Policy and public health in microbiology articles within Nature Communications

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  • Article
    | Open Access

    Severe pediatric malaria remains a concern in many countries. Here, the authors use an individual-based modeling approach to evaluate the relationship between malaria prevalence and incidence of malaria pediatric hospitalizations, and show how unsteady transmission patterns affect hospitalization rates.

    • Pablo M. De Salazar
    • , Alice Kamau
    •  & Melissa A. Penny

  • Article
    | Open Access

    This study presents a machine learning model that accurately predicts seasonal antigenic changes of influenza A H3N2 using genetic data. The model’s predictions can aid influenza surveillance, vaccine strain selection, and public health management.

    • Syed Awais W. Shah
    • , Daniel P. Palomar
    •  & Matthew R. McKay

  • Perspective
    | Open Access

    In this Perspective, the authors discuss the importance of preventing zoonotic spillover to prevent pandemics. They highlight mechanisms by which environmental changes can enable spillover, identify ecological interventions for spillover prevention and suggest policy frameworks through which interventions can be implemented.

    • Raina K. Plowright
    • , Aliyu N. Ahmed
    •  & Annika T. H. Keeley

  • Article
    | Open Access

    Evaluation of the effectiveness of COVID-19 vaccines is increasingly challenging due to high levels of exposure to infection and vaccination. Here, the authors use a model-based approach incorporating these factors and estimate that using a variant-matched rather than ancestral booster could prevent nearly twice as many hospitalisations and deaths over one year.

    • Alexandra B. Hogan
    • , Patrick Doohan
    •  & Azra C. Ghani

  • Article
    | Open Access

    There is increasing incidence of vaccine-derived poliovirus (VDPV) in countries thought to be polio free. Here, the authors report detection of VDPV in 2 UK children with primary immunodeficiency. The children did not develop paralysis, but isolated viruses showed intra-host evolution and neurovirulent potential.

    • Anika Singanayagam
    • , Dimitra Klapsa
    •  & Maria Zambon

  • Article
    | Open Access

    There is limited data on within-host SARS-CoV-2 genetic diversity and how it is affected by vaccination. The authors analysed intra-host sequence diversity and found that VOCs may have more sequence variations than non-VOCs and that breakthrough infections in vaccinated individuals do not seem to increase non-silent mutations.

    • Haogao Gu
    • , Ahmed Abdul Quadeer
    •  & Leo L. M. Poon

  • Article
    | Open Access

    Nigeria has a high burden of malaria which mostly results from Plasmodium falciparum infection, but other species are also endemic. Here, the authors estimate the prevalence of active infection and previous exposure to P malariae, P ovale, and P vivax in children in Nigeria in 2018 and determine risk factors.

    • Camelia Herman
    • , Colleen M. Leonard
    •  & Eric Rogier

  • Article
    | Open Access

    Here, analyzing paired fecal and blood metabolomics and metagenomics data in a large cohort, Deng et al. uncover disparate associations of the gut microbiota with cardiometabolic diseases when utilizing either fecal or blood metabolome data, suggesting that sampling criteria may be a relevant factor in metabolomics-based association studies.

    • Kui Deng
    • , Jin-jian Xu
    •  & Yu-ming Chen

  • Article
    | Open Access

    There have been increasing reports of extensively drug-resistant (XDR) Shigella sonnei infections in recent years. In this laboratory surveillance study from France, the authors document the rise of XDR isolates from 2005 to 2021 and perform whole genome sequencing to investigate their genomic diversity and evolutionary history.

    • Sophie Lefèvre
    • , Elisabeth Njamkepo
    •  & François-Xavier Weill

  • Article
    | Open Access

    Understanding the emergence, evolution, and transmission of antibiotic resistance genes (ARGs) is essential to combat antimicrobial resistance. Here, Munk et al. analyse ARGs in hundreds of sewage samples from 101 countries and describe regional patterns, diverse genetic environments of common ARGs, and ARG-specific transmission patterns.

    • Patrick Munk
    • , Christian Brinch
    •  & Frank M. Aarestrup

  • Article
    | Open Access

    Vaccination can provide reliable and long-lasting protection against COVID-19, however the immune response to vaccination can vary between individuals and can decline over time, leading to differences in protective effects. Here the authors assess the immune response to COVID-19 vaccination across a large cohort of previously uninfected adults and demonstrate lower post-vaccination antibody levels amongst those with immune-suppressing conditions and medications, as well as those with several other more common chronic conditions.

    • Madhumita Shrotri
    • , Ellen Fragaszy
    •  & Robert W. Aldridge

  • Article
    | Open Access

    Air surveillance offers a potential means of monitoring airborne pathogens without the need for individual sampling. Here, the authors perform continuous air sampling in 15 community settings in the US for 29 weeks and demonstrate its feasibility for routine detection of SARS-CoV-2 and other respiratory pathogens.

