Salmonella pathogenicity and host adaptation in chicken-associated serovars

SL Foley, TJ Johnson, SC Ricke, R Nayak… - Microbiology and …, 2013‏ - journals.asm.org
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 …

Navigating microbiological food safety in the era of whole-genome sequencing

J Ronholm, N Nasheri, N Petronella… - Clinical microbiology …, 2016‏ - journals.asm.org
The epidemiological investigation of a foodborne outbreak, including identification of related
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 …

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy

JP Meier-Kolthoff, M Göker - Nature communications, 2019‏ - nature.com
Microbial taxonomy is increasingly influenced by genome-based computational methods.
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

NJ Croucher, AJ Page, TR Connor… - Nucleic acids …, 2015‏ - academic.oup.com
The emergence of new sequencing technologies has facilitated the use of bacterial whole
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

TJ Treangen, BD Ondov, S Koren, AM Phillippy - Genome biology, 2014‏ - Springer
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 …

Multilocus Sequence Ty** as a Replacement for Seroty** in Salmonella enterica

M Achtman, J Wain, FX Weill, S Nair, Z Zhou… - PLoS …, 2012‏ - journals.plos.org
Salmonella enterica subspecies enterica is traditionally subdivided into serovars by
serological and nutritional characteristics. We used Multilocus Sequence Ty** (MLST) to …

Identification of Salmonella for public health surveillance using whole genome sequencing

PM Ashton, S Nair, TM Peters, JA Bale, DG Powell… - PeerJ, 2016‏ - peerj.com
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 …

Emergence of human-adapted Salmonella enterica is linked to the Neolithization process

FM Key, C Posth, LR Esquivel-Gomez… - Nature ecology & …, 2020‏ - nature.com
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 …

A reverse ecology approach based on a biological definition of microbial populations

P Arevalo, D VanInsberghe, J Elsherbini, J Gore… - Cell, 2019‏ - cell.com
Delineating ecologically meaningful populations among microbes is important for identifying
their roles in environmental and host-associated microbiomes. Here, we introduce a metric …