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Characterization of carbapenem-resistant Enterobacterales and Pseudomonas aeruginosa carrying multiple carbapenemase genes-Antimicrobial Resistance Laboratory Network, 2018-2022. 携带多种碳青霉烯酶基因的耐碳青霉烯类肠杆菌和铜绿假单胞菌的特征--抗菌药物耐药性实验室网络,2018-2022。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-20 DOI: 10.1128/jcm.01220-24
Sarah Sabour, Kristin R V Harrington, Ellen Martinson, Amelia S Bhatnagar, Jennifer Y Huang, Dustin Duffy, Katie Bantle, Joseph D Lutgring, Maria Karlsson, Allison C Brown
<p><p>Carbapenem-resistant Enterobacterales (CRE) and carbapenem-resistant <i>Pseudomonas aeruginosa</i> (CRPA) are significant public health threats, particularly when harboring carbapenemases. Literature describing the frequencies and phenotypic and genotypic characteristics of isolates harboring multiple carbapenemase genes is limited. Using data collected from the Antimicrobial Resistance Laboratory Network (AR Lab Network) in 2018-2022, we describe CRE and CRPA isolates that harbor multiple acquired carbapenemase genes. Clinical laboratories submitted CRE and CRPA isolates to AR Lab Network public health laboratories for additional characterization that included antimicrobial susceptibility testing and detection of five targeted carbapenemase genes. Isolates were classified as non-carbapenemase producing (non-CP) when negative for carbapenemase production and all targeted carbapenemase genes, or positive for a single-CP (SCP) or multiple-carbapenemase (MCP) targeted gene. Among 79,799 CREs tested, 27,599 (35%) were SCP and 611 (1%) were MCP. MCP-CRE most often carried <i>bla</i><sub>KPC</sub>/<i>bla</i><sub>NDM</sub> (<i>n</i> = 285, 47%). Both SCP-CRE and MCP-CRE were most commonly <i>Klebsiella</i> spp. <i>Enterobacter</i> spp. and <i>Escherichia coli</i> isolates harboring MCP were detected at slightly higher frequencies (18% and 15%; <i>n</i> = 109 and <i>n</i> = 88, respectively) than <i>Enterobacter</i> spp. and <i>Escherichia coli</i> isolates harboring SCP (13% and 13%; <i>n</i> = 3,653 and 3,471, respectively). The number of MCP-CRE detected increased from 54 of 5,105 (1%) in 2018 to 223 of 6,994 (3%) in 2022. Among 54,490 CRPA tested, 2% (<i>n</i> = 1,249) were SCP and 31 were MCP. MCP-CRPA most often carried <i>bla</i><sub>VIM</sub>/<i>bla</i><sub>IMP</sub> (<i>n</i> = 13, 42%). A higher proportion of MCP-CRE (97%, <i>n</i> = 330) isolates were categorized as resistant to meropenem, compared to SCP-CRE (79%; <i>n</i> = 11,227) and non-CP (13%; <i>n</i> = 2,683). Although MCP organisms represent a small proportion of total CP detected in the AR Lab Network, there is a need for continued monitoring and additional research.IMPORTANCECarbapenemase-producing organisms are of significant clinical and public health concerns, and rapid detection and containment of such threats are vital to preventing their spread. In this article, we used a collection of over 130,000 contemporary isolates to evaluate frequencies and phenotypic and genotypic properties of CRE and CRPA isolates harboring multiple carbapenemase genes across the United States, from 2018 to 2022. Of note, 95% and 100% of CRE and CRPA isolates co-harbored at least one metallo-β-lactamase gene, respectively, indicating a high proportion of isolates originating from patients with difficult-to-treat infections. Both clinical and public health professionals across the nation can use these data and key findings to better understand the molecular landscape of these isolates. Timely d
耐碳青霉烯类肠杆菌(CRE)和耐碳青霉烯类铜绿假单胞菌(CRPA)对公共卫生构成重大威胁,尤其是当它们携带碳青霉烯酶时。描述分离物携带多种碳青霉烯酶基因的频率、表型和基因型特征的文献十分有限。利用 2018-2022 年从抗菌药物耐药性实验室网络(AR Lab Network)收集的数据,我们描述了携带多种获得性碳青霉烯酶基因的 CRE 和 CRPA 分离物。临床实验室将 CRE 和 CRPA 分离物提交给 AR 实验室网络公共卫生实验室进行额外的特征描述,包括抗菌药敏感性测试和五种目标碳青霉烯酶基因的检测。如果碳青霉烯酶生成和所有目标碳青霉烯酶基因检测结果均为阴性,则分离物被归类为不产碳青霉烯酶(non-CP);如果单碳青霉烯酶(SCP)或多碳青霉烯酶(MCP)目标基因检测结果为阳性,则分离物被归类为产碳青霉烯酶(non-CP)。在检测的 79799 个 CRE 中,27599 个(35%)为 SCP,611 个(1%)为 MCP。MCP-CRE 最常携带 blaKPC/blaNDM(n = 285,47%)。检出携带 MCP 的肠杆菌属和大肠埃希菌分离物的频率(分别为 18% 和 15%; n = 109 和 n = 88)略高于携带 SCP 的肠杆菌属和大肠埃希菌分离物(分别为 13% 和 13%; n = 3,653 和 3,471 )。检测到的 MCP-CRE 数量从 2018 年 5 105 个中的 54 个(1%)增加到 2022 年 6 994 个中的 223 个(3%)。在检测的 54 490 个 CRPA 中,2%(n = 1 249)为 SCP,31 个为 MCP。MCP-CRPA 最常携带 blaVIM/blaIMP(n = 13,42%)。与 SCP-CRE(79%;n = 11,227 例)和非 MCP(13%;n = 2,683 例)相比,更高比例的 MCP-CRE 分离物(97%,n = 330 例)被归类为对美罗培南耐药。虽然 MCP 微生物在 AR 实验室网络检测到的 CP 总量中只占一小部分,但仍需继续监测和开展更多研究。在这篇文章中,我们利用收集到的超过 13 万个当代分离株,评估了 2018 年至 2022 年全美携带多种碳青霉烯酶基因的 CRE 和 CRPA 分离株的频率、表型和基因型特性。值得注意的是,分别有95%和100%的CRE和CRPA分离物至少同时携带一种金属-β-内酰胺酶基因,这表明有很高比例的分离物来源于难以治疗的感染患者。全国的临床和公共卫生专业人员都可以利用这些数据和重要发现来更好地了解这些分离物的分子状况。及时发现和控制这些微生物对于遏制抗生素耐药性的传播和确保为患者提供有效的治疗方案至关重要。
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引用次数: 0
Retrospective analysis of antimicrobial susceptibility profiles of non-diphtheriae Corynebacterium species from a tertiary hospital and reference laboratory, 2012-2023. 2012-2023年一家三甲医院和参考实验室非白喉棒状杆菌抗菌药敏感性谱的回顾性分析。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-18 DOI: 10.1128/jcm.01199-24
Ryan B Khodadadi, Said El Zein, Christina G Rivera O'Connor, Ryan W Stevens, Audrey N Schuetz, Omar M Abu Saleh, Madiha Fida

