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Outbreaks and emerging infections

Infectious disease outbreaks threaten human, animal and plant health, and they have implications for global health, food security, biodiversity and economic stability. This Collection contains articles from Nature Reviews Microbiology that explore the emergence, identification, spread, pathogenesis, impacts and management of local or global outbreaks caused by pathogens, including emerging and re-emerging viruses such as SARS-CoV-2, Ebola virus and novel influenza viruses, as well as fungi and drug-resistant bacteria. Increased knowledge of the origin and characteristics of infectious disease outbreaks are prerequisites for the successful management of current outbreaks and the prevention of future outbreaks, and thus for ensuring the planet’s health.

This Collection is editorially independent, produced with financial support from a third party. About this content.

Content

The integrative environment-health sciences including One Health, Conservation Medicine, EcoHealth and Planetary Health embody the transdisciplinary synthesis needed to understand the multitude of factors that underpin emerging infections and their management. Future successes in confronting and resolving the complex causal basis of disease emergence to generate robust, systems-oriented risk reduction strategies that preserve both human health as well as promoting sustainable futures represent the ‘Moon Shot’ for the integrative environment-health sciences.

Comment | | Nature Reviews Microbiology

In this Review, Shi and colleagues summarize the exceptional amount of research that has characterized acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease 2019 (COVID-19) since this virus has swept around the globe. They discuss what we know so far about the emergence and virology of SARS-CoV-2 and the pathogenesis and treatment of COVID-19.

Review Article | | Nature Reviews Microbiology

The COVID-19 pandemic has prompted unparalleled progress in the development of vaccines and therapeutics in many countries, but it has also highlighted the vulnerability of resource-limited countries in Africa. Margolin and colleagues review global efforts to develop SARS-CoV-2 diagnostics, therapeutics and vaccines, with a focus on the opportunities and challenges in Africa.

Review Article | | Nature Reviews Microbiology

Bats harbour a large number of different viruses, some of which have spilled over to cause human disease. In this Review, Letko, Munster and colleagues discuss the diversity of bat viruses and the factors that determine the emergence of zoonotic viruses from bats.

Review Article | | Nature Reviews Microbiology

Filoviruses such as Ebola virus pose a substantial health risk to humans. Advances in genomic technologies have enabled the rapid, large-scale generation of virus sequence data at the location of disease outbreaks and thus the use of reverse functional genomics to swiftly characterize the threat of, and treatment for, filovirus disease.

Review Article | | Nature Reviews Microbiology

Influenza A viruses cause pandemics when they cross between species. In this Review, Barclay and colleagues examine the host barriers that influenza A viruses must overcome to initiate a pandemic in humans and describe how, on crossing the species barrier, the virus mutates to establish new interactions with the human host.

Review Article | | Nature Reviews Microbiology

Over the past decade, Klebsiella pneumoniae has emerged as a major clinical and public health threat. In this Review, Wyres, Lam and Holt discuss how genomics approaches have advanced our understanding of K. pneumoniae taxonomy, ecology and evolution as well as the diversity and distribution of clinically relevant determinants of pathogenicity and antimicrobial resistance.

Review Article | | Nature Reviews Microbiology

Meningococcal disease remains an important cause of morbidity and death worldwide despite the development and increasing implementation of effective vaccines. In this Review, Caugant and Brynildsrud discuss how high-throughput sequencing approaches have advanced our understanding of the diversity and evolution of Neisseria meningitidis and the pathogenesis of N. meningitidis infection and how they are helping to explain the epidemiology of meningococcal disease.

Review Article | | Nature Reviews Microbiology

Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen both within hospitals and in the community. In this Review, Fowler and colleagues provide an overview of basic and clinical MRSA research and explore the epidemiology, transmission, genetic diversity, evolution, surveillance and treatment of MRSA.

Review Article | | Nature Reviews Microbiology

Worldwide amphibian declines caused by pathogenic chytrid fungi are emblematic of the emerging infectious diseases driven by globalization. Fisher and Garner discuss how these wildlife pathogens emerge to drive global declines in amphibian biodiversity and the implications of current research for policy and control measures.

Review Article | | Nature Reviews Microbiology

The fungal pathogen Pseudogymnoascus destructans, which causes white-nose syndrome in bats, has devastated bat populations in North America since its introduction from Eurasia in the 2000s. In this Review, Hoyt and colleagues describe the ecology of P. destructans in bats and its impacts on bats and the ecosystem.

Review Article | | Nature Reviews Microbiology