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Divergent effects of emm types 1 and 12 on invasive group A streptococcal infections-results of a retrospective cohort study, Germany 2023. 1 型和 12 型 emm 对侵袭性 A 组链球菌感染的不同影响--一项回顾性队列研究的结果,德国 2023 年。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-08-14 Epub Date: 2024-07-11 DOI: 10.1128/jcm.00637-24
Ralph Bertram, Andreas Itzek, Lisa Marr, Jana Manzke, Sebastian Voigt, Valérie Chapot, Mark van der Linden, Peter-Michael Rath, Wolfgang Hitzl, Joerg Steinmann

As a potential side effect of the severe acute respiratory syndrome coronavirus type 2 pandemic, invasive group A Streptococcus (iGAS) infections in Europe have increased dramatically in both children and adults in the end of 2022. This epidemiological and molecular study describes the distributions of streptococcal genes encoding the M antigen (emm types) and superantigens in patients with invasive and non-invasive GAS infections. From December 2022 to December 2023, a total of 163 GAS isolates were collected from sterile and non-sterile sites of patients at five hospitals in Germany including two tertiary care centers. Genes encoding M protein and superantigens were determined following the guidelines of CDC Streptococcus laboratory. Patients' characteristics were reviewed retrospectively. Correlations of clinical factors, emm types, and superantigens with rates of invasive infections were analyzed. Of the 163 included GAS cases, 112 (69%) were considered as invasive. In total, 33 different emm types were observed, of which emm1.0 (n = 49; 30%), emm89.0 (n = 15; 9%), and emm12.0 (n = 14; 9%) were most prevalent. In total, 70% of emm1.0 isolates belonged to M1UK lineage. No difference in invasive infections was observed for the M1UK lineage compared with other emm1.0 isolates. However, the emm1.0 type, presence of speA1-3, speG, or speJ, as well as adulthood were significantly associated with invasive infections. In contrast, emm12.0 isolates were significantly less associated with invasive infections. Multivariable analysis confirmed a significant influence of speJ and adulthood on iGAS infections. This study underlines the importance of continuous monitoring of genomic trends and identification of emerging GAS variants. This may aid in delineating pathogenicity factors of Streptococcus pyogenes that propel invasive infections.

作为严重急性呼吸系统综合征冠状病毒 2 型大流行的潜在副作用,2022 年底欧洲儿童和成人的侵袭性 A 组链球菌(iGAS)感染急剧增加。这项流行病学和分子研究描述了侵袭性和非侵袭性 A 组链球菌感染患者中编码 M 抗原(emm 型)和超抗原的链球菌基因的分布情况。2022 年 12 月至 2023 年 12 月期间,从德国五家医院(包括两家三级医疗中心)患者的无菌和非无菌部位共收集到 163 株 GAS 分离物。根据中国疾病预防控制中心链球菌实验室的指南,对编码 M 蛋白和超抗原的基因进行了测定。对患者的特征进行了回顾性分析。分析了临床因素、emm 类型和超抗原与侵袭性感染率的相关性。在纳入的 163 例 GAS 病例中,112 例(69%)被认为是侵袭性感染。总共观察到 33 种不同的 emm 类型,其中以 emm1.0(n = 49;30%)、emm89.0(n = 15;9%)和 emm12.0(n = 14;9%)最为普遍。总共有 70% 的 emm1.0 分离物属于 M1UK 系。与其他emm1.0分离株相比,M1UK株在侵袭性感染方面没有差异。不过,emm1.0 类型、speA1-3、speG 或 speJ 的存在以及成年期与侵袭性感染显著相关。相比之下,emm12.0分离株与侵袭性感染的相关性明显较低。多变量分析证实,speJ 和成年期对 iGAS 感染有显著影响。这项研究强调了持续监测基因组趋势和识别新出现的 GAS 变异的重要性。这可能有助于确定化脓性链球菌的致病因素,从而推动侵入性感染的发生。
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引用次数: 0
The Brief Case: A case of tinea corporis caused by drug-resistant Trichophyton indotineae identified by broad-range fungal DNA sequencing. 简要病例:一例通过广谱真菌 DNA 测序鉴定出的由抗药性毛癣菌引起的体癣。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-08-14 DOI: 10.1128/jcm.00234-24
Allison Smith, Becky Wong-O'Brien, Joshua A Lieberman, Brad T Cookson, Erica Grinager, Thao T Truong
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引用次数: 0
A single-layer spot assay for easy, fast, and high-throughput quantitation of phages against multidrug-resistant Gram-negative pathogens. 单层定点检测法,可对抗耐多药革兰氏阴性病原体的噬菌体进行简便、快速和高通量的定量检测。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-08-14 Epub Date: 2024-07-29 DOI: 10.1128/jcm.00743-24
Paschalis Paranos, Spyros Pournaras, Joseph Meletiadis

