临床微生物学杂志 (JCM) 发表与人类和动物感染的实验室诊断以及实验室在传染病管理和阐明感染流行病学方面的作用相关的最新研究。

The Journal of Clinical Microbiology publishes the latest research related to laboratory diagnostics of human and animal infections, focusing on the role of laboratories in the management of infectious diseases and elucidating the epidemiology of infections.

《Journal of Clinical Microbiology》发表与人类和动物感染的实验室诊断相关的最新研究，重点探讨实验室在传染病管理和感染流行病学阐明中的作用。

Journal of Clinical Microbiology

ABSTRACT The diagnosis of tuberculosis (TB) still lacks a rapid, user-friendly method. Recent research has revealed the significant diagnostic potential of the CRISPR system in TB detection. However, most current CRISPR-based diagnostic tests involve a two-step process, including nucleic acid amplification followed by CRISPR-guided sequence-specific detection, which raises concerns about cross-contamination and operational complexity. In this study, we introduced TB One-Pot, which combines CRISPR-Cas12b-mediated trans-cleavage with cross-priming amplification, enabling one-pot detection in a single reaction. TB One-Pot achieves a minimum detection limit of 0.8 copies/μL for H37Rv genomic DNA and a quantification limit of 50 CFU/mL. It exhibited no cross-reactivity with common nontuberculous mycobacteria and respiratory pathogens. TB One-Pot employs real-time fluorescence, enabling the process from nucleic acid extraction to result in reporting in just 80 minutes. It also includes a UV-based visual check, eliminating the need for specialized equipment. A retrospective cohort study evaluated the diagnostic performance of this method using a composite reference standard as the gold standard. TB One-Pot demonstrated a sensitivity of 67.2% and an area under the curve (AUC) of 0.820 in sputum samples, surpassing conventional methods such as culture and acid-fast bacilli (AFB) smear. Comparative analysis with Xpert (sensitivity:64.2%, AUC:0.821) showed no statistically significant difference ( P &gt; 0.05). TB One-Pot exhibited a specificity of 96.7%, similar to Xpert, culture, and AFB smear ( P &gt; 0.05). TB One-Pot excels in speed, sensitivity, specificity, and practical requirements. Ongoing refinements aim to improve sensitivity, making it a promising solution for overcoming limitations in molecular TB diagnosis, particularly in resource-constrained settings. IMPORTANCE In this study, we successfully established a new One-Pot method, named TB One-Pot, for detecting Mtb in sputum by combining CRISPR-cas12b-mediated trans-cleavage with cross-priming amplification (CPA). Our study evaluated the diagnostic performance of TB One-Pot in clinical sputum samples for tuberculosis. The findings provide evidence for the potential of TB One-Pot as a diagnostic tool for tuberculosis.

Lijun Peng

Tingting Fang

Qingshan Cai

Hao Li

Huanyu Li

Haiqiong Sun

Mingzhi Zhu

Lingshan Dai

Yanqin Shao

Long Cai

Rapid detection of Mycobacterium tuberculosis in sputum using CRISPR-Cas12b combined with cross-priming amplification in a single reaction

利用CRISPR-Cas12b结合交叉引物扩增在单次反应中快速检测痰液中的结核分枝杆菌

Viral genetic sequencing can be used to monitor the spread of HIV drug resistance, identify appropriate antiretroviral regimes, and characterize transmission dynamics. Despite decreasing costs, next-generation sequencing (NGS) is still prohibitively costly for routine use in generalized HIV epidemics in low- and middle-income countries. Here, we present veSEQ-HIV, a high-throughput, cost-effective NGS sequencing method and computational pipeline tailored specifically to HIV, which can be performed using leftover blood drawn for routine CD4 cell count testing. This method overcomes several major technical challenges that have prevented HIV sequencing from being used routinely in public health efforts; it is fast, robust, and cost-efficient, and generates full genomic sequences of diverse strains of HIV without bias. The complete veSEQ-HIV pipeline provides viral load estimates and quantitative summaries of drug resistance mutations; it also exploits information on within-host viral diversity to construct directed transmission networks. We evaluated the method's performance using 1,620 plasma samples collected from individuals attending 10 large urban clinics in Zambia as part of the HPTN 071-2 study (PopART Phylogenetics). Whole HIV genomes were recovered from 91% of samples with a viral load of >1,000 copies/ml. The cost of the assay (30 GBP per sample) compares favorably with existing VL and HIV genotyping tests, proving an affordable option for combining HIV clinical monitoring with molecular epidemiology and drug resistance surveillance in low-income settings.

