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Host blood protein biomarkers to screen for tuberculosis disease: a systematic review and meta-analysis. 用于筛查结核病的宿主血液蛋白生物标志物:系统综述和荟萃分析。
IF 5.3 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 Epub Date: 2024-10-24 DOI: 10.1128/jcm.00786-24
Mary Gaeddert, Kerstin Glaser, Bih H Chendi, Ayten Sultanli, Lisa Koeppel, Emily L MacLean, Tobias Broger, Claudia M Denkinger

Non-sputum tests are needed to improve tuberculosis (TB) diagnosis and close the diagnostic gap. The World Health Organization's target product profile (TPP) for point-of-care (POC) screening tests requires a minimum sensitivity of 90% and a specificity of 70%. Our objective was to identify host blood protein biomarkers meeting TPP criteria. A systematic review was conducted and reported following PRISMA guidelines. Data extraction and quality assessment with Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) were completed for the included studies. Heterogeneity was assessed. For biomarkers reporting sensitivity and specificity in at least four studies, a random-effects meta-analysis was performed for biomarkers with similar cut-offs. We screened 4,651 citations and included 65 studies that enrolled 16,010 participants and evaluated 156 host proteins. Most (47/65) studies enrolled adult pulmonary TB (PTB), with 15 studies in adult extra-pulmonary TB and 5 in children. Small early-stage discovery studies with case-control design were common (24/65) and had a high risk of bias. For adult PTB, CRP, IP-10, NCAM-1, and SAA met TPP criteria in high-quality studies. There was a high degree of heterogeneity in biomarker cut-offs and study design. CRP at 10 mg/L cut-off was meta-analyzed from 10 studies; pooled sensitivity 86% [95% confidence interval (CI): 80-95] and pooled specificity 67% (95% CI: 54-79). In people living with HIV (six studies), CRP pooled sensitivity was 93% (95% CI: 90-95), and pooled specificity was 59% (95% CI: 40-78). We identified promising biomarkers that performed well in high-quality studies. Data overall are limited and highly heterogenous. Further standardized validation across subgroups in prospective studies is needed before translating into POC assays.

Importance: To our knowledge, this is the first comprehensive systematic review of host blood protein biomarkers for tuberculosis (TB), and we identified promising biomarkers for a TB screening test.

要改善结核病(TB)诊断并缩小诊断差距,就需要非痰检验。世界卫生组织针对床旁(POC)筛查检验的目标产品规格(TPP)要求灵敏度至少达到 90%,特异性至少达到 70%。我们的目标是找出符合 TPP 标准的宿主血液蛋白生物标志物。我们按照 PRISMA 指南进行了系统综述和报告。对纳入的研究进行了数据提取和诊断准确性研究质量评估-2(QUADAS-2)质量评估。对异质性进行了评估。对于至少有四项研究报告了敏感性和特异性的生物标志物,我们对具有相似临界值的生物标志物进行了随机效应荟萃分析。我们筛选了 4,651 篇引文,纳入了 65 项研究,这些研究共招募了 16,010 名参与者,评估了 156 种宿主蛋白质。大多数研究(47/65)的研究对象是成人肺结核(PTB),15 项研究的对象是成人肺外结核,5 项研究的对象是儿童。采用病例对照设计的小型早期发现研究很常见(24/65),偏倚风险很高。对于成人 PTB,CRP、IP-10、NCAM-1 和 SAA 符合高质量研究的 TPP 标准。生物标志物的临界值和研究设计存在高度异质性。10 项研究对 CRP 的 10 mg/L 临界值进行了荟萃分析;汇总灵敏度为 86%[95% 置信区间 (CI):80-95],汇总特异性为 67%(95% CI:54-79)。在艾滋病毒感染者中(6 项研究),CRP 的集合灵敏度为 93%(95% CI:90-95),集合特异性为 59%(95% CI:40-78)。我们发现了在高质量研究中表现良好的有前景的生物标志物。总体数据有限且高度异质性。在转化为 POC 检测方法之前,还需要在前瞻性研究中对不同亚组进行进一步的标准化验证:据我们所知,这是对结核病(TB)宿主血液蛋白生物标志物的首次全面系统综述,我们为结核病筛查检验确定了有前景的生物标志物。
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引用次数: 0
Photo Quiz: Skin scraping of persistent lesion reveals the main course. 照片测验:刮除顽固病灶的皮肤可发现主要病变。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 DOI: 10.1128/jcm.00220-24
Christopher Attaway, Jennifer Andrasko, Anisha Misra
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引用次数: 0
Evaluation of gradient strip diffusion for susceptibility testing of aztreonam-avibactam in metallo-β-lactamase-producing Enterobacterales. 评估梯度条带扩散法在产金-β-内酰胺酶肠杆菌中对阿曲南唑-阿维菌素的药敏试验。
IF 5.3 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 Epub Date: 2024-09-30 DOI: 10.1128/jcm.00649-24
Jamie K Lemon, Cheryl Jankowsi-Romano, Scott Duong, Stefan Juretschko, Vincent A Streva

