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Salmonella pathogenicity and host adaptation in chicken-associated serovars
Enteric pathogens such as Salmonella enterica cause significant morbidity and mortality. S.
enterica serovars are a diverse group of pathogens that have evolved to survive in a wide …
enterica serovars are a diverse group of pathogens that have evolved to survive in a wide …
Navigating microbiological food safety in the era of whole-genome sequencing
The epidemiological investigation of a foodborne outbreak, including identification of related
cases, source attribution, and development of intervention strategies, relies heavily on the …
cases, source attribution, and development of intervention strategies, relies heavily on the …
Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder
MHK Johansson, V Bortolaia… - Journal of …, 2021 - academic.oup.com
Objectives Antimicrobial resistance (AMR) in clinically relevant bacteria is a growing threat
to public health globally. In these bacteria, antimicrobial resistance genes are often …
to public health globally. In these bacteria, antimicrobial resistance genes are often …
TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
Microbial taxonomy is increasingly influenced by genome-based computational methods.
Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS …
Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS …
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
The emergence of new sequencing technologies has facilitated the use of bacterial whole
genome alignments for evolutionary studies and outbreak analyses. These datasets, of …
genome alignments for evolutionary studies and outbreak analyses. These datasets, of …
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
Whole-genome sequences are now available for many microbial species and clades,
however existing whole-genome alignment methods are limited in their ability to perform …
however existing whole-genome alignment methods are limited in their ability to perform …
Multilocus Sequence Ty** as a Replacement for Seroty** in Salmonella enterica
Salmonella enterica subspecies enterica is traditionally subdivided into serovars by
serological and nutritional characteristics. We used Multilocus Sequence Ty** (MLST) to …
serological and nutritional characteristics. We used Multilocus Sequence Ty** (MLST) to …
Identification of Salmonella for public health surveillance using whole genome sequencing
In April 2015, Public Health England implemented whole genome sequencing (WGS) as a
routine ty** tool for public health surveillance of Salmonella, adopting a multilocus …
routine ty** tool for public health surveillance of Salmonella, adopting a multilocus …
Emergence of human-adapted Salmonella enterica is linked to the Neolithization process
It has been hypothesized that the Neolithic transition towards an agricultural and pastoralist
economy facilitated the emergence of human-adapted pathogens. Here, we recovered eight …
economy facilitated the emergence of human-adapted pathogens. Here, we recovered eight …
A reverse ecology approach based on a biological definition of microbial populations
Delineating ecologically meaningful populations among microbes is important for identifying
their roles in environmental and host-associated microbiomes. Here, we introduce a metric …
their roles in environmental and host-associated microbiomes. Here, we introduce a metric …