Clinical Microbiology Reviews最新文献

{"title":"Reassessment of Historical Clinical Trials Supports the Effectiveness of Phage Therapy.","authors":"Luigi Marongiu,&nbsp;Markus Burkard,&nbsp;Ulrich M Lauer,&nbsp;Ludwig E Hoelzle,&nbsp;Sascha Venturelli","doi":"10.1128/cmr.00062-22","DOIUrl":"https://doi.org/10.1128/cmr.00062-22","url":null,"abstract":"<p><p>Phage therapy has become a hot topic in medical research due to the increasing prevalence of antibiotic-resistant bacteria strains. In the treatment of bacterial infections, bacteriophages have several advantages over antibiotics, including strain specificity, lack of serious side effects, and low development costs. However, scientists dismissed the clinical success of early clinical trials in the 1940s, slowing the adoption of this promising antibacterial application in Western countries. The current study used statistical methods commonly used in modern meta-analysis to reevaluate early 20th-century studies and compare them with clinical trials conducted in the last 20 years. Using a random effect model, the development of disease after treatment with or without phages was measured in odds ratios (OR) with 95% confidence intervals (CI). Based on the findings of 17 clinical trials conducted between 1921 and 1940, phage therapy was effective (OR = 0.21, 95% CI = 0.10 to 0.44, <i>P</i> value < 0.0001). The current study includes a topic review on modern clinical trials; four could be analyzed, indicating a noneffective therapy (OR = 2.84, 95% CI = 1.53 to 5.27, <i>P</i> value = 0.0009). The results suggest phage therapy was surprisingly less effective than standard treatments in resolving bacterial infections. However, the results were affected by the small sample set size. This work also contextualizes the development of phage therapy in the early 20th century and highlights the expansion of phage applications in the last few years. In conclusion, the current review shows phage therapy is no longer an underestimated tool in the treatment of bacterial infections.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":null,"pages":null},"PeriodicalIF":36.8,"publicationDate":"2022-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769689/pdf/cmr.00062-22.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10231295","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":"Paracoccidioidomycosis: Current Status and Future Trends.","authors":"Rosane Christine Hahn,&nbsp;Ferry Hagen,&nbsp;Rinaldo Poncio Mendes,&nbsp;Eva Burger,&nbsp;Andreia Ferreira Nery,&nbsp;Nathan Pereira Siqueira,&nbsp;Armando Guevara,&nbsp;Anderson Messias Rodrigues,&nbsp;Zoilo Pires de Camargo","doi":"10.1128/cmr.00233-21","DOIUrl":"https://doi.org/10.1128/cmr.00233-21","url":null,"abstract":"<p><p>Paracoccidioidomycosis (PCM), initially reported in 1908 in the city of São Paulo, Brazil, by Adolpho Lutz, is primarily a systemic and neglected tropical mycosis that may affect individuals with certain risk factors around Latin America, especially Brazil. Paracoccidioides brasiliensis <i>sensu stricto</i>, a classical thermodimorphic fungus associated with PCM, was long considered to represent a monotypic taxon. However, advances in molecular taxonomy revealed several cryptic species, including Paracoccidioides americana, P. restrepiensis, P. venezuelensis, and P. lutzii, that show a preference for skin and mucous membranes, lymph nodes, and respiratory organs but can also affect many other organs. The classical diagnosis of PCM benefits from direct microscopy culture-based, biochemical, and immunological assays in a general microbiology laboratory practice providing a generic identification of the agents. However, molecular assays should be employed to identify <i>Paracoccidioides</i> isolates to the species level, data that would be complemented by epidemiological investigations. From a clinical perspective, all probable and confirmed cases should be treated. The choice of treatment and its duration must be considered, along with the affected organs, process severity, history of previous treatment failure, possibility of administering oral medication, associated diseases, pregnancy, and patient compliance with the proposed treatment regimen. Nevertheless, even after appropriate treatment, there may be relapses, which generally occur 5 years after the apparent cure following treatment, and also, the mycosis may be confused with other diseases. This review provides a comprehensive and critical overview of the immunopathology, laboratory diagnosis, clinical aspects, and current treatment of PCM, highlighting current issues in the identification, treatment, and patient follow-up in light of recent <i>Paracoccidioides</i> species taxonomic developments.