The emergence of metallo-β-lactamase (MBL)-producing Enterobacterales presents unique clinical treatment challenges. Recently developed β-lactam/ β-lactamase inhibitor combination agents, while effective against other carbapenemase-producing organisms, are notably ineffective against MBL producers. While MBLs do not hydrolyze monobactams (aztreonam), many MBL-producing organisms are resistant to aztreonam through alternate mechanisms, leaving cefiderocol as the sole monotherapy treatment option recommended for MBL producers. Recent guidelines for the treatment of MBL-harboring organisms have added combination therapy with aztreonam and ceftazidime-avibactam, using ceftazidime-avibactam as a source of the β-lactamase inhibitor avibactam. Current laboratory testing options for the combination of aztreonam-avibactam are limited to broth microdilution (BMD) and broth disk elution (BDE) methods, which are not practical in most clinical laboratories. In this study, we evaluated the performance of aztreonam/avibactam gradient strips on 103 MBL-producing Enterobacterales patient isolates as well as an additional 31 isolates from the CDC AR Bank. All MBL Enterobacterales patient isolates included in this study harbored a New Delhi metallo-β-lactamase (blaNDM) gene. Essential agreement of gradient strip minimal inhibitory concentrations (MICs) for patient isolates compared to BMD was 93.2%. While there are no established breakpoints for aztreonam-avibactam, category agreement (CA) for patient isolates was 97.1% when using the CLSI aztreonam breakpoints. There were no major or very major errors observed. There were three minor errors. Precision for aztreonam-avibactam gradient strip diffusion was 100%. These data demonstrate that the use of gradient strip diffusion for aztreonam-avibactam MIC determination in MBL-producing Enterobacterales is a viable option for clinical laboratories.