A total of 1,925 Corynebacterium isolates were tested for antimicrobial susceptibility at the Mayo Clinic Microbiology laboratory (Rochester, Minnesota) from January 2012 to March 2023, with C. striatum (35.6%) and C. amycolatum (24.4%) identified as the predominant species. Species known to potentially carry diphtheria toxin were excluded. Common sources of isolation included skin and soft tissue (56.8%), bone and/or native joint synovial fluid (14.2%), urine (13.1%), sputum (6.1%), and blood (5.9%). For penicillin, susceptibility decreased from 47.5% (58 of 122) in 2012 to 20.6% (14 of 68) in 2023. Isolates also showed a decrease in susceptibility to erythromycin from 22.4% (26 of 116) in 2012 to 13.2% (9 of 68) in 2023. Susceptibility to trimethoprim-sulfamethoxazole averaged around 50% throughout the period. Notably, linezolid and vancomycin were universally effective in vitro against all species. The highest susceptibility rates among tested oral agents were to linezolid and doxycycline for non-C. striatum species. Daptomycin minimal inhibitory concentrations (MICs) of >256 µg/mL were observed for one C. amycolatum isolate, one C. tuberculostearicum isolate, and for seven C. striatum isolates, all from patients with prior daptomycin exposure. Daptomycin MICs of 2 µg/mL (nonsusceptible) were observed in one C. striatum isolate recovered from a daptomycin-naïve patient and in six C. jeikeium isolates, from both daptomycin-exposed and non-exposed patients. Significant variation in susceptibility profiles across different Corynebacterium species underscores the importance of performing antimicrobial susceptibility testing to guide effective treatment. Moreover, multidrug resistance observed in C. striatum poses substantial therapeutic challenges especially in patients requiring prolonged or chronic antibiotic suppression.

2012 年 1 月至 2023 年 3 月期间,梅奥诊所微生物实验室(明尼苏达州罗切斯特市)共对 1,925 个分离出的棒状杆菌进行了抗菌药敏感性检测,其中纹状杆菌(35.6%)和淀粉样棒状杆菌(24.4%)被确定为主要菌种。已知可能携带白喉毒素的菌种被排除在外。常见的分离来源包括皮肤和软组织(56.8%)、骨和/或原始关节滑液(14.2%)、尿液(13.1%)、痰液(6.1%)和血液(5.9%)。青霉素的敏感性从 2012 年的 47.5%(122 例中的 58 例)下降到 2023 年的 20.6%(68 例中的 14 例)。分离菌株对红霉素的敏感性也从2012年的22.4%(116株中的26株)下降到2023年的13.2%(68株中的9株)。在此期间,三甲双氨-磺胺甲噁唑的平均易感率约为 50%。值得注意的是,利奈唑胺和万古霉素在体外对所有菌种普遍有效。在测试过的口服药物中,对利奈唑胺和多西环素的敏感率最高,适用于非条纹状球菌。在一个阿米科球菌分离株、一个结核杆菌分离株和七个条纹状球菌分离株中,观察到达托霉素的最小抑菌浓度(MICs)>256 µg/mL,这些菌株均来自曾接触过达托霉素的患者。从一名未使用过达托霉素的患者体内分离出的一个条纹状球菌以及从接触过达托霉素和未接触过达托霉素的患者体内分离出的六个结节性球菌中观察到的达托霉素 MIC 值为 2 µg/mL(不敏感)。不同科里纳菌种的药敏谱差异很大,这突出表明了进行抗菌药敏试验以指导有效治疗的重要性。此外,在纹杆菌中观察到的多药耐药性给治疗带来了巨大挑战,尤其是对于需要长期或慢性抗生素抑制的患者。
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引用次数: 0
A simplified pyrazinamidase test for Mycobacterium tuberculosis pyrazinamide antimicrobial susceptibility testing. 用于结核分枝杆菌吡嗪酰胺抗菌药敏感性试验的简化吡嗪酰胺酶试验。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-18 DOI: 10.1128/jcm.01227-24
Hsin-Hua Chan, Yu-Chen Wang, Ruwen Jou

