Clinical Microbiology Reviews最新文献

{"title":"Agnostic Sequencing for Detection of Viral Pathogens.","authors":"Nick P G Gauthier, Samuel D Chorlton, Mel Krajden, Amee R Manges","doi":"10.1128/cmr.00119-22","DOIUrl":"10.1128/cmr.00119-22","url":null,"abstract":"<p><p>The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on <i>a priori</i> knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"36 1","pages":"e0011922"},"PeriodicalIF":36.8,"publicationDate":"2023-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10035330/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9944638","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":"The Changing Paradigm of Drug-Resistant Tuberculosis Treatment: Successes, Pitfalls, and Future Perspectives.","authors":"Navisha Dookie,&nbsp;Senamile L Ngema,&nbsp;Rubeshan Perumal,&nbsp;Nikita Naicker,&nbsp;Nesri Padayatchi,&nbsp;Kogieleum Naidoo","doi":"10.1128/cmr.00180-19","DOIUrl":"10.1128/cmr.00180-19","url":null,"abstract":"<p><p>Drug-resistant tuberculosis (DR-TB) remains a global crisis due to the increasing incidence of drug-resistant forms of the disease, gaps in detection and prevention, models of care, and limited treatment options. The DR-TB treatment landscape has evolved over the last 10 years. Recent developments include the remarkable activity demonstrated by the newly approved anti-TB drugs bedaquiline and pretomanid against Mycobacterium tuberculosis. Hence, treatment of DR-TB has drastically evolved with the introduction of the short-course regimen for multidrug-resistant TB (MDR-TB), transitioning to injection-free regimens and the approval of the 6-month short regimens for rifampin-resistant TB and MDR-TB. Moreover, numerous clinical trials are under way with the aim to reduce pill burden and shorten the DR-TB treatment duration. While there have been apparent successes in the field, some challenges remain. These include the ongoing inclusion of high-dose isoniazid in DR-TB regimens despite a lack of evidence for its efficacy and the inclusion of ethambutol and pyrazinamide in the standard short regimen despite known high levels of background resistance to both drugs. Furthermore, antimicrobial heteroresistance, extensive cavitary disease and intracavitary gradients, the emergence of bedaquiline resistance, and the lack of biomarkers to monitor DR-TB treatment response remain serious challenges to the sustained successes. In this review, we outline the impact of the new drugs and regimens on patient treatment outcomes, explore evidence underpinning current practices on regimen selection and duration, reflect on the disappointments and pitfalls in the field, and highlight key areas that require continued efforts toward improving treatment approaches and rapid biomarkers for monitoring treatment response.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"35 4","pages":"e0018019"},"PeriodicalIF":36.8,"publicationDate":"2022-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769521/pdf/cmr.00180-19.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9185549","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":"The Microbial Etiology of Community-Acquired Pneumonia in Adults: from Classical Bacteriology to Host Transcriptional Signatures.","authors":"Naomi J Gadsby,&nbsp;Daniel M Musher","doi":"10.1128/cmr.00015-22","DOIUrl":"10.1128/cmr.00015-22","url":null,"abstract":"<p><p>All modern advances notwithstanding, pneumonia remains a common infection with substantial morbidity and mortality. Understanding of the etiology of pneumonia continues to evolve as new techniques enable identification of already known organisms and as new organisms emerge. We now review the etiology of pneumonia (at present often called \"community-acquired pneumonia\") beginning with classic bacteriologic techniques, which identified Streptococcus pneumoniae as the overwhelmingly common cause, to more modern bacteriologic studies, which emphasize Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, <i>Enterobacteriaceae</i>, Pseudomonas, and normal respiratory flora. Urine antigen detection is useful in identifying <i>Legionella</i> and pneumococcus. The low yield of bacteria in recent studies is due to the failure to obtain valid sputum samples before antibiotics are administered. The use of high-quality sputum specimens enables identification of recognized (\"typical\") bacterial pathogens as well as a role for commensal bacteria (\"normal respiratory flora\"). Nucleic acid amplification technology for viruses has revolutionized diagnosis, showing the importance of viral pneumonia leading to hospitalization with or without coinfecting bacterial organisms. Quantitative PCR study of sputum is in its early stages of application, but regular detection of high counts of bacterial DNA from organisms that are not seen on Gram stain or grown in quantitative culture presents a therapeutic dilemma. This finding may reflect the host microbiome of the respiratory tract, in which case treatment may not need to be given for them. Finally, host transcriptional signatures might enable clinicians to distinguish between viral and bacterial pneumonia, an important practical consideration.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"35 4","pages":"e0001522"},"PeriodicalIF":36.8,"publicationDate":"2022-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769922/pdf/cmr.00015-22.