产金属-β-内酰胺酶(MBL)肠杆菌的出现给临床治疗带来了独特的挑战。最近开发的 β-内酰胺/β-内酰胺酶抑制剂复方制剂虽然对其他产碳青霉烯酶的微生物有效,但对 MBL 生产者明显无效。虽然 MBL 不会水解单内酰胺(阿曲南),但许多产生 MBL 的病菌会通过其他机制对阿曲南产生耐药性,因此头孢哌酮成为针对 MBL 生产者推荐的唯一单一疗法。最近,治疗产生 MBL 的微生物的指南增加了唑曲南和头孢唑肟-阿维菌素的联合疗法,使用头孢唑肟-阿维菌素作为 β-内酰胺酶抑制剂阿维菌素的来源。目前对阿曲南类-阿维菌素复方制剂的实验室检测方法仅限于肉汤微量稀释法(BMD)和肉汤盘洗脱法(BDE),而这两种方法在大多数临床实验室并不实用。在本研究中,我们对 103 例产生 MBL 的肠杆菌患者分离物以及另外 31 例来自疾病预防控制中心 AR 库的分离物进行了唑曲南/阿维菌素梯度条的性能评估。本研究中的所有 MBL 肠杆菌患者分离物均携带新德里金属-β-内酰胺酶(blaNDM)基因。患者分离物的梯度条带最小抑菌浓度 (MIC) 与 BMD 的基本一致率为 93.2%。虽然目前还没有确立阿兹曲南-阿维巴坦的断点,但在使用 CLSI 阿兹曲南断点时,患者分离物的类别一致性(CA)为 97.1%。没有发现重大或非常重大的错误。有三个轻微错误。阿兹菌素-阿维菌素梯度条带扩散的精确度为 100%。这些数据表明,使用梯度条带扩散法测定产甲氧苄啶肠杆菌的阿兹菌素-阿维菌素 MIC 值是临床实验室的可行选择。
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引用次数: 0
Clinical performance evaluation of the BioFire Joint Infection Panel. BioFire 关节感染面板的临床性能评估。
IF 5.3 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 Epub Date: 2024-10-09 DOI: 10.1128/jcm.01022-24
Rose A Lee

The BioFire Joint Infection (JI) Panel offers a significant advancement in the rapid diagnosis of joint infections by facilitating the simultaneous detection of multiple bacterial and fungal pathogens, as well as resistance markers, directly from synovial fluid samples. An article published in the Journal of Clinical Microbiology by Moran et al. (J Clin Microbiol 62:e00182-24, 2024, https://doi.org/10.1128/jcm.00182-24) presents both prospective and retrospective analyses of the panel's real-world clinical application. The study highlights the panel's benefits, such as its rapid turnaround time and ability to identify challenging pathogens, while also discussing its limitations, particularly in detecting certain off-panel organisms.

BioFire 关节感染 (JI) 检测试剂盒可直接从滑膜液样本中同时检测多种细菌和真菌病原体以及耐药性标记物,是关节感染快速诊断的一大进步。Moran 等人在《临床微生物学杂志》(J Clin Microbiol 62:e00182-24, 2024, https://doi.org/10.1128/jcm.00182-24)上发表的一篇文章介绍了该检测板在实际临床应用中的前瞻性和回顾性分析。该研究强调了该小组的优点,如快速的周转时间和识别挑战性病原体的能力,同时也讨论了其局限性,特别是在检测某些非小组生物方面。
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引用次数: 0
Oxford Nanopore's 2024 sequencing technology for Listeria monocytogenes outbreak detection and source attribution: progress and clone-specific challenges. 牛津纳米孔公司的 2024 测序技术用于李斯特菌疫情检测和来源归因:进展与特定克隆的挑战。
IF 5.3 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 Epub Date: 2024-10-04 DOI: 10.1128/jcm.01083-24
Michael Biggel, Nicole Cernela, Jule Anna Horlbog, Roger Stephan

Whole genome sequencing is an essential cornerstone of pathogen surveillance and outbreak detection. Established sequencing technologies are currently being challenged by Oxford Nanopore Technologies (ONT), which offers an accessible and cost-effective alternative enabling gap-free assemblies of chromosomes and plasmids. Limited accuracy has hindered its use for investigating pathogen transmission, but recent technology updates have brought significant improvements. To evaluate its readiness for outbreak detection, we selected 78 Listeria monocytogenes isolates from diverse lineages or known epidemiological clusters for sequencing with ONT's V14 Rapid Barcoding Kit and R10.4.1 flow cells. The most accurate of several tested workflows generated assemblies with a median of one error (SNP or indel) per assembly. For 66 isolates, the cgMLST profiles from ONT-only assemblies were identical to those generated from Illumina data. Eight assemblies were of lower quality, with more than 20 erroneous sites each, primarily caused by methylations at the GAAGAC motif (5'-GAAG6mAC-3'/5'-GT4mCTTC-3'). This led to inaccurate clustering, failing to group isolates from a persistence-associated clone that carried the responsible restriction-modification system. Out of 50 methylation motifs detected among the 78 isolates, only the GAAGAC motif was linked to substantially increased error rates. Our study shows that most L. monocytogenes genomes assembled from ONT-only data are suitable for high-resolution genotyping, but further improvements of chemistries or basecallers are required for reliable routine use in outbreak and food safety investigations.