Pyrazinamide (PZA) is an important first-line drug for tuberculosis (TB) treatment by eradicating the persisting Mycobacterium tuberculosis complex (MTBC). Due to cost and technical challenges, end TB strategies are hampered by the lack of a simple and reliable culture-based PZA antimicrobial susceptibility testing (AST) for routine use. We initially developed a simplified chromogenic pyrazinamidase (PZase) test in the TB reference laboratory using a training set MTBC isolates with various drug-resistant profiles, and validated its performance using consecutive BACTEC MGIT 960 (MGIT)-culture-positive culture in 10 clinical laboratories. The pncA gene Sanger sequencing results were used as the reference, and compared to the MGIT-PZA AST. Differential diagnosis of Mycobacterium bovis was conducted using patented in-house real-time PCR. Of the 106 training isolates, the PZase test and MGIT-PZA AST showed 100.0% and 99.1% concordance as compared to Sanger sequencing, respectively. We found 32.1% (34/106) isolates harbored pncA mutations, including one isolate with silent mutation S65S. For validation, 1,793 clinical isolates were tested including 150 duplicate isolates from specimens of the same cases and 16 isolates with uncharacterized drug resistance (UDR)-associated mutations. Excluding duplicated and UDR isolates, we identified 2.6% (43/1,627) PZA-resistant isolates, including 1.3% (21/1,627) M. bovis isolates. The kappa values were 0.851-1.000. In addition, the accuracy of the PZase test conducted by 10 laboratories was 98.5%-100.0%. Our simplified PZase test demonstrated high concordance with Sanger sequencing and MGIT-PZA AST. Integrating the PZase test into routine first-line AST is effortless and represents an improvement in laboratory services for ending TB.

Importance: We developed and validated a simple pyrazinamidase (PZase) test for pyrazinamide (PZA) antimicrobial susceptibility testing (AST). Our results demonstrated that the PZase test had high agreement with the pncA gene sequencing and MGIT-PZA AST. Integrating PZase test into routine AST is effortless and represents an improvement in laboratory services for ending TB.

