Pub Date : 2024-06-18DOI: 10.1038/s41579-024-01058-6
Yahan Wei, Dennise Palacios Araya, Kelli L Palmer
The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.
{"title":"Enterococcus faecium: evolution, adaptation, pathogenesis and emerging therapeutics.","authors":"Yahan Wei, Dennise Palacios Araya, Kelli L Palmer","doi":"10.1038/s41579-024-01058-6","DOIUrl":"10.1038/s41579-024-01058-6","url":null,"abstract":"<p><p>The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.</p>","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":69.2,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141419806","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}
Pub Date : 2024-06-18DOI: 10.1038/s41579-024-01072-8
Andrea Du Toit
This study shows that archaea produce catalytically active ultraminimal as well as hybrid [FeFe] hydrogenases.
这项研究表明，古细菌能产生具有催化活性的超微结构氢酶和混合[FeFe]氢酶。
{"title":"Gassy archaea","authors":"Andrea Du Toit","doi":"10.1038/s41579-024-01072-8","DOIUrl":"10.1038/s41579-024-01072-8","url":null,"abstract":"This study shows that archaea produce catalytically active ultraminimal as well as hybrid [FeFe] hydrogenases.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":69.2,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141419807","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}
Pub Date : 2024-06-14DOI: 10.1038/s41579-024-01070-w
Agustina Taglialegna
In this study, Niggs et al. show that Drosophila A virus infection modulates epithelial turnover in the intestine of Drosophila melanogaster, promoting premature intestinal dysplasia and reducing fly lifespan.
在这项研究中，Niggs 等人发现，果蝇 A 病毒感染会调节黑腹果蝇肠道上皮的更替，促进肠道过早发育不良，缩短果蝇的寿命。
{"title":"A virus hastens ageing in flies","authors":"Agustina Taglialegna","doi":"10.1038/s41579-024-01070-w","DOIUrl":"10.1038/s41579-024-01070-w","url":null,"abstract":"In this study, Niggs et al. show that Drosophila A virus infection modulates epithelial turnover in the intestine of Drosophila melanogaster, promoting premature intestinal dysplasia and reducing fly lifespan.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":69.2,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141319929","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":"Supra-structures to target lipid II","authors":"Andrea Du Toit","doi":"10.1038/s41579-024-01066-6","DOIUrl":"10.1038/s41579-024-01066-6","url":null,"abstract":"This study reports that plectasin uses a supramolecular antimicrobial mode of action, whereby the oligomerized peptide sequesters lipid II.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":69.2,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141306328","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}
Pub Date : 2024-06-03DOI: 10.1038/s41579-024-01054-w
William R. Miller, Cesar A. Arias
The rise of antibiotic resistance and a dwindling antimicrobial pipeline have been recognized as emerging threats to public health. The ESKAPE pathogens — Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. — were initially identified as critical multidrug-resistant bacteria for which effective therapies were rapidly needed. Now, entering the third decade of the twenty-first century, and despite the introduction of several new antibiotics and antibiotic adjuvants, such as novel β-lactamase inhibitors, these organisms continue to represent major therapeutic challenges. These bacteria share several key biological features, including adaptations for survival in the modern health-care setting, diverse methods for acquiring resistance determinants and the dissemination of successful high-risk clones around the world. With the advent of next-generation sequencing, novel tools to track and combat the spread of these organisms have rapidly evolved, as well as renewed interest in non-traditional antibiotic approaches. In this Review, we explore the current epidemiology and clinical impact of this important group of bacterial pathogens and discuss relevant mechanisms of resistance to recently introduced antibiotics that affect their use in clinical settings. Furthermore, we discuss emerging therapeutic strategies needed for effective patient care in the era of widespread antimicrobial resistance. In this Review, Miller and Arias summarize recent advances in understanding ESKAPE pathogens, focusing on their molecular epidemiology, clinical impact, emerging mechanisms of resistance and novel therapeutic approaches.
