Pub Date : 2024-08-14Epub Date: 2024-07-11DOI: 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。
{"title":"Divergent effects of <i>emm</i> types 1 and 12 on invasive group A streptococcal infections-results of a retrospective cohort study, Germany 2023.","authors":"Ralph Bertram, Andreas Itzek, Lisa Marr, Jana Manzke, Sebastian Voigt, Valérie Chapot, Mark van der Linden, Peter-Michael Rath, Wolfgang Hitzl, Joerg Steinmann","doi":"10.1128/jcm.00637-24","DOIUrl":"10.1128/jcm.00637-24","url":null,"abstract":"<p><p>As a potential side effect of the severe acute respiratory syndrome coronavirus type 2 pandemic, invasive group A <i>Streptococcus</i> (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 (<i>emm</i> 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, <i>emm</i> 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 <i>emm</i> types were observed, of which <i>emm1.0</i> (<i>n</i> = 49; 30%), <i>emm89.0</i> (<i>n</i> = 15; 9%), and <i>emm12.0</i> (<i>n</i> = 14; 9%) were most prevalent. In total, 70% of <i>emm1.0</i> isolates belonged to M1<sub>UK</sub> lineage. No difference in invasive infections was observed for the M1<sub>UK</sub> lineage compared with other <i>emm1.0</i> isolates. However, the <i>emm1.0</i> type, presence of <i>speA1-3</i>, <i>speG</i>, or <i>speJ</i>, as well as adulthood were significantly associated with invasive infections. In contrast, <i>emm12.0</i> isolates were significantly less associated with invasive infections. Multivariable analysis confirmed a significant influence of <i>speJ</i> 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 <i>Streptococcus pyogenes</i> that propel invasive infections.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0063724"},"PeriodicalIF":6.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11323487/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141579834","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}
Allison Smith, Becky Wong-O'Brien, Joshua A Lieberman, Brad T Cookson, Erica Grinager, Thao T Truong
{"title":"The Brief Case: A case of tinea corporis caused by drug-resistant <i>Trichophyton indotineae</i> identified by broad-range fungal DNA sequencing.","authors":"Allison Smith, Becky Wong-O'Brien, Joshua A Lieberman, Brad T Cookson, Erica Grinager, Thao T Truong","doi":"10.1128/jcm.00234-24","DOIUrl":"10.1128/jcm.00234-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"62 8","pages":"e0023424"},"PeriodicalIF":6.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11323470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975833","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}
Pub Date : 2024-08-14Epub Date: 2024-07-29DOI: 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。
{"title":"A single-layer spot assay for easy, fast, and high-throughput quantitation of phages against multidrug-resistant Gram-negative pathogens.","authors":"Paschalis Paranos, Spyros Pournaras, Joseph Meletiadis","doi":"10.1128/jcm.00743-24","DOIUrl":"10.1128/jcm.00743-24","url":null,"abstract":"<p><p>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 <i>K</i>. <i>pneumoniae,</i> eight <i>P</i>. <i>aeruginosa,</i> and three <i>A</i>. <i>baumannii</i> 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 × 10<sup>4</sup>-8.3 x10<sup>12</sup> 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 log<sub>10</sub>PFU/mL, respectively, for all phage/bacterial species (ANOVA <i>P</i> = 0.1-0.43), and they were highly correlated (r > 0.77, <i>P</i> < 0.01). Moreover, plaques could be quantified at 37°C after 4-h incubation for <i>K. pneumoniae</i> phages and 6-h incubation for <i>P. aeruginosa</i> and <i>A. baumannii</i> 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.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0074324"},"PeriodicalIF":6.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11323465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141788233","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}
Pub Date : 2024-08-14Epub Date: 2024-07-11DOI: 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.