吡嗪酰胺(PZA)可根除持续存在的结核分枝杆菌复合体(MTBC),是治疗结核病(TB)的重要一线药物。由于成本和技术方面的挑战,缺乏简单可靠的常规使用的基于培养的 PZA 抗菌药敏试验 (AST),阻碍了结核病的最终治疗策略。我们最初在结核病参比实验室开发了一种简化的色原吡嗪酰胺酶(PZase)检测方法,使用的是具有各种耐药性特征的 MTBC 分离物训练集,并在 10 个临床实验室使用连续的 BACTEC MGIT 960(MGIT)培养阳性培养物验证了其性能。以 pncA 基因 Sanger 测序结果为参考,并与 MGIT-PZA AST 进行比较。使用获得专利的内部实时 PCR 技术对牛分枝杆菌进行鉴别诊断。在 106 个训练分离株中,PZase 检验和 MGIT-PZA AST 与 Sanger 测序的一致性分别为 100.0% 和 99.1%。我们发现 32.1%(34/106)的分离株携带 pncA 突变,其中一个分离株携带沉默突变 S65S。为了进行验证,我们检测了 1,793 个临床分离株,其中包括 150 个来自同一病例标本的重复分离株和 16 个具有未定性耐药性(UDR)相关突变的分离株。除去重复分离株和 UDR 分离株,我们发现了 2.6%(43/1,627)的 PZA 耐药分离株,其中包括 1.3%(21/1,627)的 M. bovis 分离株。卡帕值为 0.851-1.000。此外,10家实验室进行的PZase检测的准确率为98.5%-100.0%。我们的简化 PZase 检测与 Sanger 测序和 MGIT-PZA AST 的一致性很高。将 PZase 检测纳入常规一线 AST 不费吹灰之力,这代表着实验室服务在终结结核病方面的进步:我们开发并验证了一种用于吡嗪酰胺(PZA)抗菌药物敏感性检测(AST)的简单吡嗪酰胺酶(PZase)检测方法。结果表明,PZase 检验与 pncA 基因测序和 MGIT-PZA AST 具有很高的一致性。将 PZase 检测纳入常规 AST 不费吹灰之力,而且还能改善结核病的实验室服务。
{"title":"A simplified pyrazinamidase test for <i>Mycobacterium tuberculosis</i> pyrazinamide antimicrobial susceptibility testing.","authors":"Hsin-Hua Chan, Yu-Chen Wang, Ruwen Jou","doi":"10.1128/jcm.01227-24","DOIUrl":"10.1128/jcm.01227-24","url":null,"abstract":"<p><p>Pyrazinamide (PZA) is an important first-line drug for tuberculosis (TB) treatment by eradicating the persisting <i>Mycobacterium tuberculosis</i> complex (MTBC). Due to cost and technical challenges, end TB strategies are hampered by the lack of a simple and reliable culture-based PZA antimicrobial susceptibility testing (AST) for routine use. We initially developed a simplified chromogenic pyrazinamidase (PZase) test in the TB reference laboratory using a training set MTBC isolates with various drug-resistant profiles, and validated its performance using consecutive BACTEC MGIT 960 (MGIT)-culture-positive culture in 10 clinical laboratories. The <i>pncA</i> gene Sanger sequencing results were used as the reference, and compared to the MGIT-PZA AST. Differential diagnosis of <i>Mycobacterium bovis</i> was conducted using patented in-house real-time PCR. Of the 106 training isolates, the PZase test and MGIT-PZA AST showed 100.0% and 99.1% concordance as compared to Sanger sequencing, respectively. We found 32.1% (34/106) isolates harbored <i>pncA</i> mutations, including one isolate with silent mutation S65S. For validation, 1,793 clinical isolates were tested including 150 duplicate isolates from specimens of the same cases and 16 isolates with uncharacterized drug resistance (UDR)-associated mutations. Excluding duplicated and UDR isolates, we identified 2.6% (43/1,627) PZA-resistant isolates, including 1.3% (21/1,627) <i>M</i>. <i>bovis</i> isolates. The kappa values were 0.851-1.000. In addition, the accuracy of the PZase test conducted by 10 laboratories was 98.5%-100.0%. Our simplified PZase test demonstrated high concordance with Sanger sequencing and MGIT-PZA AST. Integrating the PZase test into routine first-line AST is effortless and represents an improvement in laboratory services for ending TB.</p><p><strong>Importance: </strong>We developed and validated a simple pyrazinamidase (PZase) test for pyrazinamide (PZA) antimicrobial susceptibility testing (AST). Our results demonstrated that the PZase test had high agreement with the <i>pncA</i> gene sequencing and MGIT-PZA AST. Integrating PZase test into routine AST is effortless and represents an improvement in laboratory services for ending TB.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0122724"},"PeriodicalIF":6.1,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647977","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}
引用次数: 0
Performance evaluation of the Specific Reveal system for rapid antibiotic susceptibility testing from positive blood cultures containing Gram-negative pathogens. 从含有革兰氏阴性病原体的阳性血液培养物中快速检测抗生素敏感性的 Specific Reveal 系统性能评估。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-15 DOI: 10.1128/jcm.00692-24
Greta Ostermann, Barbara Körber-Irrgang, Alexander Krüger, Pragya Singh, Kenny Vo, Jörg Gielen, Ute Aurbach, Hilmar Wisplinghoff, Nathalie Jazmati

Rapid antimicrobial drug administration is crucial for the efficient treatment of sepsis or septic shock, but empirical therapy is limited by the increasing prevalence of multidrug-resistant bacteria. Thus, rapid and reliable antimicrobial susceptibility testing (AST) is needed to start appropriate antimicrobial drug administration as quickly as possible. In the present study, we evaluated the performance of the Reveal rapid AST system. From February to April 2021, 102 positive blood culture bottles (BCBs) from hospitalized patients with bacteremia caused by Gram-negative bacteria were included in the study. All isolates were tested by the Reveal system directly from the positive BCBs in comparison to the DxM MicroScan WalkAway. Essential agreement (EA) and category agreement (CA) were high with 98.5% and 97.1%, respectively. We also determined the susceptibility of 10 highly resistant CDC & FDA AR strains in duplicate. Here, EA was 99.6% and CA 97.9%. The average time to result by Reveal was 5.4 h ± 1.2 h compared to an average of 16 h by DxM MicroScan WalkAway for clinical strains and 3.8 h ± 1.2 h for more resistant CDC & FDA AR strains. Susceptibility determination with the Reveal rapid AST system directly from positive BCBs is for the frequently represented bug-drug combinations a reliable and accurate approach, meeting the European ISO guideline for the performance of AST systems. Moreover, AST directly from blood cultures performed with the Reveal system saves time when compared to the conventional AST, as no subculturing is needed and time to result is very short.