{"title":"ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics","authors":"William R. Miller, Cesar A. Arias","doi":"10.1038/s41579-024-01054-w","DOIUrl":"10.1038/s41579-024-01054-w","url":null,"abstract":"The rise of antibiotic resistance and a dwindling antimicrobial pipeline have been recognized as emerging threats to public health. The ESKAPE pathogens — Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. — were initially identified as critical multidrug-resistant bacteria for which effective therapies were rapidly needed. Now, entering the third decade of the twenty-first century, and despite the introduction of several new antibiotics and antibiotic adjuvants, such as novel β-lactamase inhibitors, these organisms continue to represent major therapeutic challenges. These bacteria share several key biological features, including adaptations for survival in the modern health-care setting, diverse methods for acquiring resistance determinants and the dissemination of successful high-risk clones around the world. With the advent of next-generation sequencing, novel tools to track and combat the spread of these organisms have rapidly evolved, as well as renewed interest in non-traditional antibiotic approaches. In this Review, we explore the current epidemiology and clinical impact of this important group of bacterial pathogens and discuss relevant mechanisms of resistance to recently introduced antibiotics that affect their use in clinical settings. Furthermore, we discuss emerging therapeutic strategies needed for effective patient care in the era of widespread antimicrobial resistance. In this Review, Miller and Arias summarize recent advances in understanding ESKAPE pathogens, focusing on their molecular epidemiology, clinical impact, emerging mechanisms of resistance and novel therapeutic approaches.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":69.2,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141235958","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}
Pub Date : 2024-05-29DOI: 10.1038/s41579-024-01044-y
Timothy W. Lyons, Christopher J. Tino, Gregory P. Fournier, Rika E. Anderson, William D. Leavitt, Kurt O. Konhauser, Eva E. Stüeken
Two records of Earth history capture the evolution of life and its co-evolving ecosystems with interpretable fidelity: the geobiological and geochemical traces preserved in rocks and the evolutionary histories captured within genomes. The earliest vestiges of life are recognized mostly in isotopic fingerprints of specific microbial metabolisms, whereas fossils and organic biomarkers become important later. Molecular biology provides lineages that can be overlayed on geologic and geochemical records of evolving life. All these data lie within a framework of biospheric evolution that is primarily characterized by the transition from an oxygen-poor to an oxygen-rich world. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, fundamental transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and their links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. The evolution of microbial life and its ecological impacts directly mirror the Earth’s chemical and physical evolution through cause-and-effect relationships. In this Review, Lyons, Tino and colleagues explore the evolution of microbial life on Earth and examine the diversity of early microbial metabolic pathways, their associations with biogeochemical cycles and how they shaped and responded to changing surface environments over billions of years.
{"title":"Co‐evolution of early Earth environments and microbial life","authors":"Timothy W. Lyons, Christopher J. Tino, Gregory P. Fournier, Rika E. Anderson, William D. Leavitt, Kurt O. Konhauser, Eva E. Stüeken","doi":"10.1038/s41579-024-01044-y","DOIUrl":"10.1038/s41579-024-01044-y","url":null,"abstract":"Two records of Earth history capture the evolution of life and its co-evolving ecosystems with interpretable fidelity: the geobiological and geochemical traces preserved in rocks and the evolutionary histories captured within genomes. The earliest vestiges of life are recognized mostly in isotopic fingerprints of specific microbial metabolisms, whereas fossils and organic biomarkers become important later. Molecular biology provides lineages that can be overlayed on geologic and geochemical records of evolving life. All these data lie within a framework of biospheric evolution that is primarily characterized by the transition from an oxygen-poor to an oxygen-rich world. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, fundamental transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and their links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. The evolution of microbial life and its ecological impacts directly mirror the Earth’s chemical and physical evolution through cause-and-effect relationships. In this Review, Lyons, Tino and colleagues explore the evolution of microbial life on Earth and examine the diversity of early microbial metabolic pathways, their associations with biogeochemical cycles and how they shaped and responded to changing surface environments over billions of years.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":69.2,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141176074","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}
Pub Date : 2024-05-24DOI: 10.1038/s41579-024-01051-z
Alison E. Mather, Matthew W. Gilmour, Stuart W. J. Reid, Nigel P. French
Foodborne illnesses pose a substantial health and economic burden, presenting challenges in prevention due to the diverse microbial hazards that can enter and spread within food systems. Various factors, including natural, political and commercial drivers, influence food production and distribution. The risks of foodborne illness will continue to evolve in step with these drivers and with changes to food systems. For example, climate impacts on water availability for agriculture, changes in food sustainability targets and evolving customer preferences can all have an impact on the ecology of foodborne pathogens and the agrifood niches that can carry microorganisms. Whole-genome and metagenome sequencing, combined with microbial surveillance schemes and insights from the food system, can provide authorities and businesses with transformative information to address risks and implement new food safety interventions across the food chain. In this Review, we describe how genome-based approaches have advanced our understanding of the evolution and spread of enduring bacterial foodborne hazards as well as their role in identifying emerging foodborne hazards. Furthermore, foodborne hazards exist in complex microbial communities across the entire food chain, and consideration of these co-existing organisms is essential to understanding the entire ecology supporting pathogen persistence and transmission in an evolving food system. In this Review, Mather et al. discuss the role of genome-based approaches in deepening our understanding of both enduring and emerging bacterial foodborne pathogens in the context of evolving global food systems and environmental changes.