Double-layer agar (DLA) overlay plaque assay is the gold standard for phage enumeration. However, it is cumbersome and time-consuming. Given the great interest in phage therapy, we explored alternative assays for phage quantitation. A total of 16 different phages belonging to Myoviridae, Siphoviridae, and Podoviridae families were quantitated with five K. pneumoniae, eight P. aeruginosa, and three A. baumannii host isolates. Phages were quantitated with the standard DLA assay (10 mL of LB soft agar 0.7% on LB hard agar 1.5%) and the new single-layer agar (SLA) assay (10 mL of LB soft agar 0.7%) with phages spread (spread) into or spotted (spot) onto soft agar. Phage concentrations with each assay were correlated with the standard assay, and the relative and absolute differences between each assay and the standard double-layer agar spread were calculated. Phage concentrations 1 × 104-8.3 x1012 PFU/mL with the standard DLA assay were quantitated with SLA-spread, SLA-spot, and DLA-spot assays, and the median (range) relative and absolute differences were <10% and <0.98 log10PFU/mL, respectively, for all phage/bacterial species (ANOVA P = 0.1-0.43), and they were highly correlated (r > 0.77, P < 0.01). Moreover, plaques could be quantified at 37°C after 4-h incubation for K. pneumoniae phages and 6-h incubation for P. aeruginosa and A. baumannii phages, and estimated concentrations remained the same over 24 hours. Compared to DLA assay, the SLA-spot assay required less media, it was 10 times faster, and generated same-day results. The SLA-spot assay was cheaper, faster, easier to perform, and generated similar phage concentrations as the standard DLA-spread assay.

双层琼脂(DLA)覆盖斑块检测法是噬菌体计数的黄金标准。然而,它既麻烦又耗时。鉴于噬菌体疗法备受关注,我们探索了噬菌体定量的替代检测方法。我们用 5 个肺炎克氏菌、8 个铜绿假单胞菌和 3 个鲍曼尼氏菌宿主分离物对属于肌病毒科、西普病毒科和 Podoviridae 科的 16 种不同噬菌体进行了定量。噬菌体的定量采用标准 DLA 检测法(10 mL LB 软琼脂 0.7%,LB 硬琼脂 1.5%)和新型单层琼脂(SLA)检测法(10 mL LB 软琼脂 0.7%),将噬菌体涂抹(扩散)到软琼脂上或斑点(点状)到软琼脂上。每种测定法的噬菌体浓度都与标准测定法相关,并计算出每种测定法与标准双层琼脂涂布法之间的相对差异和绝对差异。用标准 DLA 检测法定量的噬菌体浓度为 1 × 104-8.3 x1012 PFU/mL,用 SLA-铺展、SLA-斑点和 DLA-斑点检测法定量的噬菌体浓度为 1 × 104-8.3 x1012 PFU/mL,所有噬菌体/细菌种类的相对差异和绝对差异的中位数(范围)分别为 10PFU/mL(方差分析 P = 0.1-0.43),它们之间高度相关(r > 0.77,P < 0.01)。此外,肺炎克氏菌噬菌体在 37°C 孵育 4 小时后,铜绿假单胞菌和鲍曼尼氏菌噬菌体在 37°C 孵育 6 小时后,可对斑块进行定量,估计浓度在 24 小时内保持不变。与 DLA 检测法相比,SLA-斑点检测法所需的培养基更少,速度快 10 倍,而且当天就能得出结果。SLA-斑点检测法成本更低、速度更快、操作更简便,产生的噬菌体浓度与标准的 DLA 扩增检测法相似。
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引用次数: 0
Development and implementation of a core genome multilocus sequence typing scheme for Yersinia enterocolitica: a tool for surveillance and outbreak detection. 开发和实施小肠结肠耶尔森菌核心基因组多焦点序列分型方案:监测和疫情检测工具。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-08-14 Epub Date: 2024-07-11 DOI: 10.1128/jcm.00040-24
Joao Pires, Lin T Brandal, Umaer Naseer