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10606934","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":"Osteoarticular Mycoses.","authors":"Maria N Gamaletsou, Blandine Rammaert, Barry Brause, Marimelle A Bueno, Sanjeet S Dadwal, Michael W Henry, Aspasia Katragkou, Dimitrios P Kontoyiannis, Matthew W McCarthy, Andy O Miller, Brad Moriyama, Zoi Dorothea Pana, Ruta Petraitiene, Vidmantas Petraitis, Emmanuel Roilides, Jean-Pierre Sarkis, Maria Simitsopoulou, Nikolaos V Sipsas, Saad J Taj-Aldeen, Valérie Zeller, Olivier Lortholary, Thomas J Walsh","doi":"10.1128/cmr.00086-19","DOIUrl":"10.1128/cmr.00086-19","url":null,"abstract":"<p><p>Osteoarticular mycoses are chronic debilitating infections that require extended courses of antifungal therapy and may warrant expert surgical intervention. As there has been no comprehensive review of these diseases, the International Consortium for Osteoarticular Mycoses prepared a definitive treatise for this important class of infections. Among the etiologies of osteoarticular mycoses are <i>Candida</i> spp., Aspergillus spp., Mucorales, dematiaceous fungi, non-Aspergillus hyaline molds, and endemic mycoses, including those caused by Histoplasma capsulatum, Blastomyces dermatitidis, and <i>Coccidioides</i> species. This review analyzes the history, epidemiology, pathogenesis, clinical manifestations, diagnostic approaches, inflammatory biomarkers, diagnostic imaging modalities, treatments, and outcomes of osteomyelitis and septic arthritis caused by these organisms. <i>Candida</i> osteomyelitis and <i>Candida</i> arthritis are associated with greater events of hematogenous dissemination than those of most other osteoarticular mycoses. Traumatic inoculation is more commonly associated with osteoarticular mycoses caused by Aspergillus and non-Aspergillus molds. Synovial fluid cultures are highly sensitive in the detection of <i>Candida</i> and Aspergillus arthritis. Relapsed infection, particularly in <i>Candida</i> arthritis, may develop in relation to an inadequate duration of therapy. Overall mortality reflects survival from disseminated infection and underlying host factors.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"35 4","pages":"e0008619"},"PeriodicalIF":36.8,"publicationDate":"2022-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10608060","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":"Persistent Borrelia burgdorferi <i>Sensu Lato</i> Infection after Antibiotic Treatment: Systematic Overview and Appraisal of the Current Evidence from Experimental Animal Models.","authors":"Y L Verschoor,&nbsp;A Vrijlandt,&nbsp;R Spijker,&nbsp;R M van Hest,&nbsp;H Ter Hofstede,&nbsp;K van Kempen,&nbsp;A J Henningsson,&nbsp;J W Hovius","doi":"10.1128/cmr.00074-22","DOIUrl":"10.1128/cmr.00074-22","url":null,"abstract":"<p><p>Lyme borreliosis is caused by spirochetes belonging to the Borrelia burgdorferi <i>sensu lato</i> group, which are transmitted by <i>Ixodes</i> tick species living in the temperate climate zones of the Northern Hemisphere. The clinical manifestations of Lyme borreliosis are diverse and treated with oral or intravenous antibiotics. In some patients, long-lasting and debilitating symptoms can persist after the recommended antibiotic treatment. The etiology of such persisting symptoms is under debate, and one hypothesis entails persistent infection by a subset of spirochetes after antibiotic therapy. Here, we review and appraise the experimental evidence from <i>in vivo</i> animal studies on the persistence of B. burgdorferi sensu lato infection after antibiotic treatment, focusing on the antimicrobial agents doxycycline and ceftriaxone. Our review indicates that some <i>in vivo</i> animal studies found sporadic positive cultures after antibiotic treatment. However, this culture positivity often seemed to be related to inadequate antibiotic treatment, and the few positive cultures in some studies could not be reproduced in other studies. Overall, current results from animal studies provide insufficient evidence for the persistence of viable and infectious spirochetes after adequate antibiotic treatment. Borrelial nucleic acids, on the contrary, were frequently detected in these animal studies and may thus persist after antibiotic treatment. We put forward that research into the pathogenesis of persisting complaints after antibiotic treatment for Lyme borreliosis in humans should be a top priority, but future studies should most definitely also focus on explanations other than persistent B. burgdorferi sensu lato infection after antibiotic treatment.</p>","PeriodicalId":10378,"journal":{"name":"Clinical Microbiology Reviews","volume":"35 4","pages":"e0007422"},"PeriodicalIF":36.8,"publicationDate":"2022-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769629/pdf/cmr.00074-22.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10613738","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":"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":"35 4","pages":"e0006222"},"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":"35 4","pages":"e0023321"},"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":"35 4","pages":"e0013122"},"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":"35 4","pages":"e0005222"},"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":"35 4","pages":"e0009222"},"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}