Clinical Microbiology Reviews最新文献

{"title":"<i>Staphylococcus capitis</i>: insights into epidemiology, virulence, and antimicrobial resistance of a clinically relevant bacterial species.","authors":"Deborah M Crepin, Marie Chavignon, Paul O Verhoeven, Frédéric Laurent, Jérôme Josse, Marine Butin","doi":"10.1128/cmr.00118-23","DOIUrl":"10.1128/cmr.00118-23","url":null,"abstract":"<p><p>SUMMARY<i>Staphylococcus capitis</i> is divided into two subspecies, <i>S. capitis</i> subsp. <i>ureolyticus</i> (renamed <i>urealyticus</i> in 1992; ATCC 49326) and <i>S. capitis</i> subsp. <i>capitis</i> (ATCC 27840), and fits with the archetype of clinically relevant coagulase-negative staphylococci (CoNS). <i>S. capitis</i> is a commensal bacterium of the skin in humans, which must be considered an opportunistic pathogen of interest particularly as soon as it is identified in a clinically relevant specimen from an immunocompromised patient. Several studies have highlighted the potential determinants underlying <i>S. capitis</i> pathogenicity, resistance profiles, and virulence factors. In addition, mobile genetic element acquisitions and mutations contribute to <i>S. capitis</i> genome adaptation to its environment. Over the past decades, antibiotic resistance has been identified for <i>S. capitis</i> in almost all the families of the currently available antibiotics and is related to the emergence of multidrug-resistant clones of high clinical significance. The present review summarizes the current knowledge concerning the taxonomic position of <i>S. capitis</i> among staphylococci, the involvement of this species in human colonization and diseases, the virulence factors supporting its pathogenicity, and the phenotypic and genomic antimicrobial resistance profiles of this species.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":" ","pages":"e0011823"},"PeriodicalIF":19.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11391707/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Vaccines and monoclonal antibodies to prevent healthcare-associated bacterial infections.","authors":"Léo Sauvat, Paul O Verhoeven, Julie Gagnaire, Philippe Berthelot, Stéphane Paul, Elisabeth Botelho-Nevers, Amandine Gagneux-Brunon","doi":"10.1128/cmr.00160-22","DOIUrl":"10.1128/cmr.00160-22","url":null,"abstract":"<p><p>SUMMARYHealthcare-associated infections (HAIs) represent a burden for public health with a high prevalence and high death rates associated with them. Pathogens with a high potential for antimicrobial resistance, such as ESKAPE pathogens (<i><u>E</u>nterococcus faecium, <u>S</u>taphylococcus aureus, <u>K</u>lebsiella pneumoniae, <u>A</u>cinetobacter baumannii, <u>P</u>seudomonas aeruginosa,</i> and <i><u>E</u>nterobacter species</i>) and <i>Clostridioides difficile</i>, are responsible for most HAIs. Despite the implementation of infection prevention and control intervention, globally, HAIs prevalence is stable and they are mainly due to endogenous pathogens. It is undeniable that complementary to infection prevention and control measures, prophylactic approaches by active or passive immunization are needed. Specific groups at-risk (elderly people, chronic condition as immunocompromised) and also healthcare workers are key targets. Medical procedures and specific interventions are known to be at risk of HAIs, in addition to hospital environmental exposure. Vaccines or monoclonal antibodies can be seen as attractive preventive approaches for HAIs. In this review, we present an overview of the vaccines and monoclonal antibodies in clinical development for prevention of the major bacterial HAIs pathogens. Based on the current state of knowledge, we look at the challenges and future perspectives to improve prevention by these means.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":" ","pages":"e0016022"},"PeriodicalIF":19.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11391692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Practical Guidance for Clinical Microbiology Laboratories: Updated guidance for processing respiratory tract samples from people with cystic fibrosis.","authors":"Lisa Saiman, Valerie Waters, John J LiPuma, Lucas R Hoffman, Kevin Alby, Sean X Zhang, Yvonne C Yau, Damian G Downey, Isabelle Sermet-Gaudelus, Jean-Philippe Bouchara, Timothy J Kidd, Scott C Bell, A Whitney Brown","doi":"10.1128/cmr.00215-21","DOIUrl":"10.1128/cmr.00215-21","url":null,"abstract":"<p><p>SUMMARYThis guidance presents recommendations for clinical microbiology laboratories for processing respiratory samples from