Yersinia enterocolitica (Y. enterocolitica) is the most frequent etiological agent of yersiniosis and has been responsible for several national outbreaks in Norway and elsewhere. A standardized high-resolution method, such as core genome Multilocus Sequence Typing (cgMLST), is needed for pathogen traceability at the national and international levels. In this study, we developed and implemented a cgMLST scheme for Y. enterocolitica. We designed a cgMLST scheme in SeqSphere + using high-quality genomes from different Y. enterocolitica biotype sublineages. The scheme was validated if more than 95% of targets were found across all tested Y. enterocolitica: 563 Norwegian genomes collected between 2012 and 2022 and 327 genomes from public data sets. We applied the scheme to known outbreaks to establish a threshold for identifying major complex types (CTs) based on the number of allelic differences. The final cgMLST scheme included 2,582 genes with a median of 97.9% (interquartile range 97.6%-98.8%) targets found across all tested genomes. Analysis of outbreaks identified all outbreak strains using single linkage clustering at four allelic differences. This threshold identified 311 unique CTs in Norway, of which CT18, CT12, and CT5 were identified as the most frequently associated with outbreaks. The cgMLST scheme showed a very good performance in typing Y. enterocolitica using diverse data sources and was able to identify outbreak clusters. We recommend the implementation of this scheme nationally and internationally to facilitate Y. enterocolitica surveillance and improve outbreak response in national and cross-border outbreaks.

小肠结肠炎耶尔森菌(Y. enterocolitica)是小肠结肠炎最常见的病原体,曾在挪威和其他国家多次爆发。需要一种标准化的高分辨率方法,如核心基因组多焦点序列分型(cgMLST),以便在国家和国际层面对病原体进行追溯。在这项研究中,我们为小肠结肠炎病毒(Y. enterocolitica)开发并实施了一种 cgMLST 方案。我们利用来自不同小肠结肠炎病毒生物型亚系的高质量基因组,在 SeqSphere + 中设计了一个 cgMLST 方案。如果在所有测试的小肠结肠炎病毒(2012 年至 2022 年间收集的 563 个挪威基因组和来自公共数据集的 327 个基因组)中发现 95% 以上的目标,该方案就得到了验证。我们将该方案应用于已知的疫情,根据等位基因差异的数量确定识别主要复杂类型(CT)的阈值。最终的 cgMLST 方案包括 2,582 个基因,在所有测试基因组中发现的目标中位数为 97.9%(四分位间范围 97.6%-98.8%)。对疫情爆发的分析采用单链聚类,以四个等位基因差异为阈值,确定了所有疫情爆发的菌株。这一阈值在挪威确定了 311 个独特的 CT,其中 CT18、CT12 和 CT5 被确定为最常与疫情爆发相关的 CT。cgMLST 方案在利用各种数据源对小肠结肠炎病毒进行分型方面表现出了非常好的性能,并能识别疫情集群。我们建议在国内和国际上实施这一方案,以促进对小肠结肠炎的监测,并改善国内和跨境疫情爆发时的应对措施。
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引用次数: 0
When less is more: the art of communicating clinical microbiology results. 少即是多:传达临床微生物学结果的艺术。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-08-14 Epub Date: 2024-07-02 DOI: 10.1128/jcm.00703-24
Blake W Buchan

