Pub Date : 2025-11-10DOI: 10.1038/s41579-025-01254-y
Mary K. Hayden, Sarah E. Sansom, Evan S. Snitkin
{"title":"Genome sequencing for prevention of health-care-associated bacterial infections","authors":"Mary K. Hayden, Sarah E. Sansom, Evan S. Snitkin","doi":"10.1038/s41579-025-01254-y","DOIUrl":"https://doi.org/10.1038/s41579-025-01254-y","url":null,"abstract":"","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"47 1","pages":""},"PeriodicalIF":88.1,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145478043","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 : 2025-11-10DOI: 10.1038/s41579-025-01255-x
Ryuta Uraki, Bette Korber, Michael S. Diamond, Yoshihiro Kawaoka
More than 5 years have passed since the emergence of the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), yet this virus continues to circulate globally, undergoing evolutionary changes. The effective control of SARS-CoV-2 necessitates an understanding of its antigenicity, replicative capacity, pathogenicity and transmissibility, as well as the development of preventive and treatment options. In this Review, we describe the origins and evolution of SARS-CoV-2, and outline variant and subvariant-specific characteristics. We also discuss the challenges faced in implementing prevention and treatment methods, such as the emergence of antigenically distinct variants and the phenomenon of immune imprinting. This Review provides insights into combating the ongoing COVID-19 pandemic and guidance for future research and vaccine development efforts. This Review explores the evolution of SARS-CoV-2 since its emergence in late 2019 and discusses how the changes in the various variants and subvariants have affected the viral life cycle and ongoing transmission. In addition, prevention and treatment strategies are outlined, as well as the effects of antigenically distinct variants and immune imprinting on immunity after natural infection or vaccination.
{"title":"SARS-CoV-2 variants: biology, pathogenicity, immunity and control","authors":"Ryuta Uraki, Bette Korber, Michael S. Diamond, Yoshihiro Kawaoka","doi":"10.1038/s41579-025-01255-x","DOIUrl":"10.1038/s41579-025-01255-x","url":null,"abstract":"More than 5 years have passed since the emergence of the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), yet this virus continues to circulate globally, undergoing evolutionary changes. The effective control of SARS-CoV-2 necessitates an understanding of its antigenicity, replicative capacity, pathogenicity and transmissibility, as well as the development of preventive and treatment options. In this Review, we describe the origins and evolution of SARS-CoV-2, and outline variant and subvariant-specific characteristics. We also discuss the challenges faced in implementing prevention and treatment methods, such as the emergence of antigenically distinct variants and the phenomenon of immune imprinting. This Review provides insights into combating the ongoing COVID-19 pandemic and guidance for future research and vaccine development efforts. This Review explores the evolution of SARS-CoV-2 since its emergence in late 2019 and discusses how the changes in the various variants and subvariants have affected the viral life cycle and ongoing transmission. In addition, prevention and treatment strategies are outlined, as well as the effects of antigenically distinct variants and immune imprinting on immunity after natural infection or vaccination.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"24 1","pages":"8-28"},"PeriodicalIF":103.3,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145478176","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 : 2025-11-05DOI: 10.1038/s41579-025-01251-1
Scott Sugden, Christina L. Davis, Matthew W. Quinn, Lyle G. Whyte
{"title":"Current and projected effects of climate change in cryosphere microbial ecosystems","authors":"Scott Sugden, Christina L. Davis, Matthew W. Quinn, Lyle G. Whyte","doi":"10.1038/s41579-025-01251-1","DOIUrl":"https://doi.org/10.1038/s41579-025-01251-1","url":null,"abstract":"","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"26 1","pages":""},"PeriodicalIF":88.1,"publicationDate":"2025-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145441129","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 : 2025-10-28DOI: 10.1038/s41579-025-01260-0
Andrea Du Toit
This study shows that sialokinin, which is a vasodilatory peptide that is expressed in the saliva of female Aedes aegypti, modulates immune responses and mitigates inflammation during chikungunya virus infection in mice.