people with cystic fibrosis (pwCF). Appropriate processing of respiratory samples is crucial to detect bacterial and fungal pathogens, guide treatment, monitor the epidemiology of cystic fibrosis (CF) pathogens, and assess therapeutic interventions. Thanks to CF transmembrane conductance regulator modulator therapy, the health of pwCF has improved, but as a result, fewer pwCF spontaneously expectorate sputum. Thus, the collection of sputum samples has decreased, while the collection of other types of respiratory samples such as oropharyngeal and bronchoalveolar lavage samples has increased. To optimize the detection of microorganisms, including <i>Pseudomonas aeruginosa</i>, <i>Staphylococcus aureus</i>, <i>Haemophilus influenzae</i>, and <i>Burkholderia cepacia</i> complex; other less common non-lactose fermenting Gram-negative bacilli, e.g., <i>Stenotrophomonas maltophilia</i>, <i>Inquilinus</i>, <i>Achromobacter</i>, <i>Ralstonia</i>, and <i>Pandoraea</i> species; and yeasts and filamentous fungi, non-selective and selective culture media are recommended for all types of respiratory samples, including samples obtained from pwCF after lung transplantation. There are no consensus recommendations for laboratory practices to detect, characterize, and report small colony variants (SCVs) of <i>S. aureus</i>, although studies are ongoing to address the potential clinical impact of SCVs. Accurate identification of less common Gram-negative bacilli, e.g., <i>S. maltophilia</i>, <i>Inquilinus</i>, <i>Achromobacter</i>, <i>Ralstonia</i>, and <i>Pandoraea</i> species, as well as yeasts and filamentous fungi, is recommended to understand their epidemiology and clinical importance in pwCF. However, conventional biochemical tests and automated platforms may not accurately identify CF pathogens. MALDI-TOF MS provides excellent genus-level identification, but databases may lack representation of CF pathogens to the species-level. Thus, DNA sequence analysis should be routinely available to laboratories for selected clinical circumstances. Antimicrobial susceptibility testing (AST) is not recommended for every routine surveillance culture obtained from pwCF, although selective AST may be helpful, e.g., for unusual pathogens or exacerbations unresponsive to initial therapy. While this guidance reflects current care paradigms for pwCF, recommendations will continue to evolve as CF research expands the evidence base for laboratory practices.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":" ","pages":"e0021521"},"PeriodicalIF":19.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11391703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141999506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of the intestinal microbiota in contributing to weight disorders and associated comorbidities","authors":"Matthias Van HulAudrey M. NeyrinckAmandine EverardAnne AbotLaure B. BindelsNathalie M. DelzenneClaude KnaufPatrice D. Cani1UCLouvain, Université catholique de Louvain, Louvain Drug Research Institute (LDRI), Metabolism and Nutrition Research Group (MNUT), Brussels, Belgium2Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), WELBIO department, WEL Research Institute, Wavre, Belgium3NeuroMicrobiota, International Research Program (IRP) INSERM/UCLouvain, France/Belgium4Enterosys SAS, Labège, France5INSERM U1220, Institut de Recherche en Santé Digestive (IRSD), Université Paul Sabatier, Toulouse III, CHU Purpan, Toulouse, France6UCLouvain, Université catholique de Louvain, Institute of Experimental and Clinical Research (IREC), Brussels, BelgiumChristopher Staley","doi":"10.1128/cmr.00045-23","DOIUrl":"https://doi.org/10.1128/cmr.00045-23","url":null,"abstract":"Clinical Microbiology Reviews, Ahead of Print. <br/>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"2015 1","pages":""},"PeriodicalIF":36.8,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141462951","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}

