Clinical Microbiology Reviews最新文献

Implementation of pathogen genomics in clinical microbiology laboratories. 病原基因组学在临床微生物实验室的应用。

IF 36.8 1区医学

Clinical Microbiology Reviews Pub Date : 2026-04-27 DOI: 10.1128/cmr.00177-25

Andrew P Gador-Whyte,Norelle L Sherry,Anna Brischetto,Patiyan Andersson,Katherine A Bond,Sebastiaan J van Hal,Patrick N A Harris,Benjamin P Howden,

{"title":"Implementation of pathogen genomics in clinical microbiology laboratories.","authors":"Andrew P Gador-Whyte,Norelle L Sherry,Anna Brischetto,Patiyan Andersson,Katherine A Bond,Sebastiaan J van Hal,Patrick N A Harris,Benjamin P Howden, ","doi":"10.1128/cmr.00177-25","DOIUrl":"https://doi.org/10.1128/cmr.00177-25","url":null,"abstract":"SUMMARYPathogen genomics, including whole-genome sequencing (WGS) and clinical metagenomics, is a transformative technology increasingly being implemented in clinical microbiology, including in hospital laboratories. Pathogen genomics can improve the control of healthcare-associated infections, provide rapid infection diagnosis, and could enable replacement of laborious microbiology tests. To date, real-world implementation of pathogen genome sequencing has primarily been limited to public health laboratories, but sequencing in the clinical microbiology setting has the potential to provide advantages, including turnaround time and ability to focus on local priorities. In this review, we consider the factors that represent barriers to, and potential enablers of, the implementation of pathogen genomics in clinical microbiology, including the availability of funding and genomics-trained staff. We outline key use cases and implementation models of pathogen genomics in clinical microbiology and suggest a broad framework for labs commencing sequencing. Finally, we consider future opportunities, including direct-from-specimen sequencing, the role of machine learning in genomics analysis, and the application of pathogen genomics to clinical decision support.","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"25 1","pages":"e0017725"},"PeriodicalIF":36.8,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147751316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Global emergence and rapid spread of Candidozyma auris (syn. Candida auris): epidemiology, biology, and antifungal resistance. 耳念珠菌的全球出现和快速传播：流行病学、生物学和抗真菌耐药性。

IF 36.8 1区医学

Clinical Microbiology Reviews Pub Date : 2026-04-22 DOI: 10.1128/cmr.00394-25

Jian Bing,Shuaihu Li,Lingyu Ji,Han Du,Nora M Shamoon,Clarissa J Nobile,Guanghua Huang

{"title":"Global emergence and rapid spread of Candidozyma auris (syn. Candida auris): epidemiology, biology, and antifungal resistance.","authors":"Jian Bing,Shuaihu Li,Lingyu Ji,Han Du,Nora M Shamoon,Clarissa J Nobile,Guanghua Huang","doi":"10.1128/cmr.00394-25","DOIUrl":"https://doi.org/10.1128/cmr.00394-25","url":null,"abstract":"SUMMARYThe emerging fungal pathogen Candidozyma auris (syn. Candida auris; C. auris) has attracted considerable attention from the scientific, clinical, and public health communities due to its multidrug resistance, environmental persistence, and high transmissibility. Since its first description in Japan in 2009, C. auris has spread rapidly worldwide, with a marked acceleration following the coronavirus disease 2019 (COVID-19) pandemic. As of December 2025, 84,941 colonization or infection cases have been reported across 82 countries spanning 6 continents. In this review, we summarize the current knowledge of the biology and global epidemiology of C. auris. We first examine its taxonomy, proposed origins, and key biological, genetic, and phenotypic characteristics, with particular emphasis on factors underlying environmental persistence, transmission dynamics, antifungal resistance, and virulence. Drawing on published literature and publicly available surveillance data from national public health authorities worldwide, we provide an updated overview of the global epidemiological landscape and evolving transmission patterns of C. auris. Finally, we discuss potential strategies to mitigate the continued and escalating global spread of this emerging multidrug-resistant fungal pathogen.","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"22 1","pages":"e0039425"},"PeriodicalIF":36.8,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147731558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Management of latent tuberculosis infection in patients with kidney disease. 肾病患者潜伏结核感染的处理。

IF 36.8 1区医学

Clinical Microbiology Reviews Pub Date : 2026-04-20 DOI: 10.1128/cmr.00353-25

Wiwat Chancharoenthana,Tanaya Siripoon,Supitcha Kamolratanakul,Viravarn Luvira,Weerapong Phumratanaprapin,Marcus J Schultz,Claudio Ronco,Punnee Pitisuttithum