全基因组测序是病原体监控和疫情检测的重要基石。目前,牛津纳米孔技术公司(ONT)正在对现有的测序技术提出挑战,该公司提供了一种方便、经济的替代技术,可实现染色体和质粒的无间隙组装。有限的准确性阻碍了它在病原体传播调查中的应用,但最近的技术更新带来了重大改进。为了评估其在疫情检测方面的准备情况,我们从不同的菌系或已知的流行病集群中选择了 78 个李斯特菌分离物,用 ONT 的 V14 快速条形码试剂盒和 R10.4.1 流式细胞进行测序。在几种测试的工作流程中,最准确的工作流程生成的组装结果中位数为每个组装结果只有一个错误(SNP 或 indel)。对于 66 个分离物,纯 ONT 组装生成的 cgMLST 图谱与 Illumina 数据生成的完全相同。有 8 个装配质量较低,每个装配有 20 多个错误位点,主要是由 GAAGAC 主题(5'-GAAG6mAC-3'/5'-GT4mCTTC-3')的甲基化造成的。这导致了不准确的聚类,无法将携带限制性修饰系统的持久性相关克隆中的分离物进行聚类。在 78 个分离株中检测到的 50 个甲基化主题中,只有 GAAGAC 主题与错误率大幅增加有关。我们的研究表明,仅用 ONT 数据组装的大多数单核细胞增多症基因组适合于高分辨率基因分型,但要在疫情爆发和食品安全调查中可靠地常规使用,还需要进一步改进化学试剂或唤基程序。
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引用次数: 0
Persistent bloodstream infection in children: examining the role for repeat blood cultures. 儿童持续性血流感染:研究重复血液培养的作用。
IF 5.3 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 Epub Date: 2024-10-04 DOI: 10.1128/jcm.00998-24
Christine M Puthawala, Richard S Feinn, José Rivera-Viñas, Hanna Lee, Thomas S Murray, David R Peaper

Repeat blood cultures are common in children after an initial positive culture. However, in contrast to adults, there are little data to help guide clinicians when a repeat culture is necessary to assess for persistent bacteremia. This study identifies factors associated with persistent bloodstream infections (BSI) in children to inform diagnostic stewardship. This cross-sectional study of children less than 18 years with at least one positive blood culture over a 5-year period utilized a generalized linear equation model to predict patient and microbial factors associated with persistent BSI defined as a positive blood culture with the same organism >48 hours after the index culture. Four hundred and five patients had 502 positive blood cultures yielding 556 organisms. Sixty-seven (13.2%) cultures were persistently positive. Anaerobic organisms (0/37) and Streptococcus species (0/104) were never recovered from repeat cultures. Staphylococcus aureus (OR 9.45, CI 5.15-17.35) and yeast (OR 78.18, CI 9.45-646.6) were statistically associated with persistent BSI. Patients with prior positive cultures (OR 1.44, CI 1.12-1.84) or a central venous catheter (OR 2.20, 95% CI 1.04-3.92) were also at risk for persistence. Immune dysfunction and elevated inflammatory markers at the time of the index blood culture were not significantly associated with persistence. Yeast or S. aureus were associated with persistent BSI, while anaerobes and Streptococcus species were never persistent. Patient characteristics at the time of blood draw did not predict persistence other than having previous positive blood cultures or a central venous catheter. These data can inform when repeat blood cultures have clinical value and reduce the risk of unnecessary blood draws in children.

Importance: We identify factors associated with bloodstream infection persistence in children. Our findings can help guide blood culture stewardship efforts in pediatric patients, especially in light of blood culture supply shortages.