快速使用抗菌药物对有效治疗脓毒症或脓毒性休克至关重要,但由于耐多药细菌的日益流行,经验疗法受到了限制。因此,需要进行快速、可靠的抗菌药物敏感性检测(AST),以便尽快开始适当的抗菌药物治疗。在本研究中,我们评估了 Reveal 快速 AST 系统的性能。从 2021 年 2 月到 4 月,共有 102 例由革兰氏阴性菌引起的菌血症住院患者的血培养瓶(BCB)检测结果呈阳性。所有分离菌株均由 Reveal 系统直接从阳性 BCB 中进行检测,并与 DxM MicroScan WalkAway 进行比较。基本一致度(EA)和类别一致度(CA)分别为98.5%和97.1%。我们还对 10 株高度耐药的 CDC 和 FDA AR 菌株进行了一式两份的药敏测定。其中,EA 为 99.6%,CA 为 97.9%。用 Reveal 测定结果的平均时间为 5.4 小时 ± 1.2 小时,而用 DxM MicroScan WalkAway 测定临床菌株的平均时间为 16 小时,测定耐药性更强的 CDC 和 FDA AR 菌株的平均时间为 3.8 小时 ± 1.2 小时。使用 Reveal 快速 AST 系统直接从阳性 BCB 进行药敏测定,对于常见的虫-药组合是一种可靠而准确的方法,符合欧洲 ISO AST 系统性能指南的要求。此外,与传统 AST 相比,使用 Reveal 系统直接从血液培养物中进行 AST 可节省时间,因为不需要进行亚培养,而且得出结果的时间非常短。
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引用次数: 0
Evaluation of the KPC/IMP/NDM/VIM/OXA-48 Combo Test Kit and Carbapenem-Resistant K.N.I.V.O. Detection K-Set in detecting KPC variants. 评估 KPC/IMP/NDM/VIM/OXA-48 组合检测试剂盒和耐碳青霉烯类 K.N.I.V.O. 检测 K 套件在检测 KPC 变体方面的效果。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-14 DOI: 10.1128/jcm.01123-24
Aline Valério de Lima, Keila de Oliveira Lima, Paola Cappellano, Sebastian Cifuentes, Nilton Lincopan, Suely Carlos Ferreira Sampaio, Jorge Luiz Mello Sampaio
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引用次数: 0
Clinical pilot of bacterial transcriptional profiling as a combined genotypic and phenotypic antimicrobial susceptibility test. 细菌转录谱分析作为基因型和表型抗菌药敏感性联合检测的临床试验。
IF 5.3 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 Epub Date: 2024-10-21 DOI: 10.1128/jcm.00997-24
E L Young, D J Roach, M A Martinsen, G E G McGrath, N R Holbrook, H E Cho, E Y Seyoum, V M Pierce, R P Bhattacharyya

Antimicrobial resistance is a growing health threat, but standard methods for determining antibiotic susceptibility are slow and can delay optimal treatment, which is especially consequential in severe infections such as bacteremia. Novel approaches for rapid susceptibility profiling have emerged that characterize either bacterial response to antibiotics (phenotype) or detect specific resistance genes (genotype). Genotypic and Phenotypic AST through RNA detection (GoPhAST-R) is a novel assay, performed directly on positive blood cultures, that integrates rapid transcriptional response profiling with the detection of key resistance gene transcripts, thereby providing simultaneous data on both phenotype and genotype. Here, we performed the first clinical pilot of GoPhAST-R on 42 positive blood cultures: 26 growing Escherichia coli, 15 growing Klebsiella pneumoniae, and 1 with both. An aliquot of each positive blood culture was exposed to nine different antibiotics, lysed, and underwent rapid transcriptional profiling on the NanoString platform; results were analyzed using an in-house susceptibility classification algorithm. GoPhAST-R achieved 95% overall agreement with standard antimicrobial susceptibility testing methods, with the highest agreement for beta-lactams (98%) and the lowest for fluoroquinolones (88%). Epidemic resistance genes including the extended spectrum beta-lactamase blaCTX-M-15 and the carbapenemase blaKPC were also detected within the population. This study demonstrates the clinical feasibility of using transcriptional response profiling for rapid resistance determination, although further validation with larger and more diverse bacterial populations will be essential in future work. GoPhAST-R represents a promising new approach for rapid and comprehensive antibiotic susceptibility testing in clinical settings.IMPORTANCEExposure to antibiotics causes differential transcriptional signatures in susceptible vs resistant bacteria. These differences can be leveraged to rapidly predict resistance profiles of Escherichia coli and Klebsiella pneumoniae in clinically positive blood cultures.

抗生素耐药性对健康的威胁与日俱增,但确定抗生素敏感性的标准方法进展缓慢,可能会延误最佳治疗时间,尤其是在菌血症等严重感染中。新出现的快速易感性分析方法可以描述细菌对抗生素的反应(表型)或检测特定的耐药基因(基因型)。通过 RNA 检测基因型和表型 AST(GoPhAST-R)是一种直接在阳性血液培养物上进行的新型检测方法,它将快速转录反应谱分析与关键耐药基因转录本检测结合在一起,从而同时提供表型和基因型数据。在此,我们对 42 份阳性血液培养物进行了 GoPhAST-R 的首次临床试验:其中 26 份培养出大肠埃希菌,15 份培养出肺炎克雷伯菌,1 份同时培养出两种细菌。每个阳性血培养物的等分试样都暴露于 9 种不同的抗生素,裂解后在 NanoString 平台上进行快速转录剖析;使用内部药敏性分类算法对结果进行分析。GoPhAST-R 与标准抗菌素药敏测试方法的总体一致性达到 95%,其中β-内酰胺类药物的一致性最高(98%),氟喹诺酮类药物的一致性最低(88%)。在人群中还检测到了流行性耐药基因,包括广谱β-内酰胺酶blaCTX-M-15和碳青霉烯酶blaKPC。这项研究证明了利用转录反应图谱进行快速耐药性测定的临床可行性,不过在今后的工作中还必须利用更大、更多样化的细菌群体进行进一步验证。GoPhAST-R 是在临床环境中进行快速、全面抗生素敏感性测试的一种很有前途的新方法。重要意义暴露于抗生素会导致易感细菌和耐药细菌的转录特征出现差异。利用这些差异可以快速预测临床阳性血液培养物中大肠埃希菌和肺炎克雷伯菌的耐药性特征。
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引用次数: 0
Reverse-transcriptase real-time PCR in the diagnostic strategy for invasive infections caused by Aspergillus fumigatus. 反转录酶实时荧光定量PCR技术在曲霉菌侵袭性感染诊断策略中的应用。
IF 5.3 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 Epub Date: 2024-10-24 DOI: 10.1128/jcm.00791-24
Charles Gibert, Pauline Tirard-Collet, Charline Miossec, Damien Dupont, Florence Persat, Martine Wallon, Florence Ader, Gilles Devouassoux, Sophie Ducastelle, Hélène Labussière-Wallet, Sylvie Paulus, Céline Guichon, Anne-Claire Lukaszewicz, Jean-Christophe Richard, Florent Wallet, Alexandre Alanio, Meja Rabodonirina, Jean Menotti