David Bonsall

Tanya Golubchik

Mariateresa de Cesare

Mohammed Limbada

Barry Kosloff

George MacIntyre-Cockett

Matthew Hall

Chris Wymant

M. Azim Ansari

Lucie Abeler-Dörner

Ab Schaap

Anthony Brown

Eleanor Barnes

Estelle Piwowar-Manning

Susan Eshleman

Ethan Wilson

Lynda Emel

Richard Hayes

Sarah Fidler

Helen Ayles

Rory Bowden

Christophe Fraser

A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings

Streptococcus zooepidemicus is an emerging and opportunistic zoonotic pathogen which plays an important role in the development of severe and life-threatening diseases and is potentially capable of triggering large glomerulonephritis outbreaks. Between December 2012 and February 2013, 175 cases of glomerulonephritis were confirmed in the town of Monte Santo de Minas, MG, Brazil. During the outbreak, 19 isolates of S. zooepidemicus were recovered, 1 from ice cream, 2 from the oropharynx of food handlers, and 16 from patients affected by acute poststreptococcal glomerulonephritis (APSGN). All S. zooepidemicus isolates involved in the outbreak amplified the same sequence of the hypervariable region of the SzP protein (SzPHV5) and presented indistinguishable banding patterns with high similarity (>99%) to each other by the repetitive element sequence-based PCR (rep-PCR) technique. Inspection programs on the milk supply chain should be strengthened and continuously encouraged so that the health of consumers is preserved.

Rosângela S. L. A. Torres

Talita Z. Santos

Andre F. L. Bernardes

Patricia A. Soares

Ana C. C. Soares

Ricardo S. Dias

Outbreak of Glomerulonephritis Caused by Streptococcus zooepidemicus SzPHV5 Type in Monte Santo de Minas, Minas Gerais, Brazil

巴西米纳斯吉拉斯州蒙特桑托德米纳斯由兽疫链球菌SzPHV5型引起的肾小球肾炎暴发

ABSTRACT Accurate species identification is a prerequisite for successful management of tuberculosis and non-tuberculous mycobacterial (NTM) diseases. The novel FluoroType Mycobacteria assay combines three established GenoType DNA strip assays (CM, AS, and NTM-DR), allowing detection of Mycobacterium tuberculosis and 32 NTM species/subspecies in a single assay with automatic detection and result analysis. We evaluated the clinical performance of the FluoroType assay and its feasibility in replacing the GenoType Mycobacterium CM assay as the initial method for mycobacterial identification. A total of 191 clinical mycobacterial cultures were analyzed in this study: 180 identified for one mycobacterial species, 6 for multiple, and 5 for no mycobacterial species. Positive percent agreement (PPA) for the FluoroType assay was 87.8% ( n = 158), with full agreement for 23/29 species. Weakest PPA was observed for Mycobacterium gordonae (50%, n = 9/18), Mycobacterium interjectum (40%, n = 2/5), and Mycobacterium intracellulare (42%, n = 5/12). Clinical and mixed cultures containing multiple mycobacterial species gave equally single species and genus level identifications ( n = 30). No cross-reactivity with non-mycobacterial species was observed ( n = 22). In a separate in silico analysis of 2016–2022 HUS area (Finland) register data ( n = 2,573), the FluoroType assay was estimated to produce 18.8% ( n = 471) inadequate identifications (genus/false species) if used as the primary identification method compared to 14.2% ( n = 366) with the GenoType CM assay. The FluoroType assay was significantly more convenient in terms of assay workflow and result interpretation compared to the entirely manual and subjective GenoType CM assay. However, the feasibility of the assay should be critically assessed with respect to the local NTM species distribution. IMPORTANCE This study is the first clinical evaluation report of the novel FluoroType Mycobacteria assay. The assay has the potential to replace the established GenoType NTM product family in identification of culture-enriched mycobacteria. However, our research results suggest that the assay performs suboptimally and may not be feasible for use in all clinical settings.