{"title":"<i>Clostridioides difficile</i> infection: history, epidemiology, risk factors, prevention, clinical manifestations, treatment, and future options.","authors":"Stefano Di Bella, Gianfranco Sanson, Jacopo Monticelli, Verena Zerbato, Luigi Principe, Mauro Giuffrè, Giuseppe Pipitone, Roberto Luzzati","doi":"10.1128/cmr.00135-23","DOIUrl":"10.1128/cmr.00135-23","url":null,"abstract":"<p><p>SUMMARY<i>Clostridioides difficile</i> infection (CDI) is one of the major issues in nosocomial infections. This bacterium is constantly evolving and poses complex challenges for clinicians, often encountered in real-life scenarios. In the face of CDI, we are increasingly equipped with new therapeutic strategies, such as monoclonal antibodies and live biotherapeutic products, which need to be thoroughly understood to fully harness their benefits. Moreover, interesting options are currently under study for the future, including bacteriophages, vaccines, and antibiotic inhibitors. Surveillance and prevention strategies continue to play a pivotal role in limiting the spread of the infection. In this review, we aim to provide the reader with a comprehensive overview of epidemiological aspects, predisposing factors, clinical manifestations, diagnostic tools, and current and future prophylactic and therapeutic options for <i>C. difficile</i> infection.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":" ","pages":"e0013523"},"PeriodicalIF":19.0,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11324037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139989401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chagas disease in immunocompromised patients.","authors":"Eva H Clark, Louisa A Messenger, Jeffrey D Whitman, Caryn Bern","doi":"10.1128/cmr.00099-23","DOIUrl":"10.1128/cmr.00099-23","url":null,"abstract":"<p><p>SUMMARYAs Chagas disease remains prevalent in the Americas, it is important that healthcare professionals and researchers are aware of the screening, diagnosis, monitoring, and treatment recommendations for the populations of patients they care for and study. Management of <i>Trypanosoma cruzi</i> infection in immunocompromised hosts is challenging, particularly because, regardless of antitrypanosomal treatment status, immunocompromised patients with Chagas disease are at risk for <i>T. cruzi</i> reactivation, which can be lethal. Evidence-based practices to prevent and manage <i>T. cruzi</i> reactivation vary depending on the type of immunocompromise. Here, we review available data describing Chagas disease epidemiology, testing, and management practices for various populations of immunocompromised individuals, including people with HIV and patients undergoing solid organ and hematopoietic stem cell transplantation.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":" ","pages":"e0009923"},"PeriodicalIF":19.0,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140305027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Scedosporiosis and lomentosporiosis: modern perspectives on these difficult-to-treat rare mold infections.","authors":"Chin Fen Neoh, Sharon C-A Chen, Fanny Lanternier, Shio Yen Tio, Catriona L Halliday, Sarah E Kidd, David C M Kong, Wieland Meyer, Martin Hoenigl, Monica A Slavin","doi":"10.1128/cmr.00004-23","DOIUrl":"10.1128/cmr.00004-23","url":null,"abstract":"<p><p>SUMMARYAlthough <i>Scedosporium</i> species and <i>Lomentospora prolificans</i> are uncommon causes of invasive fungal diseases (IFDs), these infections are associated with high mortality and are costly to treat with a limited armamentarium of antifungal drugs. In light of recent advances, including in the area of new antifungals, the present review provides a timely and updated overview of these IFDs, with a focus on the taxonomy, clinical epidemiology, pathogenesis and host immune response, disease manifestations, diagnosis, antifungal susceptibility, and treatment. An expansion of hosts at risk for these difficult-to-treat infections has emerged over the last two decades given the increased use of, and broader population treated with, immunomodulatory and targeted molecular agents as well as wider adoption of antifungal prophylaxis. Clinical presentations differ not only between genera but also across the different <i>Scedosporium</i> species. <i>L. prolificans</i> is intrinsically resistant to most currently available antifungal agents, and the prognosis of immunocompromised patients with lomentosporiosis is poor. Development of, and improved access to, diagnostic modalities for early detection of these rare mold infections is paramount for timely targeted antifungal therapy and surgery if indicated. New antifungal agents (e.g., olorofim, fosmanogepix) with novel mechanisms of action and less cross-resistance to existing classes, availability of formulations for oral administration, and fewer drug-drug interactions are now in late-stage clinical trials, and soon, could extend options to treat scedosporiosis/lomentosporiosis. Much work remains to increase our understanding of these infections, especially in the pediatric setting. Knowledge gaps for future research are highlighted in the review.