The clinical microbiology laboratory is capable of identifying microorganisms in clinical specimens faster and more accurately than ever before. At face value, this should enable patient care providers to make better-informed decisions and target antimicrobial therapies to deliver individualized care. Ironically, more complete and specific reporting of microorganisms isolated from specimens may result in overtreatment based on the presence of a pathogen, even in the absence of clear signs of clinical infection. This conundrum calls into question the role of the laboratory in contributing to care through selective or "exception" reporting whereby some results are selectively withheld when there is a low probability that laboratory findings correlate with the clinical infection. In a recent article published in the Journal of Clinical Microbiology, Bloomfield et al. (J Clin Microbiol 62:e00342-24, 2024, https://doi.org/10.1128/jcm.00342-24) examine the impact and safety of an exception reporting strategy applied to wound swab specimens. Canonical pathogens associated with skin and soft tissue infections including S. aureus and beta-hemolytic streptococci are withheld from the laboratory report if certain patient criteria are met that would put them at low risk of adverse outcomes if untreated, or if treated with guideline-recommended empiric therapy. Their central finding was an approximately 50% reduction in post-laboratory report antibiotic initiation without adverse events or increased 30-day admission rate (indicative of infection-related complications, e.g., disseminated disease). While effectively achieving their goal, the premise of exception reporting and other modified reporting strategies raises questions about the potential risk of underreporting and how to ensure that the message is being interpreted, and acted upon, by care providers as was intended by the laboratory.

临床微生物实验室能够比以往更快、更准确地鉴定临床样本中的微生物。从表面上看,这应该能让患者护理人员做出更明智的决定,并有针对性地使用抗菌疗法,提供个性化护理。具有讽刺意味的是,更全面、更具体地报告从标本中分离出的微生物可能会导致根据病原体的存在进行过度治疗,即使没有明确的临床感染迹象。这一难题使人们对实验室在通过选择性报告或 "例外 "报告促进护理方面所起的作用产生了疑问,因为在实验室检测结果与临床感染相关性较低的情况下,某些结果会被选择性地忽略。Bloomfield 等人最近在《临床微生物学杂志》(J Clin Microbiol 62:e00342-24, 2024, https://doi.org/10.1128/jcm.00342-24)上发表了一篇文章,探讨了例外报告策略对伤口拭子标本的影响和安全性。与皮肤和软组织感染相关的典型病原体包括金黄色葡萄球菌和乙型溶血性链球菌,如果符合特定的患者标准,且这些病原体在未经治疗的情况下或在接受指南推荐的经验疗法治疗的情况下不良后果风险较低,则实验室报告中将不报告这些病原体。他们的主要发现是,化验报告后开始使用抗生素的患者减少了约 50%,但没有发生不良事件或增加 30 天入院率(表明感染相关并发症,如播散性疾病)。在有效实现其目标的同时,例外情况报告和其他修改报告策略的前提也提出了一些问题,如报告不足的潜在风险,以及如何确保医疗服务提供者按照实验室的意图解释信息并采取行动。
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引用次数: 0
Evaluation of a BioFire multiplex PCR panel for detection of joint infections using retrospective and prospectively collected specimens. 利用回顾性和前瞻性收集的标本,评估用于检测关节感染的 BioFire 多路 PCR 小组。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-08-14 Epub Date: 2024-07-17 DOI: 10.1128/jcm.00182-24
Angelica Moran, Jekzaly Arellano, Karen Bregman, Erin McElvania