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":null,"pages":null},"PeriodicalIF":36.8,"publicationDate":"2022-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769695/pdf/cmr.00233-21.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10622354","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":"2022 Acknowledgment of CMR Reviewers.","authors":"Graeme Forrest","doi":"10.1128/cmr.00131-22","DOIUrl":"https://doi.org/10.1128/cmr.00131-22","url":null,"abstract":"","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":null,"pages":null},"PeriodicalIF":36.8,"publicationDate":"2022-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10406925","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":"Genotypic Resistance Testing of HIV-1 DNA in Peripheral Blood Mononuclear Cells.","authors":"Carolyn Chu, Daniele Armenia, Charles Walworth, Maria M Santoro, Robert W Shafer","doi":"10.1128/cmr.00052-22","DOIUrl":"10.1128/cmr.00052-22","url":null,"abstract":"<p><p>HIV-1 DNA exists in nonintegrated linear and circular episomal forms and as integrated proviruses. In patients with plasma viremia, most peripheral blood mononuclear cell (PBMC) HIV-1 DNA consists of recently produced nonintegrated virus DNA while in patients with prolonged virological suppression (VS) on antiretroviral therapy (ART), most PBMC HIV-1 DNA consists of proviral DNA produced months to years earlier. Drug-resistance mutations (DRMs) in PBMCs are more likely to coexist with ancestral wild-type virus populations than they are in plasma, explaining why next-generation sequencing is particularly useful for the detection of PBMC-associated DRMs. In patients with ongoing high levels of active virus replication, the DRMs detected in PBMCs and in plasma are usually highly concordant. However, in patients with lower levels of virus replication, it may take several months for plasma virus DRMs to reach detectable levels in PBMCs. This time lag explains why, in patients with VS, PBMC genotypic resistance testing (GRT) is less sensitive than historical plasma virus GRT, if previous episodes of virological failure and emergent DRMs were either not prolonged or not associated with high levels of plasma viremia. Despite the increasing use of PBMC GRT in patients with VS, few studies have examined the predictive value of DRMs on the response to a simplified ART regimen. In this review, we summarize what is known about PBMC HIV-1 DNA dynamics, particularly in patients with suppressed plasma viremia, the methods used for PBMC HIV-1 GRT, and the scenarios in which PBMC GRT has been used clinically.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":null,"pages":null},"PeriodicalIF":19.0,"publicationDate":"2022-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769561/pdf/cmr.00052-22.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10226088","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":"Monkeypox Virus Infections in Humans.","authors":"Sameer Elsayed, Lise Bondy, William P Hanage","doi":"10.1128/cmr.00092-22","DOIUrl":"10.1128/cmr.00092-22","url":null,"abstract":"<p><p>Human monkeypox is a viral zoonosis endemic to West and Central Africa that has recently generated increased interest and concern on a global scale as an emerging infectious disease threat in the midst of the slowly relenting COVID-2019 disease pandemic. The hallmark of infection is the development of a flu-like prodrome followed by the appearance of a smallpox-like exanthem. Precipitous person-to-person transmission of the virus among residents of 100 countries where it is nonendemic has motivated the immediate and widespread implementation of public health countermeasures. In this review, we discuss the origins and virology of monkeypox virus, its link with smallpox eradication, its record of causing outbreaks of human disease in regions where it is endemic in wildlife, its association with outbreaks in areas where it is nonendemic, the clinical manifestations of disease, laboratory diagnostic methods, case management, public health interventions, and future directions.