{"title":"Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world","authors":"Alison E. Mather, Matthew W. Gilmour, Stuart W. J. Reid, Nigel P. French","doi":"10.1038/s41579-024-01051-z","DOIUrl":"10.1038/s41579-024-01051-z","url":null,"abstract":"Foodborne illnesses pose a substantial health and economic burden, presenting challenges in prevention due to the diverse microbial hazards that can enter and spread within food systems. Various factors, including natural, political and commercial drivers, influence food production and distribution. The risks of foodborne illness will continue to evolve in step with these drivers and with changes to food systems. For example, climate impacts on water availability for agriculture, changes in food sustainability targets and evolving customer preferences can all have an impact on the ecology of foodborne pathogens and the agrifood niches that can carry microorganisms. Whole-genome and metagenome sequencing, combined with microbial surveillance schemes and insights from the food system, can provide authorities and businesses with transformative information to address risks and implement new food safety interventions across the food chain. In this Review, we describe how genome-based approaches have advanced our understanding of the evolution and spread of enduring bacterial foodborne hazards as well as their role in identifying emerging foodborne hazards. Furthermore, foodborne hazards exist in complex microbial communities across the entire food chain, and consideration of these co-existing organisms is essential to understanding the entire ecology supporting pathogen persistence and transmission in an evolving food system. In this Review, Mather et al. discuss the role of genome-based approaches in deepening our understanding of both enduring and emerging bacterial foodborne pathogens in the context of evolving global food systems and environmental changes.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":69.2,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141093737","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}
Pub Date : 2024-05-22DOI: 10.1038/s41579-024-01048-8
Mustafa Özçam, Susan V. Lynch
Communication between the gut and remote organs, such as the brain or the cardiovascular system, has been well established and recent studies provide evidence for a potential bidirectional gut–airway axis. Observations from animal and human studies indicate that respiratory insults influence the activity of the gut microbiome and that microbial ligands and metabolic products generated by the gut microbiome shape respiratory immunity. Information exchange between these two large mucosal surface areas regulates microorganism–immune interactions, with significant implications for the clinical and treatment outcomes of a range of respiratory conditions, including asthma, chronic obstructive pulmonary disease and lung cancer. In this Review, we summarize the most recent data in this field, offering insights into mechanisms of gut–airway crosstalk across spatial and temporal gradients and their relevance for respiratory health. In this Review, Özçam and Lynch examine recent findings reporting the interaction between the gut and the airway microbiomes and explore the role of gut–airway crosstalk in human health and respiratory diseases.
{"title":"The gut–airway microbiome axis in health and respiratory diseases","authors":"Mustafa Özçam, Susan V. Lynch","doi":"10.1038/s41579-024-01048-8","DOIUrl":"10.1038/s41579-024-01048-8","url":null,"abstract":"Communication between the gut and remote organs, such as the brain or the cardiovascular system, has been well established and recent studies provide evidence for a potential bidirectional gut–airway axis. Observations from animal and human studies indicate that respiratory insults influence the activity of the gut microbiome and that microbial ligands and metabolic products generated by the gut microbiome shape respiratory immunity. Information exchange between these two large mucosal surface areas regulates microorganism–immune interactions, with significant implications for the clinical and treatment outcomes of a range of respiratory conditions, including asthma, chronic obstructive pulmonary disease and lung cancer. In this Review, we summarize the most recent data in this field, offering insights into mechanisms of gut–airway crosstalk across spatial and temporal gradients and their relevance for respiratory health. In this Review, Özçam and Lynch examine recent findings reporting the interaction between the gut and the airway microbiomes and explore the role of gut–airway crosstalk in human health and respiratory diseases.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":69.2,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141079755","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}
Pub Date : 2024-05-21DOI: 10.1038/s41579-024-01063-9
Andrea Du Toit
This study reports the mechanism of plasmid clearance by the DNA defence module DdmDE of the Vibrio cholerae seventh pandemic strain.
本研究报告了霍乱弧菌第七流行株 DNA 防御模块 DdmDE 清除质粒的机制。
{"title":"Defending against plasmids","authors":"Andrea Du Toit","doi":"10.1038/s41579-024-01063-9","DOIUrl":"10.1038/s41579-024-01063-9","url":null,"abstract":"This study reports the mechanism of plasmid clearance by the DNA defence module DdmDE of the Vibrio cholerae seventh pandemic strain.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":88.1,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141074177","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}
Pub Date : 2024-05-20DOI: 10.1038/s41579-024-01059-5
Yi Shi
In this Journal Club, Yi Shi discusses a paper reporting that influenza virus infection in humans induces broadly cross-reactive and protective antibodies against the viral neuraminidase.
在本期 "期刊俱乐部 "中，Yi Shi 讨论了一篇报告人类感染流感病毒后会诱导针对病毒神经氨酸酶的广泛交叉反应性和保护性抗体的论文。
{"title":"Breaking through the concept barrier to develop broad-spectrum antiviral counter-measures","authors":"Yi Shi","doi":"10.1038/s41579-024-01059-5","DOIUrl":"10.1038/s41579-024-01059-5","url":null,"abstract":"In this Journal Club, Yi Shi discusses a paper reporting that influenza virus infection in humans induces broadly cross-reactive and protective antibodies against the viral neuraminidase.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":null,"pages":null},"PeriodicalIF":69.2,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141069445","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}
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