儿童在初次培养阳性后,重复血液培养很常见。然而,与成人不同的是,几乎没有数据可以帮助指导临床医生何时需要进行重复培养以评估持续性菌血症。本研究确定了与儿童持续性血流感染(BSI)相关的因素,为诊断管理提供参考。这项横断面研究针对 5 年内至少有一次血培养阳性的 18 岁以下儿童,利用广义线性方程模型来预测与持续性 BSI 相关的患者和微生物因素,持续性 BSI 的定义是指在指数培养后 48 小时以上同一菌体的血培养呈阳性。四百零五名患者共进行了 502 次阳性血液培养,培养出 556 种生物。67份(13.2%)培养结果持续呈阳性。重复培养中从未发现厌氧菌(0/37)和链球菌(0/104)。金黄色葡萄球菌(OR 9.45,CI 5.15-17.35)和酵母菌(OR 78.18,CI 9.45-646.6)与持续性 BSI 有统计学关联。既往培养阳性(OR 1.44,CI 1.12-1.84)或使用中心静脉导管(OR 2.20,95% CI 1.04-3.92)的患者也有持续感染的风险。免疫功能障碍和指数血培养时炎症标志物升高与持续感染无明显关系。酵母菌或金黄色葡萄球菌与 BSI 持续存在有关,而厌氧菌和链球菌从未持续存在。除了曾有过阳性血培养或中心静脉导管外,抽血时的患者特征并不能预测持续性。这些数据可帮助我们了解重复血培养何时具有临床价值,并降低儿童不必要的抽血风险:我们确定了与儿童血流感染持续存在相关的因素。我们的研究结果有助于指导儿科患者的血培养管理工作,尤其是在血培养供应短缺的情况下。
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引用次数: 0
Candida guilliermondii fungemia: a 12-year retrospective review of antimicrobial susceptibility patterns at a reference laboratory and tertiary care center. Guilliermondii 念珠菌菌血症:参考实验室和三级医疗中心抗菌药敏感性模式的 12 年回顾性研究。
IF 5.3 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 Epub Date: 2024-10-23 DOI: 10.1128/jcm.01057-24
Jack W McHugh, David R Bayless, Nischal Ranganath, Ryan W Stevens, Dalton R Kind, Nancy L Wengenack, Aditya S Shah

The prevalence of invasive candidiasis caused by non-albicans Candida species is increasing. Candida guilliermondii is an infrequent cause of candidemia but has been associated with decreased susceptibility to triazoles. Clinical data related to the infection with C. guilliermondii are sparse. Our study evaluated the antifungal susceptibility testing (AST) for C. guilliermondii isolates submitted to a reference laboratory over a 12-year period (2012-2023). AST patterns were examined using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) epidemiological cutoff values (ECVs) and breakpoints. Where isolates were identified from patients treated at our institution, retrospective chart review was performed to describe patient risk factors, treatment approaches, and outcomes associated with C. guilliermondii fungemia. One hundred twelve blood culture isolates of C. guilliermondii were identified, and clinical data were available for 21 fungemic patients. A significant number of isolates (9.8-20.5%) were observed to be non-wild type for various triazoles. All isolates were susceptible to micafungin. A majority (76.2%) of cases of C. guilliermondii fungemia treated at our tertiary care center were hospital-acquired, and two-thirds of patients were immunocompromised at the time of diagnosis. Ten of the 21 patients died within 60 days of fungemia, although mortality was directly or partially attributed to C. guilliermondii fungemia in only four cases (19.0%). Echinocandins may be used for empiric therapy for C. guilliermondii until the results of AST are available. Further research is required to determine appropriate clinical breakpoints for triazoles.