{"title":"Development and implementation of a core genome multilocus sequence typing scheme for <i>Yersinia enterocolitica:</i> a tool for surveillance and outbreak detection.","authors":"Joao Pires, Lin T Brandal, Umaer Naseer","doi":"10.1128/jcm.00040-24","DOIUrl":"10.1128/jcm.00040-24","url":null,"abstract":"<p><p><i>Yersinia enterocolitica</i> (<i>Y. enterocolitica</i>) 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 <i>Y. enterocolitica</i>. We designed a cgMLST scheme in SeqSphere + using high-quality genomes from different <i>Y. enterocolitica</i> biotype sublineages. The scheme was validated if more than 95% of targets were found across all tested <i>Y. enterocolitica</i>: 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 <i>Y. enterocolitica</i> using diverse data sources and was able to identify outbreak clusters. We recommend the implementation of this scheme nationally and internationally to facilitate <i>Y. enterocolitica</i> surveillance and improve outbreak response in national and cross-border outbreaks.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0004024"},"PeriodicalIF":6.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11325262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141579833","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}
Pub Date : 2024-08-14Epub Date: 2024-07-02DOI: 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.
{"title":"When less is more: the art of communicating clinical microbiology results.","authors":"Blake W Buchan","doi":"10.1128/jcm.00703-24","DOIUrl":"10.1128/jcm.00703-24","url":null,"abstract":"<p><p>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 <i>Journal of Clinical Microbiology</i>, 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 <i>S. aureus</i> 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.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0070324"},"PeriodicalIF":6.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11323566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492206","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}
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。
{"title":"Evaluation of a BioFire multiplex PCR panel for detection of joint infections using retrospective and prospectively collected specimens.","authors":"Angelica Moran, Jekzaly Arellano, Karen Bregman, Erin McElvania","doi":"10.1128/jcm.00182-24","DOIUrl":"10.1128/jcm.00182-24","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0018224"},"PeriodicalIF":6.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11323555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141626878","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}
{"title":"Photo Quiz: Subungual organism in a renal transplant patient.","authors":"Lucy C Crawford, Sarah E Kidd","doi":"10.1128/jcm.01710-23","DOIUrl":"10.1128/jcm.01710-23","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"62 8","pages":"e0171023"},"PeriodicalIF":6.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11323499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975832","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}
Pub Date : 2024-07-16Epub Date: 2024-06-18DOI: 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
{"title":"Correction for Köndgen et al., \"A robust, scalable, and cost-efficient approach to whole genome sequencing of RSV directly from clinical samples\".","authors":"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","doi":"10.1128/jcm.00784-24","DOIUrl":"10.1128/jcm.00784-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0078424"},"PeriodicalIF":6.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11250108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141419321","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}
Pub Date : 2024-07-16Epub Date: 2024-06-27DOI: 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.
{"title":"Comparative evaluation of the STANDARD M10 and Xpert <i>C</i>. <i>difficile</i> assays for detection of toxigenic <i>Clostridioides difficile</i> in stool specimens.","authors":"Hyun-Woo Lee, Hui-Jin Yu, Heejung Kim, Sun Ae Yun, Eunsang Suh, Minhee Kang, Tae Yeul Kim, Hee Jae Huh, Nam Yong Lee","doi":"10.1128/jcm.00524-24","DOIUrl":"10.1128/jcm.00524-24","url":null,"abstract":"<p><p>This study compared the performance of two commercial molecular assays, the STANDARD M10 <i>Clostridioides difficile</i> assay (M10) and the Xpert <i>C. difficile</i> assay (Xpert), for detecting toxigenic <i>C. difficile</i> in stool specimens. A total of 487 consecutive stool specimens submitted for routine <i>C. difficile</i> 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.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0052424"},"PeriodicalIF":6.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11250526/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141457173","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}
Anthony R Russo, Maxwell T Roth, Eric P Grewal, Eric S Rosenberg, John A Branda
{"title":"Photo Quiz: A 51-year-old man with a lung mass-a multidisciplinary diagnosis.","authors":"Anthony R Russo, Maxwell T Roth, Eric P Grewal, Eric S Rosenberg, John A Branda","doi":"10.1128/jcm.01557-23","DOIUrl":"10.1128/jcm.01557-23","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"62 7","pages":"e0155723"},"PeriodicalIF":6.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11250117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141620044","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}