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":null,"pages":null},"PeriodicalIF":36.8,"publicationDate":"2022-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769527/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9170580","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":"Updated Review on <i>Nocardia</i> Species: 2006-2021.","authors":"Rita M Traxler,&nbsp;Melissa E Bell,&nbsp;Brent Lasker,&nbsp;Brendan Headd,&nbsp;Wun-Ju Shieh,&nbsp;John R McQuiston","doi":"10.1128/cmr.00027-21","DOIUrl":"10.1128/cmr.00027-21","url":null,"abstract":"<p><p>This review serves as an update to the previous <i>Nocardia</i> review by Brown-Elliott et al. published in 2006 (B. A. Brown-Elliott, J. M. Brown, P. S. Conville, and R. J. Wallace. Jr., Clin Microbiol Rev 19:259-282, 2006, https://doi.org/10.1128/CMR.19.2.259-282.2006). Included is a discussion on the taxonomic expansion of the genus, current identification methods, and the impact of new technology (including matrix-assisted laser desorption ionization-time of flight [MALDI-TOF] and whole genome sequencing) on diagnosis and treatment. Clinical manifestations, the epidemiology, and geographic distribution are briefly discussed. An additional section on actinomycotic mycetoma is added to address this often-neglected disease.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":null,"pages":null},"PeriodicalIF":36.8,"publicationDate":"2022-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769612/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10614373","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":"Human and Animal Fascioliasis: Origins and Worldwide Evolving Scenario.","authors":"Santiago Mas-Coma, M Adela Valero, M Dolores Bargues","doi":"10.1128/cmr.00088-19","DOIUrl":"10.1128/cmr.00088-19","url":null,"abstract":"<p><p>Fascioliasis is a plant- and waterborne zoonotic parasitic disease caused by two trematode species: (i) Fasciola hepatica in Europe, Asia, Africa, the Americas, and Oceania and (ii) <i>F. gigantica</i>, which is restricted to Africa and Asia. Fasciolid liver flukes infect mainly herbivores as ruminants, equids, and camelids but also omnivore mammals as humans and swine and are transmitted by freshwater Lymnaeidae snail vectors. Two phases may be distinguished in fasciolid evolution. The long predomestication period includes the <i>F. gigantica</i> origin in east-southern Africa around the mid-Miocene, the <i>F. hepatica</i> origin in the Near-Middle East of Asia around the latest Miocene to Early Pliocene, and their subsequent local spread. The short postdomestication period includes the worldwide spread by human-guided movements of animals in the last 12,000 years and the more recent transoceanic anthropogenic introductions of <i>F. hepatica</i> into the Americas and Oceania and of <i>F. gigantica</i> into several large islands of the Pacific with ships transporting livestock in the last 500 years. The routes and chronology of the spreading waves followed by both fasciolids into the five continents are redefined on the basis of recently generated knowledge of human-guided movements of domesticated hosts. No local, zonal, or regional situation showing disagreement with historical records was found, although in a few world zones the available knowledge is still insufficient. The anthropogenically accelerated evolution of fasciolids allows us to call them \"peridomestic endoparasites.\" The multidisciplinary implications for crucial aspects of the disease should therefore lead the present baseline update to be taken into account in future research studies.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":null,"pages":null},"PeriodicalIF":36.8,"publicationDate":"2022-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10617380","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":"Controlled Human Infection Models To Accelerate Vaccine Development.","authors":"Robert K M Choy,&nbsp;A Louis Bourgeois,&nbsp;Christian F Ockenhouse,&nbsp;Richard I Walker,&nbsp;Rebecca L Sheets,&nbsp;Jorge Flores","doi":"10.1128/cmr.00008-21","DOIUrl":"10.1128/cmr.00008-21","url":null,"abstract":"<p><p>The timelines for developing vaccines against infectious diseases are lengthy, and often vaccines that reach the stage of large phase 3 field trials fail to provide the desired level of protective efficacy. The application of controlled human challenge models of infection and disease at the appropriate stages of development could accelerate development of candidate vaccines and, in fact, has done so successfully in some limited cases. Human challenge models could potentially be used to gather critical information on pathogenesis, inform strain selection for vaccines, explore cross-protective immunity, identify immune correlates of protection and mechanisms of protection induced by infection or evoked by candidate vaccines, guide decisions on appropriate trial endpoints, and evaluate vaccine efficacy. We prepared this report to motivate