Importance: Our study addresses a significant knowledge gap in the clinical management of this non-Candida albicans species. Our retrospective review includes comprehensive AST data for 112 Candida guilliermondii isolates, which is the largest number of isolates reported from the United States to date. Susceptibility data are supplemented by clinical outcomes, where isolates were identified for patients treated at Mayo Clinic. Key findings from our study include the observation that a notable proportion of C. guilliermondii isolates exhibit non-wild-type profiles for various triazoles. Importantly, all isolates remained susceptible to echinocandins, suggesting their efficacy as first-line therapy in the absence of timely susceptibility results. Furthermore, our study highlights the high mortality associated with C. guilliermondii fungemia in immunocompromised patients, emphasizing the urgent need for optimized treatment strategies.

由非阿氏念珠菌引起的侵袭性念珠菌病的发病率正在上升。guilliermondii 念珠菌是念珠菌血症的一个不常见原因,但与对三唑类药物的敏感性降低有关。与guilliermondii念珠菌感染有关的临床数据很少。我们的研究评估了 12 年内(2012-2023 年)提交给参考实验室的 C. guilliermondii 分离物的抗真菌药敏试验 (AST)。采用临床与实验室标准协会(CLSI)和欧洲抗菌药物敏感性检测委员会(EUCAST)的流行病学截断值(ECV)和断点对 AST 模式进行了检测。在本机构接受治疗的患者中发现分离物时,我们进行了回顾性病历审查,以描述与吉氏真菌血症相关的患者风险因素、治疗方法和结果。共鉴定出 112 株血液培养分离出的吉氏真菌,并获得了 21 例真菌血症患者的临床数据。观察到大量分离株(9.8%-20.5%)对各种三唑类药物均为非野生型。所有分离株都对米卡芬净敏感。在我们的三级医疗中心治疗的大多数(76.2%)吉氏真菌血症病例都是在医院获得的,三分之二的患者在确诊时免疫力低下。21例患者中有10例在真菌血症发生后60天内死亡,但只有4例(19.0%)患者的死亡直接或部分归因于吉氏真菌血症。在获得 AST 结果之前,棘白菌素可用于治疗吉氏真菌的经验疗法。需要进一步研究确定三唑类药物的适当临床断点:重要意义:我们的研究填补了非白色念珠菌临床治疗方面的一个重大知识空白。我们的回顾性研究包括 112 株 Guilliermondii 念珠菌分离株的全面 AST 数据,这是迄今为止从美国报告的最大数量的分离株。在梅奥诊所接受治疗的患者的分离物中发现的临床结果补充了易感性数据。我们研究的主要发现包括观察到相当一部分吉列蒙第孢子菌分离株对各种三唑类药物表现出非野生型特征。重要的是,所有分离株对棘白菌素仍然敏感,这表明在没有及时获得药敏结果的情况下,棘白菌素可作为一线治疗药物。此外,我们的研究还突显了免疫力低下的患者中与吉氏真菌病相关的高死亡率,强调了优化治疗策略的迫切需要。
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引用次数: 0
An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022-2023. 关于 2022-2023 年描述的从水生宿主物种中分离的细菌的新分类群和修订分类地位的最新情况。
IF 5.3 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 Epub Date: 2024-10-24 DOI: 10.1128/jcm.01043-24
Claire R Burbick, Sara D Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson

The description of new taxa and nomenclature updates to currently known taxa from aquatic animal species continues. After a review of the literature from 2022 and 2023, multiple lists of bacteria, including members of Phylum Planctomycetota, were compiled. As with the previous review, most bacteria are oxidase-positive Gram-negative bacilli with familiar families including new taxa in Aeromonadaceae, Flavobacteriaceae, and Vibrionaceae. A number of Gram-positive bacilli are described including new taxa in the Nocardioides, Paenibacillus, and Streptomyces genera. Two anaerobic species are listed, and one new member of Family Planctomycetaceae is noted. Revised taxa are briefly mentioned. The majority of new and revised taxa are isolated from healthy aquatic animals, and therefore, the role of these new bacteria in health and disease is unknown. Bacteria with pathogenic association and potential production of bioactive substances are highlighted.

