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Article
Open AccessContext-specific emergence and growth of the SARS-CoV-2 Delta variant
The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide1,2. The emergence of the Delta variant in the UK occurred on the background of a hetero...
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Article
Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic
Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic an...
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Article
Open AccessCLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance
In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strateg...
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Article
Open AccessA global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch
As whole-genome sequencing capacity becomes increasingly decentralized, there is a growing opportunity for collaboration and the sharing of surveillance data within and between countries to inform typhoid cont...
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Article
Open AccessA community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch
Antimicrobial-resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant to at least one of the two last-line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone a...
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Article
Open AccessPopulation genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments
Aquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance. However, the population diversity and the genetic elements that drive the dynamics of resistant b...
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Article
Open AccessIntegrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines
National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor resistance trends and disseminate these data to AMR stakeholders. Whole-genome sequencing (WGS) can support surveill...
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Article
Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread
Public health interventions to control the current epidemic of carbapenem-resistant Klebsiella pneumoniae rely on a comprehensive understanding of its emergence and spread over a wide range of geographical scales...
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Article
Open AccessThe phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa
There is paucity of data regarding the geographical distribution, incidence, and phylogenetics of multi-drug resistant (MDR) Salmonella Typhi in sub-Saharan Africa. Here we present a phylogenetic reconstruction o...
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Article
Gene exchange drives the ecological success of a multi-host bacterial pathogen
The capacity for some pathogens to jump into different host-species populations is a major threat to public health and food security. Staphylococcus aureus is a multi-host bacterial pathogen responsible for impor...
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Article
Open AccessDevelopment and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi
Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into culture for research purposes. However, ...
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Article
Open AccessEmergence and clonal spread of colistin resistance due to multiple mutational mechanisms in carbapenemase-producing Klebsiella pneumoniae in London
Carbapenemase-producing Enterobacteriaceae (CPE) are emerging worldwide, limiting therapeutic options. Mutational and plasmid-mediated mechanisms of colistin resistance have both been reported. The emergence a...
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Article
Species Mash-up
This month's Genome Watch describes how Mash can be used to tackle comparisons between large amounts of genomic and metagenomic sequence data for taxonomic applications.
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Article
Open AccessWhole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection
Schistosoma mansoni is a parasitic fluke that infects millions of people in the develo** world. This study presents the first application of population genomics to S. mansoni based on high-coverage resequencing...
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Article
Dense genomic sampling identifies highways of pneumococcal recombination
Stephen Bentley, Paul Turner and colleagues report whole-genome sequencing of 3,085 pneumococci collected from a densely sampled pneumococcal carriage cohort in a Thai refugee camp over a 3-year period. They p...
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Article
Open AccessBayesian semi-supervised classification of bacterial samples using MLST databases
Worldwide effort on sampling and characterization of molecular variation within a large number of human and animal pathogens has lead to the emergence of multi-locus sequence ty** (MLST) databases as an impo...
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Article
Open AccessAssigning strains to bacterial species via the internet
Methods for assigning strains to bacterial species are cumbersome and no longer fit for purpose. The concatenated sequences of multiple house-kee** genes have been shown to be able to define and circumscribe...
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Protocol
WebACT
Comparison of related genomes is an enormously powerful technique for explaining phenotypic differences and revealing recent evolutionary events. Genomes evolve through a host of mechanisms including long- and...