The aim was to develop an RT-qPCR targeting Aspergillus fumigatus and compare its performance to that of Aspergillus fumigatus qPCR for the diagnosis of invasive aspergillosis (IA). Samples from patients of the Lyon University hospitals for whom a suspicion of IA led to the realization of an Aspergillus fumigatus qPCR molecular diagnostic test over a 2-year period were included. The patients were classified according to the European Organization for Research and Treatment of Cancer/Mycoses Study Group (EORTC-MSGERC) criteria for suspected IA; RT-qPCR and qPCR assays were performed on all included samples. The sensitivities and specificities of RT-qPCR and qPCR were calculated and compared using the results of the EORTC-MSGERC classification as reference. The cycle threshold (Ct) results were compared according to IA classification and sample type. Among the 193 samples analyzed, 91 were classified as IA excluded, 46 as possible IA, 53 as probable IA, and 3 as proven IA. For all sample types, RT-qPCR was significantly more sensitive than qPCR for all IA classifications with an additional 17/102 samples detected (P-value < 0.01). For plasma samples, sensitivity was significantly higher and specificity significantly lower using RT-qPCR for all IA classifications (P-value < 0.001). The mean Ct obtained with RT-qPCR were significantly lower than those obtained with qPCR for all IA classifications and all sample types (P-value < 0.001 and P-value < 0.0001, respectively). RT-qPCR presents a higher sensitivity than qPCR for the diagnosis of IA due to Aspergillus fumigatus, particularly in samples with an intrinsically low fungal load.IMPORTANCEAspergillus fumigatus belongs to the critical priority group of the World Health Organization fungal priority pathogens list. Invasive aspergillosis (IA) is a life-threatening infection with poor prognosis and challenging diagnosis. PCR has been integrated into the 2020 European Organization for Research and Treatment of Cancer/Mycoses Study Group consensus definitions for IA diagnosis. However, due to frequent low fungal burdens, its sensitivity needs to be improved. This work presents an innovative method for detecting total nucleic acids, corresponding to both ribosomal RNA and DNA, that enables IA diagnosis with greater sensitivity than conventional techniques, especially in non-invasive samples such as blood, enhancing the monitoring of this infection in high-risk patients.

我们的目的是开发一种针对曲霉菌的 RT-qPCR,并比较其与烟曲霉菌 qPCR 在诊断侵袭性曲霉菌病(IA)方面的性能。里昂大学医院在两年内对怀疑患有侵袭性曲霉菌病的患者进行了曲霉菌 qPCR 分子诊断检测。根据欧洲癌症研究和治疗组织/霉菌病研究小组(EORTC-MSGERC)的疑似 IA 标准对患者进行了分类;对所有纳入的样本进行了 RT-qPCR 和 qPCR 检测。以 EORTC-MSGERC 分类结果为参考,计算并比较了 RT-qPCR 和 qPCR 的敏感性和特异性。根据 IA 分类和样本类型对周期阈值(Ct)结果进行了比较。在分析的 193 份样本中,91 份被归类为排除 IA,46 份被归类为可能 IA,53 份被归类为可能 IA,3 份被归类为已证实 IA。在所有样本类型中,RT-qPCR 对所有 IA 分类的灵敏度明显高于 qPCR,多检测出 17/102 个样本(P 值 < 0.01)。对于血浆样本,使用 RT-qPCR 检测所有 IA 分类的灵敏度明显更高,特异性明显更低(P 值 < 0.001)。就所有 IA 分类和所有样本类型而言,使用 RT-qPCR 获得的平均 Ct 值明显低于使用 qPCR 获得的平均 Ct 值(P 值分别 < 0.001 和 P 值 < 0.0001)。在诊断由烟曲霉引起的侵袭性曲霉病时,RT-qPCR 比 qPCR 具有更高的灵敏度,尤其是在真菌含量固有较低的样本中。重要意义烟曲霉属于世界卫生组织真菌优先病原体名单中的关键优先组。侵袭性曲霉菌病(IA)是一种危及生命的感染,预后不良,诊断困难。PCR 已被纳入 2020 年欧洲癌症研究和治疗组织/真菌病研究小组关于 IA 诊断的共识定义。然而,由于真菌负担经常较低,其灵敏度有待提高。本研究提出了一种检测核糖体RNA和DNA总核酸的创新方法,与传统技术相比,该方法可提高IA诊断的灵敏度,尤其是在血液等非侵入性样本中,从而加强对高危患者感染情况的监测。
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引用次数: 0
Characterization of neurologic disease-associated Streptococcus suis strains within the United States swine herd and use of diagnostic tools. 美国猪群中与神经系统疾病相关的猪链球菌菌株特征及诊断工具的使用。
IF 5.3 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 Epub Date: 2024-10-08 DOI: 10.1128/jcm.00374-24
Jessica Santos Streauslin, Daniel W Nielsen, Kent J Schwartz, Rachel J Derscheid, Drew R Magstadt, Eric R Burrough, Phillip C Gauger, Loni L Schumacher, Michael C Rahe, Alyona Michael, Panchan Sitthicharoenchai, Christopher L Siepker, Franco Matias Ferreyra, Marcelo Nunes de Almeida, Rodger Main, Laura K Bradner, Xiao Hu, Ganwu Li, Ana Paula S Poeta Silva, Orhan Sahin, Bailey L Arruda