{"title":"Management of latent tuberculosis infection in patients with kidney disease.","authors":"Wiwat Chancharoenthana,Tanaya Siripoon,Supitcha Kamolratanakul,Viravarn Luvira,Weerapong Phumratanaprapin,Marcus J Schultz,Claudio Ronco,Punnee Pitisuttithum","doi":"10.1128/cmr.00353-25","DOIUrl":"https://doi.org/10.1128/cmr.00353-25","url":null,"abstract":"SUMMARYLatent tuberculosis infection (LTBI) is common and preventable among patients with chronic kidney disease (CKD), where uremia and iatrogenic immunosuppression heighten reactivation risk. This narrative review synthesizes evidence across pre-dialysis CKD, dialysis, and kidney transplantation to propose a pragmatic care pathway. In advanced CKD, the tuberculin skin test performs poorly, whereas interferon-γ release assays (IGRAs) are preferred. Screening should be risk-targeted in pre-dialysis CKD, systematic at dialysis initiation, and mandatory pre-transplant for candidates and living donors. Following a positive test, clinicians must exclude active tuberculosis via clinical assessment and chest imaging before starting preventive therapy. Short-course rifamycin-based regimens (4 months of daily rifampin [4R], 3 months of once‑weekly isoniazid plus rifapentine [3HP], or 3 months of daily isoniazid plus rifampin [3HR]) enhance completion rates compared with 9 months of daily isoniazid (9H). In transplant recipients, rifamycin interactions with calcineurin and Mammalian target of rapamycin (mTOR) inhibitors typically favor 9H; rifamycins demand expert multidisciplinary management with intensive therapeutic drug monitoring. Programmatic data from dialysis units show high completion with tolerable toxicity, affirming routine feasibility. We integrate IGRA-based screening at critical transitions with tailored regimen selection, pyridoxine coadministration for isoniazid, and structured safety monitoring. Priorities include validating novel Mycobacterium tuberculosis antigen-based skin tests in CKD and developing implementation strategies to standardize renal care. We delineate setting-specific approaches for high- versus low-burden countries, addressing subclinical and incipient TB challenges in high-burden contexts. Adopting this framework can curb active TB progression, safeguard grafts, and enhance patient outcomes.","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"129 1","pages":"e0035325"},"PeriodicalIF":36.8,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147719389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The ecological dynamics of skin microbiota in skin health and diseases. 皮肤健康和疾病中皮肤微生物群的生态动态。

IF 36.8 1区医学

Clinical Microbiology Reviews Pub Date : 2026-04-17 DOI: 10.1128/cmr.00305-25

Pu Pu,Yimeng Wang,Xiaoli Liu,Yanli Pang,Li Qiang,Wenhui Wang

引用次数: 0

Mechanistic insights into the pathogenesis and therapeutic recalcitrance of Staphylococcus aureus osteomyelitis. 金黄色葡萄球菌骨髓炎的发病机制和治疗顽固性。

IF 36.8 1区医学

Clinical Microbiology Reviews Pub Date : 2026-04-16 DOI: 10.1128/cmr.00259-25

Karen E Beenken,Mara J Campbell,Humberto Reyes-Pardo,Charles A O'Brien,Mark S Smeltzer

{"title":"Mechanistic insights into the pathogenesis and therapeutic recalcitrance of Staphylococcus aureus osteomyelitis.","authors":"Karen E Beenken,Mara J Campbell,Humberto Reyes-Pardo,Charles A O'Brien,Mark S Smeltzer","doi":"10.1128/cmr.00259-25","DOIUrl":"https://doi.org/10.1128/cmr.00259-25","url":null,"abstract":"SUMMARYOsteomyelitis refers to inflammation in the bone and is most often a consequence of bacterial infection. The most common cause, and the pathogen that causes the most severe form of infection, is Staphylococcus aureus. S. aureus is a common commensal of healthy humans, and this contributes to its predominance as a cause of osteomyelitis, but this does not account for the severity of S. aureus bone infections or their therapeutic recalcitrance to conventional antibiotic therapy. Clinical characteristics of osteomyelitis implicated in this regard include cortical bone destruction resulting in a compromised local blood supply, formation of a biofilm, the ability to invade and survive inside osteoblasts, osteoclasts, and osteocytes, the formation of small-colony variants and persister cells, and invasion of the osteocyte lacuno-canalicular network. This review summarizes evidence implicating these features in the pathogenesis and therapeutic recalcitrance of osteomyelitis, and the attributes of S. aureus that contribute to these features and define S. aureus as the predominant orthopedic pathogen.","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"1 1","pages":"e0025925"},"PeriodicalIF":36.8,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147685100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