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":" ","pages":"e0000423"},"PeriodicalIF":19.0,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140317920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"COVID-19 therapeutics.","authors":"Daniele Focosi, Massimo Franchini, Fabrizio Maggi, Shmuel Shoham","doi":"10.1128/cmr.00119-23","DOIUrl":"10.1128/cmr.00119-23","url":null,"abstract":"<p><p>SUMMARYSince the emergence of COVID-19 in 2020, an unprecedented range of therapeutic options has been studied and deployed. Healthcare providers have multiple treatment approaches to choose from, but efficacy of those approaches often remains controversial or compromised by viral evolution. Uncertainties still persist regarding the best therapies for high-risk patients, and the drug pipeline is suffering fatigue and shortage of funding. In this article, we review the antiviral activity, mechanism of action, pharmacokinetics, and safety of COVID-19 antiviral therapies. Additionally, we summarize the evidence from randomized controlled trials on efficacy and safety of the various COVID-19 antivirals and discuss unmet needs which should be addressed.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":" ","pages":"e0011923"},"PeriodicalIF":19.0,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141070805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pathogenesis of viral infections during pregnancy.","authors":"Patrick S Creisher, Sabra L Klein","doi":"10.1128/cmr.00073-23","DOIUrl":"10.1128/cmr.00073-23","url":null,"abstract":"<p><p>SUMMARYViral infections during pregnancy are associated with significant adverse perinatal and fetal outcomes. Pregnancy is a unique immunologic and physiologic state, which can influence control of virus replication, severity of disease, and vertical transmission. The placenta is the organ of the maternal-fetal interface and provides defense against microbial infection while supporting the semi-allogeneic fetus via tolerogenic immune responses. Some viruses, such as cytomegalovirus, Zika virus, and rubella virus, can breach these defenses, directly infecting the fetus and having long-lasting consequences. Even without direct placental infection, other viruses, including respiratory viruses like influenza viruses and severe acute respiratory syndrome coronavirus 2, still cause placental damage and inflammation. Concentrations of progesterone and estrogens rise during pregnancy and contribute to immunological adaptations, placentation, and placental development and play a pivotal role in creating a tolerogenic environment at the maternal-fetal interface. Animal models, including mice, nonhuman primates, rabbits, and guinea pigs, are instrumental for mechanistic insights into the pathogenesis of viral infections during pregnancy and identification of targetable treatments to improve health outcomes of pregnant individuals and offspring.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":" ","pages":"e0007323"},"PeriodicalIF":19.0,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139989531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Testing for SARS-CoV-2: lessons learned and current use cases.","authors":"Elitza S Theel, James E Kirby, Nira R Pollock","doi":"10.1128/cmr.00072-23","DOIUrl":"10.1128/cmr.00072-23","url":null,"abstract":"<p><p>SUMMARYThe emergence and worldwide dissemination of SARS-CoV-2 required both urgent development of new diagnostic tests and expansion of diagnostic testing capacity on an unprecedented scale. The rapid evolution of technologies that allowed testing to move out of traditional laboratories and into point-of-care testing centers and the home transformed the diagnostic landscape. Four years later, with the end of the formal public health emergency but continued global circulation of the virus, it is important to take a fresh look at available SARS-CoV-2 testing technologies and consider how they should be used going forward. This review considers current use case scenarios for SARS-CoV-2 antigen, nucleic acid amplification, and immunologic tests, incorporating the latest evidence for analytical/clinical performance characteristics and advantages/limitations for each test type to inform current debates about how tests should or should not be used.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":" ","pages":"e0007223"},"PeriodicalIF":19.0,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237512/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140130931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}