blaKPC-79 (1/42)、blaKPC-100 (1/42)、blaKPC-127 (1/42)、blaKPC-128 (1/42)、blaKPC-144 (1/42)、blaKPC-157 (2/42) 和 blaKPC-180 (1/42)。对于 KPC-2 菌株,所有四种检测方法与测序结果的阴性一致率 (NPA) 和阳性一致率 (PPA) 均为 100%。对于所有 16 个 KPC-2 变异株,GeneXpert Carba-R 显示出 100% 的 NPA 和 100% 的 PPA,三种胶体金免疫测定显示出 100% 的 NPA,而 Gold Mountainriver CGI 检验、Dynamiker CGI 检验和 NG-Test CARBA5 的 PPA 分别为 87.5%、87.5% 和 68.8%。我们还发现变体氨基酸的突变位点与胶体金免疫测定的假阴性结果之间存在相关性。总之,GeneXpert Carba-R 已被证明是检测 KPC-2 及其变体的可靠方法,而胶体金免疫测定试验则为检测它们提供了一种实用且经济有效的方法。对于胶体金免疫测定检测结果为阴性但不符合耐药表型的样本,建议使用其他类型的试剂盒或 GeneXpert Carba-R 检测法进行复检,这样可以大大提高检测的准确性。
{"title":"Comparison of three colloidal gold immunoassays and GeneXpert Carba-R for the detection of <i>Klebsiella pneumoniae bla</i><sub>KPC-2</sub> variants.","authors":"Jinghao Zhang, Jieli Xu, Siquan Shen, Li Ding, Weiwei Yang, Chengkang Tang, Qingyu Shi, Hu Zhao, Yan Guo, Renru Han, Fupin Hu","doi":"10.1128/jcm.00154-24","DOIUrl":"10.1128/jcm.00154-24","url":null,"abstract":"<p><p>The increasing use of ceftazidime-avibactam has led to the emergence of a wide range of ceftazidime-avibactam-resistant <i>bla</i><sub>KPC-2</sub> variants. Particularly, the conventional carbapenemase phenotypic assay exhibited a high false-negative rate for KPC-2 variants. In this study, three colloidal gold immunoassays, including the Gold Mountainriver CGI test, Dynamiker CGI test and NG-Test CARBA5, and GeneXpert Carba-R, were used to detect the presence of KPC-2 carbapenemase and its various variants in 42 <i>Klebsiella pneumoniae</i> strains. These strains covered <i>bla</i><sub>KPC-2</sub> (13/42) and 16 other <i>bla</i><sub>KPC-2</sub> variants including <i>bla</i><sub>KPC-12</sub> (1/42), <i>bla</i><sub>KPC-23</sub> (1/42), <i>bla</i><sub>KPC-25</sub> (1/42), <i>bla</i><sub>KPC-33</sub> (6/42), <i>bla</i><sub>KPC-35</sub> (1/42), <i>bla</i><sub>KPC-44</sub> (1/42), <i>bla</i><sub>KPC-71</sub> (1/42), <i>bla</i><sub>KPC-76</sub> (8/42), <i>bla</i><sub>KPC-78</sub> (1/42), <i>bla</i><sub>KPC-79</sub> (1/42), <i>bla</i><sub>KPC-100</sub> (1/42), <i>bla</i><sub>KPC-127</sub> (1/42), <i>bla</i><sub>KPC-128</sub> (1/42), <i>bla</i><sub>KPC-144</sub> (1/42), <i>bla</i><sub>KPC-157</sub> (2/42), and <i>bla</i><sub>KPC-180</sub> (1/42). For KPC-2 strains, all four assays showed 100% negative percentage agreement (NPA) and 100% positive percentage agreement (PPA) with sequencing results. For all 16 KPC-2 variants, GeneXpert Carba-R showed 100% NPA and 100% PPA, and the three colloidal gold immunoassays showed 100% NPA, while the PPAs of the Gold Mountainriver CGI test, Dynamiker CGI test, and NG-Test CARBA5 were 87.5%, 87.5%, and 68.8%, respectively. We also found a correlation between the mutation site in the amino acid of the variants and false-negative results by colloidal gold immunoassays. In conclusion, the GeneXpert Carba-R has been proven to be a reliable method in detecting KPC-2 and its variants, and the colloidal gold immunoassay tests offer a practical and cost-effective approach for their detection. For the sample with a negative result by a colloidal gold immunoassay test but not matching the drug-resistant phenotype, it is recommended to retest using another type of kit or the GeneXpert Carba-R assay, which can significantly improve the accuracy of detection.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0015424"},"PeriodicalIF":6.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11250111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141161178","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