{"title":"A soothing bite for chikungunya","authors":"Andrea Du Toit","doi":"10.1038/s41579-025-01260-0","DOIUrl":"10.1038/s41579-025-01260-0","url":null,"abstract":"This study shows that sialokinin, which is a vasodilatory peptide that is expressed in the saliva of female Aedes aegypti, modulates immune responses and mitigates inflammation during chikungunya virus infection in mice.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"24 1","pages":"3-3"},"PeriodicalIF":103.3,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145381936","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 : 2025-10-28DOI: 10.1038/s41579-025-01261-z
Shimona Starling
This study assessed the ability of a replicating RNA vaccine expressing H5 haemagglutinin to protect cynomolgus macaques from lethal challenge with a clade 2.3.4.4b highly pathogenic avian influenza A H5N1 virus.
{"title":"A replicating RNA vaccine takes flight against H5N1","authors":"Shimona Starling","doi":"10.1038/s41579-025-01261-z","DOIUrl":"10.1038/s41579-025-01261-z","url":null,"abstract":"This study assessed the ability of a replicating RNA vaccine expressing H5 haemagglutinin to protect cynomolgus macaques from lethal challenge with a clade 2.3.4.4b highly pathogenic avian influenza A H5N1 virus.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"24 1","pages":"3-3"},"PeriodicalIF":103.3,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145380917","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 : 2025-10-28DOI: 10.1038/s41579-025-01248-w
Yan Wang,Francine Govers,Yuanchao Wang
Oomycete plant pathogens are among the most serious global threats to crop production and food security, causing devastating diseases in a wide and diverse range of plant species. Best known are the Phytophthora species in the genus that includes the notorious Irish Potato Famine pathogen, Phytophthora infestans. In addition, the downy mildews are also notable plant destroyers. Oomycetes are eukaryotes that share several characteristics with fungi but evolved independently. Both have filamentous growth, form spores for reproduction and dispersal, have a global distribution, thrive in diverse environments as saprobes and pathogens, and share the top position as the most devastating plant pathogens worldwide. Since the late 1990s, in-depth research on oomycetes was boosted by access to genetic tools, advanced technology and genomic resources. Digging into the biology of oomycetes, deciphering their genomes and exploring their pathogenicity mechanisms have uncovered a treasure trove of novelties and peculiarities that opens avenues for tailor-made strategies for disease control.
{"title":"Oomycete plant pathogens: biology, pathogenesis and emerging control strategies.","authors":"Yan Wang,Francine Govers,Yuanchao Wang","doi":"10.1038/s41579-025-01248-w","DOIUrl":"https://doi.org/10.1038/s41579-025-01248-w","url":null,"abstract":"Oomycete plant pathogens are among the most serious global threats to crop production and food security, causing devastating diseases in a wide and diverse range of plant species. Best known are the Phytophthora species in the genus that includes the notorious Irish Potato Famine pathogen, Phytophthora infestans. In addition, the downy mildews are also notable plant destroyers. Oomycetes are eukaryotes that share several characteristics with fungi but evolved independently. Both have filamentous growth, form spores for reproduction and dispersal, have a global distribution, thrive in diverse environments as saprobes and pathogens, and share the top position as the most devastating plant pathogens worldwide. Since the late 1990s, in-depth research on oomycetes was boosted by access to genetic tools, advanced technology and genomic resources. Digging into the biology of oomycetes, deciphering their genomes and exploring their pathogenicity mechanisms have uncovered a treasure trove of novelties and peculiarities that opens avenues for tailor-made strategies for disease control.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"69 1","pages":""},"PeriodicalIF":88.1,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145380916","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 : 2025-10-27DOI: 10.1038/s41579-025-01257-9
Shimona Starling
This study combines high-throughput RNA sequencing analysis of Mycobacterium tuberculosis clinical isolates with global population genomics to link diversity in gene expression with variants in genes encoding regulators.
{"title":"M. tuberculosis regulatory evolution levels up transmission and resistance","authors":"Shimona Starling","doi":"10.1038/s41579-025-01257-9","DOIUrl":"10.1038/s41579-025-01257-9","url":null,"abstract":"This study combines high-throughput RNA sequencing analysis of Mycobacterium tuberculosis clinical isolates with global population genomics to link diversity in gene expression with variants in genes encoding regulators.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 12","pages":"754-754"},"PeriodicalIF":103.3,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145373841","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 : 2025-10-22DOI: 10.1038/s41579-025-01253-z
Uri Neri
This Genome Watch explores how a new antisense oligomer-based approach enables functional genomics of genetically intractable bacteriophages, revealing essential genes and infection mechanisms without requiring genetic modification.
