{"title":"COVID-19 drug discovery and treatment options","authors":"Jasper Fuk-Woo Chan, Shuofeng Yuan, Hin Chu, Siddharth Sridhar, Kwok-Yung Yuen","doi":"10.1038/s41579-024-01036-y","DOIUrl":"10.1038/s41579-024-01036-y","url":null,"abstract":"The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused substantial morbidity and mortality, and serious social and economic disruptions worldwide. Unvaccinated or incompletely vaccinated older individuals with underlying diseases are especially prone to severe disease. In patients with non-fatal disease, long COVID affecting multiple body systems may persist for months. Unlike SARS-CoV and Middle East respiratory syndrome coronavirus, which have either been mitigated or remained geographically restricted, SARS-CoV-2 has disseminated globally and is likely to continue circulating in humans with possible emergence of new variants that may render vaccines less effective. Thus, safe, effective and readily available COVID-19 therapeutics are urgently needed. In this Review, we summarize the major drug discovery approaches, preclinical antiviral evaluation models, representative virus-targeting and host-targeting therapeutic options, and key therapeutics currently in clinical use for COVID-19. Preparedness against future coronavirus pandemics relies not only on effective vaccines but also on broad-spectrum antivirals targeting conserved viral components or universal host targets, and new therapeutics that can precisely modulate the immune response during infection. In this Review, Chan et al. explore major drug discovery approaches, preclinical antiviral evaluation models, virus-targeting and host-targeting therapeutic strategies, and key treatments currently used in clinical settings for COVID-19.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 7","pages":"391-407"},"PeriodicalIF":88.1,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140553359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Microbial adaptability in changing environments","authors":"Sharon Greenblum","doi":"10.1038/s41579-024-01046-w","DOIUrl":"10.1038/s41579-024-01046-w","url":null,"abstract":"This Genome Watch article highlights the recent use of large-scale monitoring of natural microbiomes to examine feedback between environmental change and microbial adaptation.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 6","pages":"327-327"},"PeriodicalIF":88.1,"publicationDate":"2024-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140550617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Aayushi Uberoi, Amelia McCready-Vangi, Elizabeth A. Grice
{"title":"The wound microbiota: microbial mechanisms of impaired wound healing and infection","authors":"Aayushi Uberoi, Amelia McCready-Vangi, Elizabeth A. Grice","doi":"10.1038/s41579-024-01035-z","DOIUrl":"10.1038/s41579-024-01035-z","url":null,"abstract":"The skin barrier protects the human body from invasion by exogenous and pathogenic microorganisms. A breach in this barrier exposes the underlying tissue to microbial contamination, which can lead to infection, delayed healing, and further loss of tissue and organ integrity. Delayed wound healing and chronic wounds are associated with comorbidities, including diabetes, advanced age, immunosuppression and autoimmune disease. The wound microbiota can influence each stage of the multi-factorial repair process and influence the likelihood of an infection. Pathogens that commonly infect wounds, such as Staphylococcus aureus and Pseudomonas aeruginosa, express specialized virulence factors that facilitate adherence and invasion. Biofilm formation and other polymicrobial interactions contribute to host immunity evasion and resistance to antimicrobial therapies. Anaerobic organisms, fungal and viral pathogens, and emerging drug-resistant microorganisms present unique challenges for diagnosis and therapy. In this Review, we explore the current understanding of how microorganisms present in wounds impact the process of skin repair and lead to infection through their actions on the host and the other microbial wound inhabitants. In this Review, Uberoi, McCready-Vangi and Grice explore the diversity of microorganisms present in wounds and examine the mechanisms through which they invade skin tissues, impair skin repair and cause infection.