The BioFire Joint Infection Panel (JI panel) is a newly FDA-approved multiplex PCR assay for detection of common bone and joint pathogens with 39 targets which include select Gram-positive and Gram-negative bacteria, yeast, and antimicrobial resistance genes. We evaluated the performance of the JI panel in detecting joint infections in our patient population. Sixty-three frozen, residual joint fluid specimens were retrospectively tested using the JI panel. An additional 104 residual joint fluid specimens were de-identified and prospectively tested within 1 week of collection. Results from routine bacterial cultures were used as the reference standard, which included inoculation to agar plates and blood culture bottles. For the frozen specimens, the JI panel showed a positive percent agreement (PPA) of 92.8% and a negative percent agreement (NPA) of 97.1%. PPA was 71.4% and NPA was 94.8% for fresh specimens. A total of 12 discrepancies were observed among the 167 specimens tested. The JI panel demonstrated good overall agreement with routine culture for the detection of joint infections and may improve timely diagnosis when used in conjunction with bacterial culture. However, potential false-positive and false-negative results were observed in both retrospective and prospective testing of specimens.IMPORTANCEThe BioFire JI panel is a new commercially available multiplex PCR assay for detecting common pathogens causing bone and joint infections. The test is performed directly on joint fluids with a fast turnaround time of 1 hour. Our study shows that while the JI panel overall shows good agreement with routine culture, discrepancies were observed in 7% of cases and results should be interpreted with appropriate clinical context.

BioFire 关节感染检测试剂盒(JI 检测试剂盒)是一种新近获得 FDA 批准的多重 PCR 检测试剂盒,用于检测常见的骨关节病原体,有 39 个靶点,包括精选的革兰氏阳性和革兰氏阴性细菌、酵母菌和抗菌药耐药基因。我们评估了 JI 面板在检测患者关节感染方面的性能。我们使用 JI 面板对 63 份冷冻的残留关节液标本进行了回顾性检测。对另外 104 份残留关节液标本进行了去标识化处理,并在采集后一周内进行了前瞻性检测。常规细菌培养的结果被用作参考标准,包括接种到琼脂平板和血液培养瓶中。对于冷冻标本,联合检测小组的阳性一致率(PPA)为 92.8%,阴性一致率(NPA)为 97.1%。新鲜标本的 PPA 为 71.4%,NPA 为 94.8%。在检测的 167 份样本中,共发现 12 项差异。在检测关节感染方面,联合检测小组与常规培养的总体一致性良好,与细菌培养结合使用可提高诊断的及时性。然而,在对标本进行回顾性和前瞻性检测时,都发现了潜在的假阳性和假阴性结果。重要意义BioFire JI 检测试剂盒是一种新型的商用多重 PCR 检测试剂盒,用于检测引起骨关节感染的常见病原体。该检测可直接在关节液中进行,检测时间仅需 1 小时。我们的研究表明,虽然 JI 检测板总体上与常规培养显示出良好的一致性,但在 7% 的病例中发现了差异,因此在解释结果时应结合适当的临床背景。
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引用次数: 0
Photo Quiz: Subungual organism in a renal transplant patient. 照片测验:肾移植患者的舌下生物。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-08-14 DOI: 10.1128/jcm.01710-23
Lucy C Crawford, Sarah E Kidd
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引用次数: 0
Correction for Köndgen et al., "A robust, scalable, and cost-efficient approach to whole genome sequencing of RSV directly from clinical samples". 更正:Köndgen 等人,"直接从临床样本对 RSV 进行全基因组测序的稳健、可扩展且经济高效的方法"。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-18 DOI: 10.1128/jcm.00784-24
Sophie Köndgen, Djin-Ye Oh, Andrea Thürmer, Somayyeh Sedaghatjoo, Livia V Patrono, Sébastien Calvignac-Spencer, Barbara Biere, Thorsten Wolff, Ralf Dürrwald, Stephan Fuchs, Janine Reiche
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引用次数: 0
Comparative evaluation of the STANDARD M10 and Xpert C. difficile assays for detection of toxigenic Clostridioides difficile in stool specimens. 对 STANDARD M10 和 Xpert 艰难梭菌检测法进行比较评估,以检测粪便标本中的毒性艰难梭菌。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 Epub Date: 2024-06-27 DOI: 10.1128/jcm.00524-24
Hyun-Woo Lee, Hui-Jin Yu, Heejung Kim, Sun Ae Yun, Eunsang Suh, Minhee Kang, Tae Yeul Kim, Hee Jae Huh, Nam Yong Lee