Streptococcus suis negatively impacts swine health, posing diagnostic and preventative challenges. S. suis can induce disease and also quietly reside on mucosal surfaces. The limited use of diagnostic tools to identify disease-associated strains and rule out differential diagnoses, alongside the complex ecology of S. suis, poses significant challenges in comprehending this important pathogen and defining pathotypes. This study evaluated 2,379 S. suis central nervous system (CNS) isolates from diagnostic submissions between 2015 and 2019. Isolates originating from submissions with histologic evidence of CNS infection (n = 1,032) were further characterized by standard and advanced diagnostic techniques. We identified 29 S. suis serotypes and 4 reclassified serotypes as putative causes of CNS disease. Among these, serotypes 1 and 7 emerged as the predominant putative causes of CNS infection (32% of submissions). Furthermore, 51 sequence types (STs), of which 15 were novel, were detected with ST1 predominating. Through whole-genome sequencing of 145 isolates, we observed that five commonly used virulence-associated genes (VAGs; epf, mrp, sly, ofs, and srtF) were not present in most disease-associated isolates, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) yielded false-positive results in 7% of isolates. These data indicate that (i) clinical signs and site of isolation alone are insufficient for defining a pathotype, (ii) S. suis serotypes and STs associated with CNS infection are more diverse than previously reported, (iii) MALDI-TOF MS may need to be supplemented with additional diagnostic tools for precise S. suis identification, and (iv) VAGs remain an unreliable means for identifying isolates associated with CNS disease.IMPORTANCEStreptococcus suis is an important and complex systemic bacterial pathogen of swine. Characterization of S. suis strains originating from pigs with histologic confirmation of neurologic disease is limited. Review of swine diagnostic submissions revealed that fewer than half of cases from which S. suis was isolated from the brain had histologic evidence of neurologic disease. This finding demonstrates that clinical signs and site of isolation alone are not sufficient for identifying a neurologic disease-associated strain. Characterization of strains originating from cases with evidence of disease using classic and advanced diagnostic techniques revealed that neurologic disease-associated strains are diverse and commonly lack genes previously associated with virulence.

猪链球菌对猪的健康有负面影响,给诊断和预防带来挑战。猪链球菌可诱发疾病,也可静静地栖息在粘膜表面。由于使用的诊断工具有限,无法确定与疾病相关的菌株和排除鉴别诊断,再加上猪链球菌的生态环境复杂,这给了解这种重要病原体和确定病原体类型带来了巨大挑战。本研究评估了 2015 年至 2019 年期间从诊断呈文中分离出的 2379 株猪链球菌中枢神经系统(CNS)分离株。通过标准和先进的诊断技术,对来自有中枢神经系统感染组织学证据(n = 1,032)的分离物进行了进一步鉴定。我们确定了 29 个猪链球菌血清型和 4 个重新分类的血清型可能是中枢神经系统疾病的病因。其中,血清型 1 和 7 成为中枢神经系统感染的主要推定病因(占提交病例的 32%)。此外,还发现了 51 种序列类型(ST),其中 15 种是新的,以 ST1 型为主。通过对 145 株分离株进行全基因组测序,我们观察到大多数与疾病相关的分离株中不存在五个常用的毒力相关基因(VAGs:epf、mrp、sly、ofs 和 srtF),基质辅助激光解吸电离飞行时间质谱法(MALDI-TOF MS)在 7% 的分离株中产生了假阳性结果。这些数据表明:(i) 仅凭临床症状和分离部位不足以确定病原体类型;(ii) 与中枢神经系统感染相关的猪链球菌血清型和 ST 比以前报道的更为多样;(iii) MALDI-TOF MS 可能需要辅以其他诊断工具才能精确鉴定猪链球菌;(iv) VAG 仍是鉴定与中枢神经系统疾病相关分离物的不可靠方法。猪链球菌是一种重要而复杂的全身性细菌病原体,对来自猪的猪链球菌菌株进行特征描述并经组织学证实患有神经系统疾病的情况非常有限。对猪诊断报告的审查显示,从脑中分离出猪链球菌的病例中,只有不到一半有神经系统疾病的组织学证据。这一发现表明,仅凭临床症状和分离部位不足以确定神经系统疾病相关菌株。使用传统和先进的诊断技术对来自有疾病证据的病例的菌株进行特征描述后发现,神经系统疾病相关菌株多种多样,通常缺乏以前与毒力相关的基因。
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引用次数: 0
Whole-genome sequencing resolves biochemical misidentification of Neisseria species from urogenital specimens. 全基因组测序解决了从泌尿生殖系统标本中对奈瑟菌种的生化鉴别错误。
IF 5.3 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 Epub Date: 2024-10-03 DOI: 10.1128/jcm.00704-24
Amanda C Smith, Apurva Shrivastava, John C Cartee, Myriam Bélanger, Samera Sharpe, Jorden Lewis, Suzanna Budionno, Raquel Gomez, Manjeet K Khubbar, Cau D Pham, Kim M Gernert, Matthew W Schmerer, Brian H Raphael, Emily R Learner, Ellen N Kersh, Sandeep J Joseph