Performance of rapid on-site evaluation of touch imprints of bronchoscopic biopsies or lung tissue biopsies for the diagnosis of invasive pulmonary filamentous fungi infections in non-neutropenic patients. 对支气管镜活检组织或肺组织活检组织的触摸印迹进行现场快速评估,用于诊断非中性卫生患者的侵袭性肺丝状真菌感染。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-10 DOI: 10.1128/jcm.00479-24
Hansheng Wang, Dan Yu, Xiao Chen, Yanhui Zhou, Xin Qian, Dan Liu, Lei Wang, Yijun Tang, Meifang Wang

The diagnosis of invasive pulmonary fungal disease depends on histopathology and mycological culture; there are few studies on touch imprints of bronchoscopic biopsies or lung tissue biopsies for the diagnosis of pulmonary filamentous fungi infections. The purpose of the present study was to explore the detection accuracy of rapid on-site evaluation of touch imprints of bronchoscopic biopsies or lung tissue biopsies for the filamentous fungi, and it aims to provide a basis for initiating antifungal therapy before obtaining microbiological evidence. We retrospectively analyzed the diagnosis and treatment of 44 non-neutropenic patients with invasive pulmonary filamentous fungi confirmed by glactomannan assay, histopathology, and culture from February 2017 to December 2023. The diagnostic positive rate and sensitivity of rapid on-site evaluation for these filamentous fungi identification, including diagnostic turnaround time, were calculated. Compared with the final diagnosis, the sensitivity of rapid on-site evaluation was 81.8%, and the sensitivity of histopathology, culture of bronchoalveolar lavage fluid, and glactomannan assay of bronchoalveolar lavage fluid was 86.4%, 52.3%, and 68.2%, respectively. The average turnaround time of detecting filamentous fungi by rapid on-site evaluation was 0.17 ± 0.03 hours, which was significantly faster than histopathology, glactomannan assay, and mycological culture. A total of 29 (76.3%) patients received earlier antifungal therapy based on ROSE diagnosis and demonstrated clinical improvement. Rapid on-site evaluation showed good sensitivity and accuracy that can be comparable to histopathology in identification of pulmonary filamentous fungi. Importantly, it contributed to the triage of biopsies for further microbial culture or molecular detection based on the preliminary diagnosis, and the decision on early antifungal therapy before microbiological evidence is available.

侵袭性肺部真菌病的诊断依赖于组织病理学和真菌学培养,而关于支气管镜活检组织或肺组织活检组织的触摸印迹用于肺部丝状真菌感染诊断的研究却很少。本研究的目的是探讨现场快速评估支气管镜活检组织或肺组织活检组织触摸印迹对丝状真菌的检测准确性,旨在为在获得微生物学证据之前启动抗真菌治疗提供依据。我们回顾性分析了2017年2月至2023年12月期间44例非中性粒细胞减少症患者的诊断和治疗情况,这些患者均经glactomannan测定、组织病理学和培养证实为侵袭性肺丝状真菌。计算了这些丝状真菌鉴定的诊断阳性率和现场快速评估的灵敏度,包括诊断周转时间。与最终诊断结果相比,现场快速评估的灵敏度为 81.8%,组织病理学、支气管肺泡灌洗液培养和支气管肺泡灌洗液葡聚甘露聚糖检测的灵敏度分别为 86.4%、52.3% 和 68.2%。通过现场快速评估检测丝状真菌的平均周转时间为 0.17 ± 0.03 小时,明显快于组织病理学、胶乳甘露聚糖检测和真菌学培养。共有 29 例(76.3%)患者根据 ROSE 诊断提前接受了抗真菌治疗,临床症状得到改善。现场快速评估显示出良好的灵敏度和准确性,在鉴定肺丝状真菌方面可与组织病理学相媲美。重要的是,它有助于根据初步诊断对活检组织进行分流,以便进一步进行微生物培养或分子检测,并有助于在获得微生物学证据之前决定是否进行早期抗真菌治疗。
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引用次数: 0