{"title":"Licence to knockdown — the phage gene silencer","authors":"Uri Neri","doi":"10.1038/s41579-025-01253-z","DOIUrl":"10.1038/s41579-025-01253-z","url":null,"abstract":"This Genome Watch explores how a new antisense oligomer-based approach enables functional genomics of genetically intractable bacteriophages, revealing essential genes and infection mechanisms without requiring genetic modification.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 12","pages":"756-756"},"PeriodicalIF":103.3,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145339434","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 : 2025-10-13DOI: 10.1038/s41579-025-01247-x
Charalampos Ntallis, Nathaniel I Martin, Andrew M Edwards, Markus Weingarth
The emergence of multidrug-resistant bacteria presents a critical threat to global health. These multidrug-resistant bacteria are often protected by complex cell envelopes that many antibiotics cannot penetrate, creating an important barrier to treatment. In response, targeting bacterial envelopes has long been recognized as an effective strategy, offering potential to bypass the challenges of drug entry and efflux resistance mechanisms. Moreover, many unique bacterial envelope sites remain clinically untapped, and new compounds directed at them have the potential to diversify the space of antimicrobial mechanisms, lowering the risk for cross-resistance. Compounds that target non-proteinaceous envelope components, such as lipopolysaccharide or prenylated peptidoglycan-precursors, are particularly attractive owing to their reduced susceptibility to antimicrobial resistance development. In this Review, we explore both recently discovered compounds and established envelope-targeting antibiotics, including compounds that target Gram-positive bacteria, more complex Gram-negative bacteria and mycobacterial pathogens, shedding light on this still clinically underexplored and vital therapeutic approach.
{"title":"Bacterial cell envelope-targeting antibiotics.","authors":"Charalampos Ntallis, Nathaniel I Martin, Andrew M Edwards, Markus Weingarth","doi":"10.1038/s41579-025-01247-x","DOIUrl":"https://doi.org/10.1038/s41579-025-01247-x","url":null,"abstract":"<p><p>The emergence of multidrug-resistant bacteria presents a critical threat to global health. These multidrug-resistant bacteria are often protected by complex cell envelopes that many antibiotics cannot penetrate, creating an important barrier to treatment. In response, targeting bacterial envelopes has long been recognized as an effective strategy, offering potential to bypass the challenges of drug entry and efflux resistance mechanisms. Moreover, many unique bacterial envelope sites remain clinically untapped, and new compounds directed at them have the potential to diversify the space of antimicrobial mechanisms, lowering the risk for cross-resistance. Compounds that target non-proteinaceous envelope components, such as lipopolysaccharide or prenylated peptidoglycan-precursors, are particularly attractive owing to their reduced susceptibility to antimicrobial resistance development. In this Review, we explore both recently discovered compounds and established envelope-targeting antibiotics, including compounds that target Gram-positive bacteria, more complex Gram-negative bacteria and mycobacterial pathogens, shedding light on this still clinically underexplored and vital therapeutic approach.</p>","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":" ","pages":""},"PeriodicalIF":103.3,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145286605","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 : 2025-10-08DOI: 10.1038/s41579-025-01252-0
Andrea Du Toit
This study shows that metabolic inactivity confers tolerance against polymyxin antibiotics and proposes a model for polymyxin-mediated killing of metabolically active bacterial cells.
{"title":"Energizing antibiotic killing","authors":"Andrea Du Toit","doi":"10.1038/s41579-025-01252-0","DOIUrl":"10.1038/s41579-025-01252-0","url":null,"abstract":"This study shows that metabolic inactivity confers tolerance against polymyxin antibiotics and proposes a model for polymyxin-mediated killing of metabolically active bacterial cells.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 12","pages":"753-753"},"PeriodicalIF":103.3,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251969","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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