Neisseria meningitidis (Nm) and Neisseria gonorrhoeae (Ng) are human pathogens that sometimes occupy the same anatomical niche. Ng, the causative agent of gonorrhea, infects 87 million individuals annually worldwide and is an urgent threat due to increasing drug resistance. Ng is a pathogen of the urogenital tract and may infect the oropharyngeal or rectal site, often asymptomatically. Conversely, Nm is an opportunistic pathogen. While often a commensal in the oropharyngeal tract, it is also the leading cause of bacterial meningitis with 1.2 million cases globally, causing significant morbidity and mortality. Horizontal gene transfer (HGT) is likely to occur between Ng and Nm due to their shared anatomical niches and genetic similarity, which poses challenges for accurate detection and treatment. Routine surveillance through the Gonococcal Isolate Surveillance Project and Strengthening the U.S. Response to Resistant Gonorrhea detected six concerning urogenital Neisseria isolates with contradicting species identification in Milwaukee (MIL). While all six isolates were positive for Ng using nucleic acid amplification testing (NAAT) and matrix-assisted laser desorption/ionization time of flight identified the isolates as Ng, two biochemical tests, Gonochek-II and API NH, classified them as Nm. To address this discrepancy, we performed whole-genome sequencing (WGS) using Illumina MiSeq on all isolates and employed various bioinformatics tools. Species detection analysis using BMScan, which uses WGS data, identified all isolates as Ng. Furthermore, Kraken revealed over 98% of WGS reads mapped to the Ng genome and <1% to Nm. Recombination analysis identified putative HGT in all MIL isolates within the γ-glutamyl transpeptidase (ggt) gene, a key component in the biochemical tests used to differentiate between Nm and Ng. Further analysis identified Nm as the source of HGT event. Specifically, the active Nm ggt gene replaced the Ng pseudogenes, ggt1 and ggt2. Together, this study demonstrates that closely related Neisseria species sharing a niche underwent HGT, which led to the misidentification of species following biochemical testing. Importantly, NAAT accurately detected Ng. The misidentification highlights the importance of using WGS to continually evaluate diagnostic or bacterial identification tests.

脑膜炎奈瑟菌(Neisseria meningitidis,Nm)和淋病奈瑟菌(Neisseria gonorrhoeae,Ng)是人类病原体,有时会占据相同的解剖位置。淋病奈瑟菌是淋病的致病菌,每年全球有 8700 万人感染淋病,由于耐药性不断增加,淋病奈瑟菌已成为一个紧迫的威胁。Ng 是泌尿生殖道的病原体,也可能感染口咽部或直肠部位,通常无症状。相反,Nm 是一种机会性病原体。虽然 Nm 通常是口咽道的共生菌,但它也是细菌性脑膜炎的主要病因,全球有 120 万病例,造成严重的发病率和死亡率。由于 Ng 和 Nm 具有共同的解剖壁龛和基因相似性,它们之间很可能发生水平基因转移 (HGT),这给准确检测和治疗带来了挑战。在密尔沃基(MIL),通过淋球菌分离监测项目和加强美国对耐药淋病的应对措施进行的常规监测发现了六例与泌尿生殖器奈瑟菌有关的分离株,其菌种鉴定相互矛盾。通过核酸扩增检测(NAAT)和基质辅助激光解吸/电离飞行时间检测,这六例分离物均呈伍氏杆菌阳性,但 Gonochek-II 和 API NH 这两种生化检测却将它们归类为奈瑟氏杆菌。为了解决这一差异,我们使用 Illumina MiSeq 对所有分离物进行了全基因组测序(WGS),并使用了多种生物信息学工具。利用 WGS 数据进行的物种检测分析(BMScan)确定所有分离物均为 Ng。此外,Kraken 发现超过 98% 的 WGS 读数映射到 Ng 基因组和 ggt)基因上,该基因是用于区分 Nm 和 Ng 的生化测试的关键成分。进一步分析发现,Nm 是 HGT 事件的源头。具体来说,活跃的 Nm ggt 基因取代了 Ng 伪基因 ggt1 和 ggt2。总之,这项研究表明,共享一个生态位的近缘奈瑟氏菌物种发生了 HGT,这导致了生化检测中物种的错误识别。重要的是,NAAT 准确检测到了 Ng。这次错误鉴定凸显了使用 WGS 对诊断或细菌鉴定测试进行持续评估的重要性。
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引用次数: 0
The Brief Case: A fatal case of Legionella pneumophila in an elderly patient. 简要病例:一名老年患者感染嗜肺军团菌的致命病例。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 DOI: 10.1128/jcm.00863-24
Andrew Sulaiman, Emily Gisriel, Karen C Carroll
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引用次数: 0
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Journal of Clinical Microbiology
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