新类群的描述和目前已知水生动物类群的命名更新工作仍在继续。在对 2022 年和 2023 年的文献进行回顾后,编制了多个细菌列表,其中包括 Planctomycetota 门的成员。与之前的回顾一样,大多数细菌都是氧化酶阳性革兰氏阴性杆菌,其中包括熟悉的科,包括气单胞菌科(Aeromonadaceae)、黄杆菌科(Flavobacteriaceae)和弧菌科(Vibrionaceae)中的新类群。描述了一些革兰氏阳性杆菌,包括 Nocardioides 属、Paenibacillus 属和 Streptomyces 属中的新类群。还列出了两个厌氧菌种,并指出了 Planctomycetaceae 科的一个新成员。简要提及了修订类群。大多数新分类群和修订分类群都是从健康水生动物中分离出来的,因此这些新细菌在健康和疾病中的作用尚不清楚。重点介绍了具有致病性和可能产生生物活性物质的细菌。
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引用次数: 0
A novel machine-learning aided platform for rapid detection of urine ESBLs and carbapenemases: URECA-LAMP. 用于快速检测尿液中 ESBLs 和碳青霉烯酶的新型机器学习辅助平台:URECA-LAMP。
IF 5.3 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 Epub Date: 2024-10-24 DOI: 10.1128/jcm.00869-24
L Ricardo Castellanos, Ryan Chaffee, Hitendra Kumar, Biniyam Kahsay Mezgebo, Pawulos Kassau, Gisele Peirano, Johann D D Pitout, Keekyoung Kim, Dylan R Pillai

Pathogenic gram-negative bacteria frequently carry genes encoding extended-spectrum beta-lactamases (ESBL) and/or carbapenemases. Of great concern are carbapenem resistant Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Despite the need for rapid AMR diagnostics globally, current molecular detection methods often require expensive equipment and trained personnel. Here, we present a novel machine-learning-aided platform for the rapid detection of ESBLs and carbapenemases using Loop-mediated isothermal Amplification (LAMP). The platform consists of (i) an affordable device for sample lysis, LAMP amplification, and visual fluorometric detection; (ii) a LAMP screening panel to detect the most common ESBL and carbapenemase genes; and (iii) a smartphone application for automated interpretation of results. Validation studies on clinical isolates and urine samples demonstrated percent positive and negative agreements above 95% for all targets. Accuracy, precision, and recall values of the machine learning model deployed in the smartphone application were all above 92%. Providing a simplified workflow, minimal operation training, and results in less than an hour, this study demonstrated the platform's feasibility for near-patient testing in resource-limited settings.IMPORTANCEExtended-spectrum beta-lactamases (ESBL) and carbapenemases confer resistance to third-generation cephalosporins and carbapenems in pathogenic Gram-negative bacteria such as Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Conventional antimicrobial susceptibility testing is based on phenotypic methods, and results can take several days to be obtained. Current genotypic detection methods can be rapid but require expensive equipment and trained personnel. In this study, we present a novel machine learning-aided platform for the rapid detection of ESBLs and carbapenemases using Loop-mediated isothermal Amplification (LAMP). The validation of the platform demonstrated percent positive and negative agreements above 95% for all targets. The newly developed platform provided a simplified workflow, minimal technical training, and results in less than an hour. This study demonstrated the platform's feasibility for rapid testing of ESBL and carbapenemases in bacteria and urine specimens.