Broad-range amplification and sequencing of the rpoB gene: a novel assay for bacterial identification in clinical microbiology. rpoB 基因的大范围扩增和测序:临床微生物学细菌鉴定的新型检测方法。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-17 DOI: 10.1128/jcm.00266-24
Joanna Małgorzata Bivand, Ruben Dyrhovden, Audun Sivertsen, Marit Gjerde Tellevik, Robin Patel, Øyvind Kommedal

The rpoB gene has been proposed as a promising phylogenetic marker for bacterial identification, providing theoretically improved species-level resolution compared to the 16S rRNA gene for a range of clinically important taxa. However, its utility in diagnostic microbiology has been limited by the lack of broad-range primers allowing for its amplification from most species with a single PCR assay. Here, we present an assay for broad-range partial amplification and Sanger sequencing of the rpoB gene. To reduce cross-reactivity and allow for rpoB amplification directly from patient samples, primers were based on the dual priming oligonucleotide principle. The resulting amplicon is ~550 base pairs in length and appropriate for species-level identification. Systematic in silico evaluation of a wide selection of taxa demonstrated improved resolution within multiple important genera, including Enterococcus, Fusobacterium, Mycobacterium, Streptococcus, and Staphylococcus species and several genera within the Enterobacteriaceae family. Broad-range rpoB amplification and Sanger sequencing of 115 bacterial isolates provided unambiguous species-level identification for 97 (84%) isolates, as compared to 57 (50%) using a clinical 16S rRNA gene assay. Several unresolved taxonomic matters disguised by the low resolution of the 16S rRNA gene were revealed using the rpoB gene. Using a collection of 33 clinical specimens harboring bacteria and assumed to contain high concentrations of human DNA, the rpoB assay identified the pathogen in 29 specimens (88%). Broad-range rpoB amplification and sequencing provides a promising tool for bacterial identification, improving discrimination between closely related species and making it amenable for use in culture-based and culture-independent diagnostic approaches.

与 16S rRNA 基因相比,rpoB 基因理论上可提高一系列临床重要类群的物种级分辨率,被认为是一种很有前景的细菌鉴定系统发育标记。然而,由于缺乏可通过单次 PCR 检测扩增大多数物种的广谱引物,其在诊断微生物学中的应用受到了限制。在此,我们介绍一种对 rpoB 基因进行大范围部分扩增和 Sanger 测序的检测方法。为了减少交叉反应并能直接从患者样本中扩增 rpoB,引物采用了双引物寡核苷酸原理。由此产生的扩增片段长度约为 550 碱基对,适用于物种级鉴定。对多种分类群进行的系统性硅学评估表明,在多个重要菌属中,包括肠球菌属、镰刀菌属、分枝杆菌属、链球菌属和葡萄球菌属以及肠杆菌科的多个菌属中,分辨率都有所提高。对 115 株细菌分离物进行广谱 rpoB 扩增和 Sanger 测序后,97 株(84%)分离物得到了明确的物种鉴定,而使用临床 16S rRNA 基因测定的结果为 57 株(50%)。由于 16S rRNA 基因的分辨率较低,一些尚未解决的分类问题被 rpoB 基因所掩盖。利用收集的 33 份临床标本,假定其中含有高浓度的人类 DNA,rpoB 检测确定了 29 份标本(88%)中的病原体。广谱 rpoB 扩增和测序为细菌鉴定提供了一种前景广阔的工具,提高了近亲物种之间的鉴别能力,并使其适用于基于培养和不依赖培养的诊断方法。
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引用次数: 0
Mitigation of errors on an FDA-approved platform for cytomegalovirus viral load assay. 减少 FDA 批准的巨细胞病毒载量检测平台的误差。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-06 DOI: 10.1128/jcm.00416-24
Jung-Ho Youn, Lorenzo Walker, Seth Carlson, Craig Soutar, Karen Frank, Adrian Zelazny, Sanchita Das
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引用次数: 0
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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Journal of Clinical Microbiology
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