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 8","pages":"507-521"},"PeriodicalIF":69.2,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140346292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Microbial food spoilage: impact, causative agents and control strategies","authors":"Abigail B. Snyder, Nicole Martin, Martin Wiedmann","doi":"10.1038/s41579-024-01037-x","DOIUrl":"10.1038/s41579-024-01037-x","url":null,"abstract":"Microbial food spoilage is a major contributor to food waste and, hence, to the negative environmental sustainability impacts of food production and processing. Globally, it is estimated that 15–20% of food is wasted, with waste, by definition, occurring after primary production and harvesting (for example, in households and food service establishments). Although the causative agents of food spoilage are diverse, many microorganisms are major contributors across different types of foods. For example, the genus Pseudomonas causes spoilage in various raw and ready-to-eat foods. Aerobic sporeformers (for example, members of the genera Bacillus, Paenibacillus and Alicyclobacillus) cause spoilage across various foods and beverages, whereas anaerobic sporeformers (for example, Clostridiales) cause spoilage in a range of products that present low-oxygen environments. Fungi are also important spoilage microorganisms, including in products that are not susceptible to bacterial spoilage due to their low water activity or low pH. Strategies that can reduce spoilage include improved control of spoilage microorganisms in raw material and environmental sources as well as application of microbicidal or microbiostatic strategies (for example, to products and packaging). Emerging tools (for example, systems models and improved genomic tools) represent an opportunity for rational design of systems, processes and products that minimize microbial food spoilage. In this Review, Snyder et al. discuss the global impacts of food spoilage, mechanisms and causative agents, and strategies and emerging tools to control microbial food spoilage.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 9","pages":"528-542"},"PeriodicalIF":69.2,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140343358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Author Correction: Conservation and similarity of bacterial and eukaryotic innate immunity","authors":"Hannah E. Ledvina, Aaron T. Whiteley","doi":"10.1038/s41579-024-01043-z","DOIUrl":"10.1038/s41579-024-01043-z","url":null,"abstract":"","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 7","pages":"451-451"},"PeriodicalIF":88.1,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41579-024-01043-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140293998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Maha Farhat, Helen Cox, Marwan Ghanem, Claudia M. Denkinger, Camilla Rodrigues, Mirna S. Abd El Aziz, Handaa Enkh-Amgalan, Debrah Vambe, Cesar Ugarte-Gil, Jennifer Furin, Madhukar Pai
{"title":"Drug-resistant tuberculosis: a persistent global health concern","authors":"Maha Farhat, Helen Cox, Marwan Ghanem, Claudia M. Denkinger, Camilla Rodrigues, Mirna S. Abd El Aziz, Handaa Enkh-Amgalan, Debrah Vambe, Cesar Ugarte-Gil, Jennifer Furin, Madhukar Pai","doi":"10.1038/s41579-024-01025-1","DOIUrl":"10.1038/s41579-024-01025-1","url":null,"abstract":"Drug-resistant tuberculosis (TB) is estimated to cause 13% of all antimicrobial resistance-attributable deaths worldwide and is driven by both ongoing resistance acquisition and person-to-person transmission. Poor outcomes are exacerbated by late diagnosis and inadequate access to effective treatment. Advances in rapid molecular testing have recently improved the diagnosis of TB and drug resistance. Next-generation sequencing of Mycobacterium tuberculosis has increased our understanding of genetic resistance mechanisms and can now detect mutations associated with resistance phenotypes. All-oral, shorter drug regimens that can achieve high cure rates of drug-resistant TB within 6–9 months are now available and recommended but have yet to be scaled to global clinical use. Promising regimens for the prevention of drug-resistant TB among high-risk contacts are supported by early clinical trial data but final results are pending. A person-centred approach is crucial in managing drug-resistant TB to reduce the risk of poor treatment outcomes, side effects, stigma and mental health burden associated with the diagnosis. In this Review, we describe current surveillance of drug-resistant TB and the causes, risk factors and determinants of drug resistance as well as the stigma and mental health considerations associated with it. We discuss recent advances in diagnostics and drug-susceptibility testing and outline the progress in developing better treatment and preventive therapies. In this Review, Pai and colleagues examine the global landscape of drug-resistant tuberculosis, exploring its epidemiology, causes, risk factors, stigma and associated mental health burden as well as discussing the most recent developments in diagnostics, treatment and preventive regimens.