    • Mitchell D. Ramuta
    • , Christina M. Newman
    •  & Shelby L. O’Connor

  • Article
    | Open Access

    The impact of prior infection on the immune response to COVID-19 vaccination has not been fully characterised. Here, the authors use data from ~100,000 adults in the UK and find that a single vaccine dose in those with prior infection produces a comparable or stronger response to two doses in those without infection.

    • Jia Wei
    • , Philippa C. Matthews
    •  & Chris Cunningham

  • Article
    | Open Access

    Post-international travel quarantine has been widely implemented to mitigate SARS-CoV-2 transmission, but the impacts of such policies are unclear. Here, the authors used linked genomic and contact tracing data to assess the impacts of a 14-day quarantine on return to England in summer 2020.

    • Dinesh Aggarwal
    • , Andrew J. Page
    •  & Ewan M. Harrison

  • Comment
    | Open Access

    The COVID-19 pandemic has accelerated the demand for near real-time analysis and dissemination of pathogen genomic data. In this comment, the authors describe how Australia has developed and rolled out its SARS-CoV-2 genomics platform, AusTrakka, and used it to support public health action.

    • Tuyet Hoang
    • , Anders Gonçalves da Silva
    •  & Torsten Seemann

  • Article
    | Open Access

    Lab-based surveillance of Shigella has traditionally been based on serotyping but increasing availability of whole genome sequencing could enable higher resolution typing. Here, the authors apply a core genome multilocus sequence typing scheme to Shigella sequence data and describe its population structure.

    • Iman Yassine
    • , Sophie Lefèvre
    •  & François-Xavier Weill

  • Article
    | Open Access

    Trends in antimicrobial resistance (AMR) in aquatic food animals are seldom documented, particularly in Asia. Here, Schar et al. review 749 point prevalence surveys, describing AMR trends in Asian aquaculture and fisheries over two decades, and identifying resistance hotspots as well as regions that would benefit most from future surveillance efforts.

    • Daniel Schar
    • , Cheng Zhao
    •  & Thomas P. Van Boeckel

  • Article
    | Open Access

    Antibiotic resistance genes are common but not all are of high risk to human health. Here, the authors develop an omics-based framework for ranking genes by risk that incorporates level of enrichment in human associated environments, gene mobility, and host pathogenicity.

    • An-Ni Zhang
    • , Jeffry M. Gaston
    •  & Tong Zhang

  • Article
    | Open Access

    Whole genome sequencing data are increasingly becoming routinely available but generating actionable insights is challenging. Here, the authors describe Pathogenwatch, a web tool for genomic surveillance of S. Typhi, and demonstrate its use for antimicrobial resistance assignment and strain risk assessment.

    • Silvia Argimón
    • , Corin A. Yeats
    •  & David M. Aanensen

  • Article
    | Open Access

    Massive unemployment during the COVID-19 pandemic could result in an eviction crisis in US cities. Here, the authors model the effect of evictions on SARS-CoV-2 epidemics, simulating viral transmission within and among households in a theoretical and applied urban settings.

    • Anjalika Nande
    • , Justin Sheen
    •  & Alison L. Hill

  • Article
    | Open Access

    COVID-19-related travel restrictions were imposed in China around the same time as major annual holiday migrations, with unknown combined impacts on mobility patterns. Here, the authors show that restructuring of the travel network in response to restrictions was temporary, whilst holiday-related travel increased pressure on healthcare services with lower capacity.

    • Hamish Gibbs
    • , Yang Liu
    •  & Rosalind M. Eggo

  • Article
    | Open Access

    Carbapenem-resistance in Klebsiella pneumoniae sequence type ST258 can be enhanced by modification of the porins OmpK35 and OmpK36. Here, Wong et al. solve the crystal structure of a clinical ST258 OmpK36 variant, elucidating the mechanism of resistance and consequences on pathogenicity in vivo.

    • Joshua L. C. Wong
    • , Maria Romano
    •  & Gad Frankel

  • Article
    | Open Access

    Copper is well known for its high antimicrobial efficacy; however, cost, appearance and metallic properties limit application. Here the authors describe a stable, water dispersible copper-glass ceramic powder with long-term antimicrobial activity as an additive for antimicrobial surfaces.

    • Timothy M. Gross
    • , Joydeep Lahiri
    •  & Michael J. Snyder

  • Article
    | Open Access

    The WHO targets measles elimination by 2020, a goal that relies on high vaccination coverage. Here, Takahashiet al. identify ‘coldspots’ in the African Great Lakes region where measles vaccine coverage is below 80%, suggesting that these regions should be targeted in future vaccination campaigns.

    • Saki Takahashi
    • , C. Jessica E. Metcalf
    •  & Justin Lessler

  • Article
    | Open Access

    Several drug combinations with different properties are used for malaria treatment. Here, Okell et al. use a mathematical model to simulate malaria transmission and treatment with two drug combinations in Africa, and find that locally optimized policies can be highly cost effective for reducing malaria burden.

    • Lucy C. Okell
    • , Matthew Cairns
    •  & Azra C. Ghani

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