Bruno Luukinen

Jenni Antikainen

Janne Aittoniemi

Terhi Miikkulainen-Lahti

Hanne-Leena Hyyryläinen

Anu Pätäri-Sampo

Evaluation of the FluoroType Mycobacteria assay for identification of mycobacteria

Identification of biomarkers for latent Mycobacterium tuberculosis infection and risk of progression to tuberculosis (TB) disease are needed to better identify individuals to target for preventive therapy, predict disease risk, and potentially predict preventive therapy efficacy. Our group developed multiple reaction monitoring mass spectrometry (MRM-MS) assays that detected M. tuberculosis peptides in serum extracellular vesicles from TB patients. We subsequently optimized this MRM-MS assay to selectively identify 40 M. tuberculosis peptides from 19 proteins that most commonly copurify with serum vesicles of patients with TB.

Carolina Mehaffy

Nicole A. Kruh-Garcia

Barbara Graham

Leah G. Jarlsberg

Charis E. Willyerd

Andrey Borisov

Timothy R. Sterling

Payam Nahid

Karen M. Dobos

J Clin Microbiol

Identification of Mycobacterium tuberculosis Peptides in Serum Extracellular Vesicles from Persons with Latent Tuberculosis Infection

ABSTRACT Genotypic methods for detecting antibiotic resistance in Helicobacter pylori infection offer a rapid, convenient, and accurate approach for tailored therapy. However, existing studies predominantly examine single sample types and lack comparative analyses across different samples. This study comprehensively detects and compares genotypic resistance to clarithromycin and levofloxacin in gastric mucosa, gastric fluid, and fecal samples from the same patients. The study enrolled 183 participants, comprising 124 H . pylori -positive and 59 H . pylori -negative patients. All participants provided fecal samples and underwent gastroscopy for the collection of gastric mucosa and gastric fluid. Real-time PCR was employed to detect genotypic resistance to clarithromycin and levofloxacin in conjunction with bacterial culture and antibiotic susceptibility testing. Genotypic resistance detection rates for clarithromycin were 100% in gastric mucosa, 99.2% in gastric fluid, and 79.8% in fecal samples. For levofloxacin, detection rates were 97.6%, 96.8%, and 72.6%, respectively. The results showed that PCR detection for clarithromycin exhibited high sensitivity (0.94–0.95) and specificity (0.88–0.89) across all sample types. However, PCR detection for levofloxacin demonstrated slightly lower sensitivity (0.79–0.89) and specificity (0.79–0.83). The comparison of genotypic resistance results by PCR among the three sample types showed that gastric mucosa and gastric juice exhibited higher consistency, while the consistency between feces and both gastric mucosa and gastric juice was lower. This study confirmed good consistency between genotypic and phenotypic resistance in clarithromycin and levofloxacin. While both gastric mucosa and gastric fluid samples demonstrated high detection performance, the efficiency of detecting fecal samples was constrained by challenges in DNA extraction. IMPORTANCE This study, with a large sample size, comprehensively tested both Helicobacter pylori-negative and -positive patients, including rapid urease test, histopathological evaluation and staining, bacterial culture, susceptibility testing, and resistance gene mutation analysis. By simultaneously examining gastric mucosa, gastric juice, and fecal samples from the same individuals, we minimized confounding factors arising from different sample sources, ensuring the reliability of our results. This approach effectively delineated the differences and characteristics in detection performance among different sample types, offering crucial reference data for selecting appropriate detection samples and identifying areas for improvement. The findings revealed robust concordance between genotypic and phenotypic resistance, with both gastric mucosa and gastric juice samples demonstrating excellent detection performance. However, the efficiency of detecting resistance in fecal samples was hampered by challenges in DNA extraction.