This study compared the performance of two commercial molecular assays, the STANDARD M10 Clostridioides difficile assay (M10) and the Xpert C. difficile assay (Xpert), for detecting toxigenic C. difficile in stool specimens. A total of 487 consecutive stool specimens submitted for routine C. difficile testing between June and November 2023 were included. Following routine testing using C. DIFF QUIK CHEK COMPLETE (QCC), M10 and Xpert were tested in parallel, alongside toxigenic culture (reference standard). Additionally, two-step algorithms, using QCC on the first step and either M10 or Xpert on the second step, were assessed. Both M10 and Xpert demonstrated a sensitivity and negative predictive value (NPV) of 100%. M10 exhibited significantly higher specificity and positive predictive value (PPV; 91.9% and 64.2%, respectively) than Xpert (90.3% and 59.8%, respectively). Both two-step algorithms showed a sensitivity and NPV of 98.4% and 99.8%, respectively. The specificity and PPV of the two-step algorithm using M10 (95.2% and 75.0%, respectively) were slightly higher than those of the one using Xpert (94.8% and 73.2%, respectively), without statistical significance. Receiver operating characteristic curve analysis, assessing the predictive ability of cycle threshold (Ct) values for the detection of free toxin, exhibited an area under the curve of 0.825 for M10 and 0.843 for Xpert. This indicates the utility of Ct values as predictors for the detection of free toxin in both assays. In conclusion, M10 proves to be an effective diagnostic tool with performance comparable to Xpert, whether utilized independently or as part of a two-step algorithm.

本研究比较了 STANDARD M10 艰难梭菌测定法(M10)和 Xpert 艰难梭菌测定法(Xpert)这两种商业分子测定法在检测粪便标本中毒性艰难梭菌方面的性能。在 2023 年 6 月至 11 月期间,共纳入了 487 份连续送检的艰难梭菌常规粪便标本。在使用 C. DIFF QUIK CHEK COMPLETE (QCC) 进行常规检测后,M10 和 Xpert 与毒性培养(参考标准)同时进行检测。此外,还对两步法进行了评估,第一步使用 QCC,第二步使用 M10 或 Xpert。M10 和 Xpert 的灵敏度和阴性预测值 (NPV) 均为 100%。M10 的特异性和阳性预测值(PPV;分别为 91.9% 和 64.2%)明显高于 Xpert(分别为 90.3% 和 59.8%)。两种两步算法的灵敏度和 NPV 分别为 98.4% 和 99.8%。使用 M10 的两步法的特异性和 PPV(分别为 95.2% 和 75.0%)略高于使用 Xpert 的两步法(分别为 94.8% 和 73.2%),但无统计学意义。接受者操作特征曲线分析评估了周期阈值(Ct)对检测游离毒素的预测能力,结果显示 M10 的曲线下面积为 0.825,Xpert 为 0.843。这表明在这两种检测方法中,Ct 值都可以作为检测游离毒素的预测因子。总之,无论是独立使用还是作为两步算法的一部分,M10 都被证明是一种有效的诊断工具,其性能可与 Xpert 相媲美。
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引用次数: 0
Photo Quiz: A 51-year-old man with a lung mass-a multidisciplinary diagnosis. 照片测验:一名 51 岁男子的肺部肿块--多学科诊断。
IF 6.1 2区 医学 Q1 MICROBIOLOGY Pub Date : 2024-07-16 DOI: 10.1128/jcm.01557-23
Anthony R Russo, Maxwell T Roth, Eric P Grewal, Eric S Rosenberg, John A Branda
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引用次数: 0
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Journal of Clinical Microbiology
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