fellow scientists to exploit the potential capacity of controlled human challenge experiments to advance vaccine development. In this review, we considered available challenge models for 17 infectious diseases in the context of the public health importance of each disease, the diversity and pathogenesis of the causative organisms, the vaccine candidates under development, and each model's capacity to evaluate them and identify correlates of protective immunity. Our broad assessment indicated that human challenge models have not yet reached their full potential to support the development of vaccines against infectious diseases. On the basis of our review, however, we believe that describing an ideal challenge model is possible, as is further developing existing and future challenge models.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":null,"pages":null},"PeriodicalIF":36.8,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9491212/pdf/cmr.00008-21.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10133947","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":"Tuberculosis Treatment Monitoring and Outcome Measures: New Interest and New Strategies.","authors":"Jan Heyckendorf,&nbsp;Sophia B Georghiou,&nbsp;Nicole Frahm,&nbsp;Norbert Heinrich,&nbsp;Irina Kontsevaya,&nbsp;Maja Reimann,&nbsp;David Holtzman,&nbsp;Marjorie Imperial,&nbsp;Daniela M Cirillo,&nbsp;Stephen H Gillespie,&nbsp;Morten Ruhwald","doi":"10.1128/cmr.00227-21","DOIUrl":"https://doi.org/10.1128/cmr.00227-21","url":null,"abstract":"<p><p>Despite the advent of new diagnostics, drugs and regimens, tuberculosis (TB) remains a global public health threat. A significant challenge for TB control efforts has been the monitoring of TB therapy and determination of TB treatment success. Current recommendations for TB treatment monitoring rely on sputum and culture conversion, which have low sensitivity and long turnaround times, present biohazard risk, and are prone to contamination, undermining their usefulness as clinical treatment monitoring tools and for drug development. We review the pipeline of molecular technologies and assays that serve as suitable substitutes for current culture-based readouts for treatment response and outcome with the potential to change TB therapy monitoring and accelerate drug development.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":null,"pages":null},"PeriodicalIF":36.8,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9491169/pdf/cmr.00227-21.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9148262","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":"Machine Learning for Antimicrobial Resistance Prediction: Current Practice, Limitations, and Clinical Perspective.","authors":"Jee In Kim, Finlay Maguire, Kara K Tsang, Theodore Gouliouris, Sharon J Peacock, Tim A McAllister, Andrew G McArthur, Robert G Beiko","doi":"10.1128/cmr.00179-21","DOIUrl":"10.1128/cmr.00179-21","url":null,"abstract":"<p><p>Antimicrobial resistance (AMR) is a global health crisis that poses a great threat to modern medicine. Effective prevention strategies are urgently required to slow the emergence and further dissemination of AMR. Given the availability of data sets encompassing hundreds or thousands of pathogen genomes, machine learning (ML) is increasingly being used to predict resistance to different antibiotics in pathogens based on gene content and genome composition. A key objective of this work is to advocate for the incorporation of ML into front-line settings but also highlight the further refinements that are necessary to safely and confidently incorporate these methods. The question of what to predict is not trivial given the existence of different quantitative and qualitative laboratory measures of AMR. ML models typically treat genes as independent predictors, with no consideration of structural and functional linkages; they also may not be accurate when new mutational variants of known AMR genes emerge. Finally, to have the technology trusted by end users in public health settings, ML models need to be transparent and explainable to ensure that the basis for prediction is clear. We strongly advocate that the next set of AMR-ML studies should focus on the refinement of these limitations to be able to bridge the gap to diagnostic implementation.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":null,"pages":null},"PeriodicalIF":19.0,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9491192/pdf/cmr.00179-21.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9520536","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}