Xinlu Ren

Baojun Suo

Cailing Li

Guangjie Ping

Lingling Ma

Yanyan Shi

Kai Zhou

Yuxin Wang

Xueli Tian

Liya Zhou

Zhiqiang Song

Comparative analysis of the detection of antibiotic genotypic resistance with gastric mucosa, gastric fluid, and fecal samples in patients with Helicobacter pylori infection

幽门螺杆菌感染患者胃黏膜、胃液及粪便样本抗生素基因型耐药性检测的比较分析

ABSTRACT Mosquito-borne viruses represent a large global health burden. With geographic expansion of competent vectors for chikungunya virus (CHIKV), dengue virus (DENV), and Zika virus (ZIKV) in Europe, it is anticipated that the number of autochthonous cases of these tropical viruses in Europe will increase. Therefore, regular assessment of diagnostic capabilities in Europe is important. Our aim was to evaluate the mosquito-borne virus molecular detection capability of expert European laboratories by conducting an external quality assessment in October 2023. Molecular panels included 12 plasma samples: one alphavirus (CHIKV), four orthoflaviviruses (ZIKV, yellow fever virus [YFV], DENV, and Japanese encephalitis virus [JEV]), and two negative control samples. Mosquito-borne virus detection was assessed among 36 laboratories in 24 European countries. Adequate capabilities were lacking for YFV and JEV. Many laboratories relied on a mix of laboratory-developed tests (some of which were pan-orthoflavivirus or pan-alphavirus in combination with sequencing) and commercial assays. 47.2% of laboratories characterized all external quality assessment (EQA) samples correctly. Correct result rates were 100% for CHIKV and ZIKV and &gt;99% for DENV, but laboratories lacked capacity, specificity, and sensitivity for JEV and YFV. Three of the viruses in this panel emerged and transiently circulated in Europe: CHIKV, ZIKV, and DENV. Molecular detection was excellent for those viruses, but &lt;50% is accurate for the remainder of the panel. With the possibility or continuation of imported cases and a growing global concern about climate change and vector expansion, progress toward rapid, accurate mosquito-borne virus diagnostics in Europe is recommended, as well as regular EQAs to monitor it. IMPORTANCE The external quality assessment (EQA) focused on Aedes -borne viruses: chikungunya virus (CHIKV), dengue virus (DENV), Zika virus (ZIKV), and yellow fever virus (YFV). Japanese encephalitis virus, an orthoflavivirus that is spread by mosquito species belonging to the genus Culex , was included in the quality assessment as well. CHIKV, DENV, and ZIKV have proven potential for transient and limited circulation in Europe upon introduction of viremic travelers returning to Aedes albopictus -endemic regions. Results of this EQA were excellent for those viruses, but &lt;50% is accurate for the remainder of the panel (YFV and Japanese encephalitis virus). Considering imported cases and the threat of climate change and competent vector expansion, progress toward rapid, accurate mosquito-borne virus diagnostics in Europe is recommended.

Lance D. Presser

Cécile Baronti

Ramona Moegling

Laura Pezzi

Yaniv Lustig

Céline M. Gossner

Chantal B. E. M. Reusken

Rémi N. Charrel

Excellent capability for molecular detection of Aedes -borne dengue, Zika, and chikungunya viruses but with a need for increased capacity for yellow fever and Japanese encephalitis viruses: an external quality assessment in 36 European laboratories