IgY passive immunotherapy for pandemic preparedness: a One Health platform approach against pathogen X. IgY被动免疫疗法用于大流行防范：针对病原体X的一个健康平台方法。

IF 36.8 1区医学

Clinical Microbiology Reviews Pub Date : 2026-04-15 DOI: 10.1128/cmr.00249-25

Sherif A El-Kafrawy,Aymn T Abbas,Umama A Abdel-Dayem,Menatalla S El-Kafrawy,Esam I Azhar

{"title":"IgY passive immunotherapy for pandemic preparedness: a One Health platform approach against pathogen X.","authors":"Sherif A El-Kafrawy,Aymn T Abbas,Umama A Abdel-Dayem,Menatalla S El-Kafrawy,Esam I Azhar","doi":"10.1128/cmr.00249-25","DOIUrl":"https://doi.org/10.1128/cmr.00249-25","url":null,"abstract":"SUMMARYThe rising threat of emerging infectious diseases, especially zoonotic pathogens crossing species barriers, highlights the urgent global need for scalable, rapid-response passive immunotherapy platforms. Chicken egg yolk-derived immunoglobulin Y (IgY) antibodies offer unique conceptual and practical advantages. This review critically evaluates IgY antibodies (IgY-Abs) as a One Health immunotherapeutic strategy with strong potential for mitigating zoonotic spillover risks. Drawing on insights from SARS-CoV-2, we highlight the advantages of IgY-Abs over traditional approaches in specific scenarios while emphasizing their role as a complementary rather than replacement platform within the broader passive immunotherapy landscape. We discuss key strategic considerations, regulatory challenges, and essential knowledge gaps. Finally, we propose a forward-looking research and development roadmap that emphasizes interdisciplinary collaboration, optimized production methods, targeted regulatory frameworks, and integrated One Health strategies to facilitate the rapid deployment of IgY-based countermeasures against WHO-priority zoonotic pathogens.","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"107 1","pages":"e0024925"},"PeriodicalIF":36.8,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147680627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Erratum for Gopalaswamy and Subbian, "The power of resistance: mechanisms of antimicrobial resistance in Mycobacterium tuberculosis and its impact on tuberculosis management". Gopalaswamy和Subbian的勘误，“耐药性的力量：结核分枝杆菌抗微生物药物耐药性的机制及其对结核病管理的影响”。

IF 36.8 1区医学

Clinical Microbiology Reviews Pub Date : 2026-04-02 DOI: 10.1128/cmr.00093-26

Radha Gopalaswamy,Selvakumar Subbian

引用次数: 0

Coenzyme A metabolism in fungi: a new frontier in antifungal therapy. 真菌中的辅酶A代谢：抗真菌治疗的新前沿。

IF 36.8 1区医学

Clinical Microbiology Reviews Pub Date : 2026-03-31 DOI: 10.1128/cmr.00307-25

Jae-Yeon Choi,Abigail Chiang,Choukri Ben Mamoun

{"title":"Coenzyme A metabolism in fungi: a new frontier in antifungal therapy.","authors":"Jae-Yeon Choi,Abigail Chiang,Choukri Ben Mamoun","doi":"10.1128/cmr.00307-25","DOIUrl":"https://doi.org/10.1128/cmr.00307-25","url":null,"abstract":"SUMMARYFungal infections are the leading cause of mortality among eukaryotic pathogens. They are responsible for approximately 150 million cases of severe illness and 3.8 million deaths annually. This global health threat is exacerbated by the limited arsenal of clinically approved antifungal drugs, particularly for the treatment of life-threatening invasive infections. The rise of multidrug-resistant fungal strains further underscores the urgent need for new classes of antifungals with novel mechanisms of action. In this context, the fungal coenzyme A (CoA) biosynthesis pathway has emerged as a promising therapeutic target due to its essential role in fungal physiology and key differences from its human counterpart. This review explores the critical role of CoA biosynthesis in fungal metabolism and highlights recent advances in the discovery and characterization of novel compounds targeting this pathway. Some of these emerging candidates act both as standalone inhibitors and as broad-spectrum potentiators of existing antifungals through their ability to enhance strain susceptibility and counteract mechanisms of drug detoxification and multidrug resistance. Collectively, these findings establish CoA metabolism as a compelling target for the next generation of antifungal therapies, offering a multipronged strategy to overcome the limitations of current treatment options and reduce fungal-related mortality.","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"192 1","pages":"e0030725"},"PeriodicalIF":36.8,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147578308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An update on Clostridioides difficile population structure and genomics. 艰难梭菌种群结构和基因组学研究进展。

