Clinical Microbiology Reviews最新文献

{"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":"35 4","pages":"e0002721"},"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":"35 4","pages":"e0008819"},"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":"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":"35 3","pages":"e0017921"},"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}

{"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":"35 3","pages":"e0000821"},"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":"35 3","pages":"e0022721"},"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":"Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease.","authors":"Sabrina Naud,&nbsp;Ahmad Ibrahim,&nbsp;Camille Valles,&nbsp;Mohamad Maatouk,&nbsp;Fadi Bittar,&nbsp;Maryam Tidjani Alou,&nbsp;Didier Raoult","doi":"10.1128/cmr.00140-21","DOIUrl":"https://doi.org/10.1128/cmr.00140-21","url":null,"abstract":"<p><p>Candidate phyla radiation (CPR) is an emerging division of the bacterial domain within the human microbiota. Still poorly known, these microorganisms were first described in the environment in 1981 as \"ultramicrobacteria\" with a cell volume under 0.1 μm³ and were first associated with the human oral microbiota in 2007. The evolution of technology has been paramount for the study of CPR within the human microbiota. In fact, since these ultramicrobacteria have yet to be axenically cultured despite ongoing efforts, progress in imaging technology has allowed their observation and morphological description. Although their genomic abilities and taxonomy are still being studied, great strides have been made regarding their taxonomic classification, as well as their lifestyle. In addition, advancements in next-generation sequencing and the continued development of bioinformatics tools have allowed their detection as commensals in different human habitats, including the oral cavity and gastrointestinal and genital tracts, thus highlighting CPR as a nonnegligible part of the human microbiota with an impact on physiological settings. Conversely, several pathologies present dysbiosis affecting CPR levels, including inflammatory, mucosal, and infectious diseases. In this exhaustive review of the literature, we provide a historical perspective on the study of CPR, an overview of the methods available to study these organisms and a description of their taxonomy and lifestyle. In addition, their distribution in the human microbiome is presented in both homeostatic and dysbiotic settings. Future efforts should focus on developing cocultures and, if possible, axenic cultures to obtain isolates and therefore genomes that would provide a better understanding of these ultramicrobacteria, the importance of which in the human microbiome is undeniable.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"35 3","pages":"e0014021"},"PeriodicalIF":36.8,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9491188/pdf/cmr.00140-21.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9583801","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":"Helicobacter pylori Infection, Its Laboratory Diagnosis, and Antimicrobial Resistance: a Perspective of Clinical Relevance.","authors":"Shamshul Ansari, Yoshio Yamaoka","doi":"10.1128/cmr.00258-21","DOIUrl":"10.1128/cmr.00258-21","url":null,"abstract":"<p><p>Despite the recent decrease in overall prevalence of Helicobacter pylori infection, morbidity and mortality rates associated with gastric cancer remain high. The antimicrobial resistance developments and treatment failure are fueling the global burden of H. pylori-associated gastric complications. Accurate diagnosis remains the opening move for treatment and eradication of infections caused by microorganisms. Although several reports have been published on diagnostic approaches for H. pylori infection, most lack the data regarding diagnosis from a clinical perspective. Therefore, we provide an intensive, comprehensive, and updated description of the currently available diagnostic methods that can help clinicians, infection diagnosis professionals, and H. pylori researchers working on infection epidemiology to broaden their understanding and to select appropriate diagnostic methods. We also emphasize appropriate diagnostic approaches based on clinical settings (either clinical diagnosis or mass screening), patient factors (either age or other predisposing factors), and clinical factors (either upper gastrointestinal bleeding or partial gastrectomy) and appropriate methods to be considered for evaluating eradication efficacy. Furthermore, to cope with the increasing trend of antimicrobial resistance, a better understanding of its emergence and current diagnostic approaches for resistance detection remain inevitable.