优秀的能力用于检测Aedes传播的登革热、寨卡和基孔肯雅病毒，但对黄热病和日本脑炎病毒的检测能力需提升：一项针对36个欧洲实验室的外部质量评估

ABSTRACT The laboratory diagnosis of Clostridioides difficile infection (CDI) is controversial. Nucleic acid amplification tests (NAAT) and toxin enzyme immunoassays (EIA) are most widely used, often in combination. However, the interpretation of a positive NAAT and negative toxin immunoassay (NAAT+/EIA−) is uncertain. PubMed and EMBASE were searched for studies reporting clinical outcomes in NAAT+/EIA− versus NAAT+/EIA+ patients. Forty-six studies comprising 33,959 patients were included in this meta-analysis. All-cause mortality (RR 0.96, 95% CI 0.80–1.15), attributable mortality (RR 0.61, 95% CI 0.20–1.91), fulminant CDI (RR 0.83, 95% CI 0.57–1.20), radiographic evidence of CDI (RR 0.87, 95% CI 0.65–1.16), total CDI complications (RR 0.95, 95% CI 0.59–1.53), colectomies (RR 0.78, 95% CI 0.34–1.79), and ICU admission (RR 1.04, 95% CI 0.84–1.30) did not significantly differ between NAAT+/EIA− and NAAT+/EIA+ patients. However, rates of recurrent (RR 0.62, 95% CI 0.50–0.77) or severe (RR 0.74, 95% CI 0.63–0.88) CDI were significantly lower in NAAT+/EIA− patients than in NAAT+/EIA+ patients. The pooled prevalence of NAAT+/EIA− patients who were treated with antibiotics for CDI was 73.4% (pooled proportion 0.72, 95% CI 0.52–0.88). NAAT+/EIA− patients have lower rates of recurrence and are at reduced risk for severe CDI compared with NAAT+/EIA+ patients but have a risk of CDI-related complications and mortality comparable to that of NAAT+/EIA+ patients. Toxin results cannot rule in or rule out CDI, and the decision whether to treat symptomatic NAAT+/EIA− patients for CDI should be based on clinical presentation and not on the toxin result. IMPORTANCE Clostridioides difficile infection (CDI) is a common cause of healthcare-associated infections and the leading cause of antibiotic-associated diarrhea. However, the laboratory diagnosis of CDI, primarily done by nucleic acid amplification test (NAAT) and enzyme immunoassay (EIA), is controversial, especially in patients who test positive by NAAT but negative by EIA. In this systematic review, we compared the clinical outcomes of NAAT+/EIA− versus NAAT+/EIA+ patients and found that the two groups have similar risk of mortality and CDI-related complications. However, NAAT+/EIA− patients had significantly lower rates of recurrence and severe CDI than NAAT+/EIA+ patients, and most NAAT+/EIA− patients received CDI therapy. Toxin testing can help to predict the likelihood of CDI recurrence or severe infection, but the toxin result should not be a determining factor in the administration of CDI therapy. The decision on whether to treat NAAT+/EIA− patients should be based on clinical assessment.

Giannoula S. Tansarli

Matthew E. Falagas

Ferric C. Fang

Clinical significance of toxin EIA positivity in patients with suspected Clostridioides difficile infection: systematic review and meta-analysis

疑似艰难梭菌感染患者中毒素EIA阳性的临床意义：系统综述与meta分析

Cara P. Heath

Poonam C. Sharma

Sumit Sontakke

Dallas J. Smith

Tulip A. Jhaveri

The Brief Case: Hidden in plain sight— Exophiala jeanselmei subcutaneous phaeohyphomycosis of hand masquerading as a hematoma

简要病例：明处藏匿——表现为手部血肿的皮下暗色丝孢霉病，由外瓶霉引起

Veronica Vine Nicholas

Iain Miller

Jordan Mah

Kerri E. Rieger

Indre Budvytiene

Niaz Banaei

Photo Quiz: PAS- and GMS-positive filamentous branching organisms in an immunocompromised patient

光镜测验：免疫功能低下患者PAS和GMS阳性分枝丝状生物

Abbreviation	J Clin Microbiol
Journal Impact	6.21
Quartiles(Global)	MICROBIOLOGY(Q1)

ISSN	0095-1137, 1098-660X
h-index	285
Top Journals	Yes

Publication Information	Publisher: American Society for Microbiology，Publishing cycle: Monthly，Journal Type: journal，Open Access Journals: No
Basic data	Year of publication: 1975，Proportion of original research papers: 85.71%，Self Citation Rate:4.90%， Gold OA Rate: 28.84%
Average review cycle	网友分享经验：平均3.0个月
Average recruitment ratio	网友分享经验：约65%

Journal of Clinical Microbiology

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