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This Genome Watch discusses recent advances in genomic epidemiology that enable the reconstruction of transmission events, with greater resolution and across more complex settings at scale.
In this Review, Kocher, Krause and Spyrou explore how ancient pathogen genomics is providing new perspectives on the history and evolution of infectious agents. They show how ancient DNA has revealed the aetiology and unfolding of historic outbreaks, pathogen evolutionary timescales, patterns of dissemination and functional evolution, and discuss existing limitations and perspectives of the field.
In this Review, Basler and colleagues examine the type VI secretion system (T6SS), focusing on the diversity of antibacterial T6SS effectors and the evolutionary forces that shape them. They explain how effectors diversify and highlight interbacterial antagonism as a key driver of this process.
The gut microbiome can influence brain activity and complex behaviours. In this Review, Griffiths et al. discuss microbiome-associated effects on social behaviour in laboratory model organisms, free-living animals and humans, and consider potential mechanistic pathways.
Surface layers (S-layers) are ubiquitous protein assemblies that coat prokaryotic cells, with their functional roles increasingly coming into focus. In this Review, Isbilir and colleagues discuss recent insights into S-layer architecture, assembly and function, highlighting the importance of S-layers in microbial interactions and community organization.
This study identifies multiple low-density lipoprotein receptor family members, including LRP4, LRP1 and VLDLR, as entry receptors for yellow fever virus.
Microbial whole-genome sequencing is an important element of health-care-associated infection (HAI) prevention strategies. Focusing on specific high-priority antibiotic-resistant bacterial pathogens, this Review outlines the epidemiology and microbiology of HAIs and discusses the role of whole-genome sequencing in HAI prevention and surveillance.
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.
The cryosphere remains one of the least-understood microbial ecosystems on Earth, but as climate change accelerates, cryosphere microbial communities will have an increasingly prominent role in Earth’s biogeochemical cycles. In this Review, Whyte and co-workers discuss the effects of climate change on cryosphere microbial ecosystems.
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.
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.
Oomycete plant pathogens are a serious global threat to crop production and food security. This Review outlines oomycete biology, diversity and lifestyle, discusses the disease cycle in plants, highlights pathogenicity mechanisms and the impact of oomycete plant pathogens, and considers emerging strategies for disease management.
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.
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.
In this Review, Weingarth and colleagues discuss both recently discovered compounds and established envelope-targeting antibiotics, including compounds that target Gram-positive bacteria, more complex Gram-negative bacteria and mycobacterial pathogens, with a particular focus on their drug–target interactions.
This study shows that metabolic inactivity confers tolerance against polymyxin antibiotics and proposes a model for polymyxin-mediated killing of metabolically active bacterial cells.
In this Review, Sikkema and Koopmans examine the drivers of viral emergence and how these insights could inform prevention strategies and the development of risk-targeted One Health early warning surveillance. They discuss tools for diagnostics, surveillance and virus characterization, and propose strengthening integrated One Health strategies for early warning, prevention and control of emerging infections at the human–animal interface.
This study reports the identification of cell-surface low-density lipoprotein receptor-related protein 8 (LRP8) as the crucial host factor that mediates tick-borne encephalitis virus entry and infection.
Clostridioides difficile infection is challenging to diagnose and treat and is associated with considerable mortality, morbidity and economic costs worldwide. In this Review, Chilton et al. discuss changes in global epidemiology, breakthroughs in pathogenesis and antibiotic resistance, the role of microbiota dysbiosis and the potential for microbiota-based therapeutics for Clostridioides difficile infection.