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"35 3","pages":"e0025821"},"PeriodicalIF":19.0,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9491184/pdf/cmr.00258-21.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9277985","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":"Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks.","authors":"Raphael Nyaruaba, Caroline Mwaliko, David Dobnik, Pavel Neužil, Patrick Amoth, Matilu Mwau, Junping Yu, Hang Yang, Hongping Wei","doi":"10.1128/cmr.00168-21","DOIUrl":"10.1128/cmr.00168-21","url":null,"abstract":"<p><p>The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"35 3","pages":"e0016821"},"PeriodicalIF":19.0,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9491181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662592","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":"Diagnosis, Management, and Future Control of Cholera.","authors":"Fahima Chowdhury, Allen G Ross, Md Taufiqul Islam, Nigel A J McMillan, Firdausi Qadri","doi":"10.1128/cmr.00211-21","DOIUrl":"10.1128/cmr.00211-21","url":null,"abstract":"<p><p>Cholera, caused by Vibrio cholerae, persists in developing countries due to inadequate access to safe water, sanitation, and hygiene. There are approximately 4 million cases and 143,000 deaths each year due to cholera. The disease is transmitted fecally-orally via contaminated food or water. Severe dehydrating cholera can progress to hypovolemic shock due to the rapid loss of fluids and electrolytes, which requires a rapid infusion of intravenous (i.v.) fluids. The case fatality rate exceeds 50% without proper clinical management but can be less than 1% with prompt rehydration and antibiotics. Oral cholera vaccines (OCVs) serve as a major component of an integrated control package during outbreaks or within zones of endemicity. Water, sanitation, and hygiene (WaSH); health education; and prophylactic antibiotic treatment are additional components of the prevention and control of cholera. The World Health Organization (WHO) and the Global Task Force for Cholera Control (GTFCC) have set an ambitious goal of eliminating cholera by 2030 in high-risk areas.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"35 3","pages":"e0021121"},"PeriodicalIF":19.0,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9491185/pdf/cmr.00211-21.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9756037","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 Convalescent Plasma and Clinical Trials: Understanding Conflicting Outcomes.","authors":"Daniele Focosi,&nbsp;Massimo Franchini,&nbsp;Liise-Anne Pirofski,&nbsp;Thierry Burnouf,&nbsp;Nigel Paneth,&nbsp;Michael J Joyner,&nbsp;Arturo Casadevall","doi":"10.1128/cmr.00200-21","DOIUrl":"10.1128/cmr.00200-21","url":null,"abstract":"<p><p>Convalescent plasma (CP) recurs as a frontline treatment in epidemics because it is available as soon as there are survivors. The COVID-19 pandemic represented the first large-scale opportunity to shed light on the mechanisms of action, safety, and efficacy of CP using modern evidence-based medicine approaches. Studies ranging from observational case series to randomized controlled trials (RCTs) have reported highly variable efficacy results for COVID-19 CP (CCP), resulting in uncertainty. We analyzed variables associated with efficacy, such as clinical settings, disease severity, CCP SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) antibody levels and function, dose, timing of administration (variously defined as time from onset of symptoms, molecular diagnosis, diagnosis of pneumonia, or hospitalization, or by serostatus), outcomes (defined as hospitalization, requirement for ventilation, clinical improvement, or mortality), CCP provenance and time for collection, and criteria for efficacy. The conflicting trial results, along with both recent WHO guidelines discouraging CCP usage and the recent expansion of the FDA emergency use authorization (EUA) to include outpatient use of CCP, create confusion for both clinicians and patients about the appropriate use of CCP. A review of 30 available RCTs demonstrated that signals of efficacy (including reductions in mortality) were more likely if the CCP neutralizing titer was >160 and the time to randomization was less than 9 days. The emergence of the Omicron variant also reminds us of the benefits of polyclonal antibody therapies, especially as a bridge to the development and availability of more specific therapies.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"35 3","pages":"e0020021"},"PeriodicalIF":36.8,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9491201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9828745","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}