致病性革兰氏阴性菌经常携带编码广谱β-内酰胺酶(ESBL)和/或碳青霉烯酶的基因。耐碳青霉烯类的大肠埃希菌、肺炎克雷伯氏菌、铜绿假单胞菌和鲍曼不动杆菌最令人担忧。尽管全球都需要快速的 AMR 诊断,但目前的分子检测方法往往需要昂贵的设备和训练有素的人员。在此,我们介绍一种新型机器学习辅助平台,利用环路介导等温扩增(LAMP)技术快速检测 ESBLs 和碳青霉烯酶。该平台包括:(i) 用于样品裂解、LAMP 扩增和可视荧光检测的经济型设备;(ii) 用于检测最常见 ESBL 和碳青霉烯酶基因的 LAMP 筛选面板;(iii) 用于自动解读结果的智能手机应用程序。对临床分离物和尿液样本进行的验证研究表明,所有目标的阳性和阴性一致率均超过 95%。智能手机应用中部署的机器学习模型的准确度、精确度和召回值均超过 92%。这项研究提供了简化的工作流程、最少的操作培训和不到一小时的结果,证明了该平台在资源有限的环境中进行就近病人检测的可行性。重要意义扩展谱β-内酰胺酶(ESBL)和碳青霉烯酶使大肠埃希菌、肺炎克雷伯菌、铜绿假单胞菌和鲍曼不动杆菌等致病性革兰氏阴性菌对第三代头孢菌素和碳青霉烯类产生耐药性。传统的抗菌药敏感性检测以表型法为基础,需要几天时间才能得出结果。目前的基因型检测方法虽然快速,但需要昂贵的设备和训练有素的人员。在本研究中,我们提出了一种新型机器学习辅助平台,利用环路介导等温扩增法(LAMP)快速检测 ESBLs 和碳青霉烯酶。该平台的验证结果表明,所有目标的阳性和阴性一致率均超过 95%。新开发的平台简化了工作流程,只需极少的技术培训,不到一小时就能得出结果。这项研究证明了该平台在快速检测细菌和尿液标本中的 ESBL 和碳青霉烯酶方面的可行性。
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引用次数: 0
Approaches to developing and implementing a molecular diagnostics stewardship program for infectious diseases: an ASM Laboratory Practices Subcommittee report. 制定和实施传染病分子诊断监管计划的方法:ASM 实验室规范小组委员会报告。
IF 5.3 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-11-13 Epub Date: 2024-10-21 DOI: 10.1128/jcm.00941-24
Frances Valencia-Shelton, Neil Anderson, Elizabeth L Palavecino, Maria E Navas, Paige M K Larkin, Rosemary She, Laura M Filkins

Diagnostic stewardship (DxS) for infectious disease testing requires a multi-disciplinary approach to optimize test selection, performance, interpretation and patient treatment. Nucleic acid amplification-based tests for the diagnosis of infectious diseases, or "molecular microbiology tests," have rapidly expanded over the past two decades. With the increased availability and complexity of these tests, there is also an increased need for collaborative approaches to optimize test use to promote positive impacts on patient care, while mitigating potential negative impact or resource waste. In this review, we provide recommendations on building collaborative DxS teams, including microbiologists and the diverse stakeholders that use and interpret molecular microbiology tests. We then detail approaches to identify high-priority molecular microbiology tests that may need utilization assessment, select appropriate diagnostic stewardship interventions, and monitor the impact of implemented interventions. This strategic process may be employed by laboratories to realize optimal testing for selected tests at their institution.

传染病检测的诊断管理(DxS)要求采用多学科方法来优化检测的选择、性能、解释和患者治疗。过去二十年来,基于核酸扩增的传染病诊断检测(或称 "分子微生物学检测")迅速发展。随着这些检验的可用性和复杂性的增加,人们也越来越需要通过合作的方式来优化检验的使用,以促进对患者护理的积极影响,同时减少潜在的负面影响或资源浪费。在本综述中,我们就建立 DxS 协作团队(包括微生物学家以及使用和解释分子微生物学检验的不同利益相关者)提出了建议。然后,我们详细介绍了确定可能需要进行利用率评估的高优先级分子微生物学检验、选择适当的诊断监管干预措施以及监控已实施干预措施的影响的方法。实验室可采用这一战略流程,以实现对其机构所选检验项目的最佳检验。
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引用次数: 0
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Journal of Clinical Microbiology
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