IF 36.8 1区医学

Clinical Microbiology Reviews Pub Date : 2026-03-31 DOI: 10.1128/cmr.00296-25

Merilyn A Beebe,Joseph A Sorg

{"title":"An update on Clostridioides difficile population structure and genomics.","authors":"Merilyn A Beebe,Joseph A Sorg","doi":"10.1128/cmr.00296-25","DOIUrl":"https://doi.org/10.1128/cmr.00296-25","url":null,"abstract":"SUMMARYSince its first isolation in 1935, several thousand Clostridioides difficile isolates have been collected and analyzed. These isolates belong to a diverse phylogeny consisting of five main clades and at least three cryptic clades. While clade 1 represents the largest and most diverse of the clades, clades 2 and 5 are the best studied, consisting of several strains attributed to the most severe clinical outcomes and increased rates of spread/recurrence. Strains belonging to clades 3 and 4 are typically minor constituents of C. difficile infection (CDI) outbreaks but possess several distinctive genetic features (e.g., unique pathogenicity loci) that provide unique targets for clinical treatments. Much of the divergence between these clades is attributable to variation within the accessory C. difficile genome. These factors, in turn, are often associated with mobile genetic elements (e.g., prophage, transposons, and plasmids). The transfer of these elements between strains is implicated in the acquisition and co-evolution of antibiotic resistance and virulence factors. The continued transfer of these elements between strains and their variation across the C. difficile phylogeny emphasizes the need to include strains spanning multiple ribotypes/clades in phylogenetic and phenotypic studies.","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"727 1","pages":"e0029625"},"PeriodicalIF":36.8,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147578309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

From T-cell sensitization to molecular-intelligent stratification: a roadmap for precision diagnosis of latent tuberculosis infection. 从t细胞致敏到分子智能分层：精确诊断潜伏性结核感染的路线图。

IF 36.8 1区医学

Clinical Microbiology Reviews Pub Date : 2026-03-30 DOI: 10.1128/cmr.00258-25

Ruizi Ni,Yanhua Liu,Alice Armanni,Giulia Ghisleni,Sara Fumagalli,Yajing An,Yufeng Li,Li Zhuang,Yang Ling,Linsheng Li,Zhaoyang Ye,Antonia Bruno,Lingxia Zhang,Wenping Gong

{"title":"From T-cell sensitization to molecular-intelligent stratification: a roadmap for precision diagnosis of latent tuberculosis infection.","authors":"Ruizi Ni,Yanhua Liu,Alice Armanni,Giulia Ghisleni,Sara Fumagalli,Yajing An,Yufeng Li,Li Zhuang,Yang Ling,Linsheng Li,Zhaoyang Ye,Antonia Bruno,Lingxia Zhang,Wenping Gong","doi":"10.1128/cmr.00258-25","DOIUrl":"https://doi.org/10.1128/cmr.00258-25","url":null,"abstract":"SUMMARYOne quarter of the world's population carries latent tuberculosis infection (LTBI), an invisible reservoir that must be drained to end the global tuberculosis (TB) epidemic. This review charts the evolution of LTBI diagnosis from the tuberculin skin test (TST) and interferon-gamma release assays (IGRAs) to a new molecular-intelligent paradigm. At the clinical level, we propose a CD4/age-stratified, resource-matched decision framework that delivers actionable screening and sequencing strategies for people living with HIV, children, the immunosuppressed, and pregnant women. At the biomarker level, we integrate host-derived analytes (CXCL1, CCL8, IP-10, CD38+CD27⁻ T cells, and Fc-glycosylated antibodies) with pathogen-derived antigens (dormancy survival regulator [DosR], resuscitation-promoting factor [Rpf], heparin-binding hemagglutinin [HBHA], and PE/PPE) to create a three-tier index: single-analyte triage, multi-analyte confirmation, and dynamic treatment monitoring. At the technology level, we benchmark multi-omics-plus-AI models, single-molecule Simoa arrays, and microfluidic point-of-care testing (POCT) platforms for sensitivity, accessibility, and cost. High-quality cross-population validation, standardized thresholds, and resource-tiered deployment remain the principal translational bottlenecks. We call for integrated programs that combine key-population multicenter cohorts, explainable AI, and ASSURED criteria to propel LTBI management from the T-cell-sensitization era into the molecular-intelligent age. Achieving this vision within 5 years is technically feasible and will accelerate global elimination targets by enabling precision preventive therapy at an unprecedented scale.","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"29 1","pages":"e0025825"},"PeriodicalIF":36.8,"publicationDate":"2026-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147536514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0