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 10","pages":"617-635"},"PeriodicalIF":69.2,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140188953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Antimicrobial treatment and resistance in sexually transmitted bacterial infections","authors":"Jorgen S. Jensen, Magnus Unemo","doi":"10.1038/s41579-024-01023-3","DOIUrl":"10.1038/s41579-024-01023-3","url":null,"abstract":"Sexually transmitted infections (STIs) have been part of human life since ancient times, and their symptoms affect quality of life, and sequelae are common. Socioeconomic and behavioural trends affect the prevalence of STIs, but the discovery of antimicrobials gave hope for treatment, control of the spread of infection and lower rates of sequelae. This has to some extent been achieved, but increasing antimicrobial resistance and increasing transmission in high-risk sexual networks threaten this progress. For Neisseria gonorrhoeae, the only remaining first-line treatment (with ceftriaxone) is at risk of becoming ineffective, and for Mycoplasma genitalium, for which fewer alternative antimicrobial classes are available, incurable infections have already been reported. For Chlamydia trachomatis, in vitro resistance to first-line tetracyclines and macrolides has never been confirmed despite decades of treatment of this highly prevalent STI. Similarly, Treponema pallidum, the cause of syphilis, has remained susceptible to first-line penicillin. In the Review, Jensen and Unemo examine the epidemiology and clinical features, treatment options, and antimicrobial resistance of Neisseria gonorrhoeae and Mycoplasma genitalium, while briefly covering Chlamydia trachomatis and Treponema pallidum.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 7","pages":"435-450"},"PeriodicalIF":88.1,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140164899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nianzhi Jiao, Tingwei Luo, Quanrui Chen, Zhao Zhao, Xilin Xiao, Jihua Liu, Zhimin Jian, Shucheng Xie, Helmuth Thomas, Gerhard J. Herndl, Ronald Benner, Micheal Gonsior, Feng Chen, Wei-Jun Cai, Carol Robinson
{"title":"The microbial carbon pump and climate change","authors":"Nianzhi Jiao, Tingwei Luo, Quanrui Chen, Zhao Zhao, Xilin Xiao, Jihua Liu, Zhimin Jian, Shucheng Xie, Helmuth Thomas, Gerhard J. Herndl, Ronald Benner, Micheal Gonsior, Feng Chen, Wei-Jun Cai, Carol Robinson","doi":"10.1038/s41579-024-01018-0","DOIUrl":"10.1038/s41579-024-01018-0","url":null,"abstract":"The ocean has been a regulator of climate change throughout the history of Earth. One key mechanism is the mediation of the carbon reservoir by refractory dissolved organic carbon (RDOC), which can either be stored in the water column for centuries or released back into the atmosphere as CO2 depending on the conditions. The RDOC is produced through a myriad of microbial metabolic and ecological processes known as the microbial carbon pump (MCP). Here, we review recent research advances in processes related to the MCP, including the distribution patterns and molecular composition of RDOC, links between the complexity of RDOC compounds and microbial diversity, MCP-driven carbon cycles across time and space, and responses of the MCP to a changing climate. We identify knowledge gaps and future research directions in the role of the MCP, particularly as a key component in integrated approaches combining the mechanisms of the biological and abiotic carbon pumps for ocean negative carbon emissions. In this Review, Jiao, Robinson and colleagues examine recent advances related to the microbial carbon pump, exploring its role in the carbon cycle and climate change, and proposing future research directions and approaches to ocean negative carbon emissions.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 7","pages":"408-419"},"PeriodicalIF":88.1,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140139374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Effects of climate change and human activities on vector-borne diseases","authors":"William M. de Souza, Scott C. Weaver","doi":"10.1038/s41579-024-01026-0","DOIUrl":"10.1038/s41579-024-01026-0","url":null,"abstract":"Vector-borne diseases are transmitted by haematophagous arthropods (for example, mosquitoes, ticks and sandflies) to humans and wild and domestic animals, with the largest burden on global public health disproportionately affecting people in tropical and subtropical areas. Because vectors are ectothermic, climate and weather alterations (for example, temperature, rainfall and humidity) can affect their reproduction, survival, geographic distribution and, consequently, ability to transmit pathogens. However, the effects of climate change on vector-borne diseases can be multifaceted and complex, sometimes with ambiguous consequences. In this Review, we discuss the potential effects of climate change, weather and other anthropogenic factors, including land use, human mobility and behaviour, as possible contributors to the redistribution of vectors and spread of vector-borne diseases worldwide. In this Review, de Souza and Weaver discuss the potential effects on vector-borne diseases of climate change, weather and other anthropogenic factors, including land use, human mobility and behaviour, as possible contributors to the redistribution of vectors and spread of vector-borne diseases worldwide.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 8","pages":"476-491"},"PeriodicalIF":69.2,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140123863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}