Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm

The plasmidome of a Salmonella enterica serovar Derby isolated from pork meat

(2013) Anne Bleicher et al.   PLASMID

Tracking the establishment of local endemic populations of an emergent enteric pathogen

(2013) K. E. Holt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona

(2013) Zhemin Zhou et al.   PLoS Genetics

Comprehensive Assignment of Roles for Salmonella Typhimurium Genes in Intestinal Colonization of Food-Producing Animals

(2013) Roy R. Chaudhuri et al.   PLoS Genetics

Characterization of a Novel Microcin That Kills Enterohemorrhagic Escherichia coli O157:H7 and O26

(2012) Lauren J. Eberhart et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Short read sequence typing (SRST): multi-locus sequence types from short reads

(2012) Michael Inouye et al.   BMC GENOMICS

High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach

(2012) Marc W Allard et al.   BMC GENOMICS

Improving resolution of public health surveillance for human Salmonella entericaserovar Typhimurium infection: 3 years of prospective multiple-locus variable-number tandem-repeat analysis (MLVA)

(2012) Vitali Sintchenko et al.   BMC INFECTIOUS DISEASES

Draft Genome Sequence of Salmonella enterica Serovar Typhimurium ST1660/06, a Multidrug-Resistant Clinical Strain Isolated from a Diarrheic Patient

(2012) L. Li et al.   JOURNAL OF BACTERIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

(2012) Chinyere K Okoro et al.   NATURE GENETICS

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

(2012) Kathryn E Holt et al.   NATURE GENETICS

Characterization and Differential Gene Expression between Two Phenotypic Phase Variants in Salmonella enterica Serovar Typhimurium

(2012) Sheila K. Patterson et al.   PLoS One

DNA Sequence Analysis of Plasmids from Multidrug Resistant Salmonella enterica Serotype Heidelberg Isolates

(2012) Jing Han et al.   PLoS One

Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2

(2012) Sanaa A. Ahmed et al.   PLoS One

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

(2012) Y. H. Grad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

(2011) Colin T Archer et al.   BMC GENOMICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Dutch patients, retail chicken meat and poultry share the same ESBL genes, plasmids and strains

(2011) M.A. Leverstein-van Hall et al.   CLINICAL MICROBIOLOGY AND INFECTION

Global Monitoring of Salmonella Serovar Distribution from the World Health Organization Global Foodborne Infections Network Country Data Bank: Results of Quality Assured Laboratories from 2001 to 2007

(2011) Rene S. Hendriksen et al.   Foodborne Pathogens and Disease

Salmonella in chicken meat, eggs and humans; Adelaide, South Australia, 2008

(2011) Emily Fearnley et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Genome Sequences and Phylogenetic Analysis of K88- and F18-Positive Porcine Enterotoxigenic Escherichia coli

(2011) S. M. Shepard et al.   JOURNAL OF BACTERIOLOGY

Complete Genome Sequence of the Universal Killer Salmonella enterica Serovar Typhimurium UK-1 (ATCC 68169)

(2011) Y. Luo et al.   JOURNAL OF BACTERIOLOGY

Comparative Genomics of 28 Salmonella enterica Isolates: Evidence for CRISPR-Mediated Adaptive Sublineage Evolution

(2011) W. F. Fricke et al.   JOURNAL OF BACTERIOLOGY

Genome Sequences of Salmonella enterica Serovar Typhimurium, Choleraesuis, Dublin, and Gallinarum Strains of Well- Defined Virulence in Food-Producing Animals

(2011) E. J. Richardson et al.   JOURNAL OF BACTERIOLOGY

Optical mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements, and multiple tandem copies of the Zymomonas mobilis pdc and adhB genes

(2011) Peter C. Turner et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

The genome sequence of the incompatibility group Iγ plasmid R621a: Evolution of IncI plasmids

(2011) Hiroyuki Takahashi et al.   PLASMID

Comparative genomics and phylogeny of the IncI1 plasmids: A common plasmid type among porcine enterotoxigenic Escherichia coli

(2011) Timothy J. Johnson et al.   PLASMID

Whole-Genome Analysis ofSalmonella entericaSerovar Typhimurium T000240 Reveals the Acquisition of a Genomic Island Involved in Multidrug Resistance via IS1Derivatives on the Chromosome

(2010) Hidemasa Izumiya et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The Global Burden of NontyphoidalSalmonellaGastroenteritis

(2010) Shannon E. Majowicz et al.   CLINICAL INFECTIOUS DISEASES

A Commensal Gone Bad: Complete Genome Sequence of the Prototypical Enterotoxigenic Escherichia coli Strain H10407

(2010) L. C. Crossman et al.   JOURNAL OF BACTERIOLOGY

Complete Nucleotide Sequence of CTX-M-15-Plasmids from Clinical Escherichia coli Isolates: Insertional Events of Transposons and Insertion Sequences

(2010) Annemieke Smet et al.   PLoS One

Complete Nucleotide Sequences of Plasmids pEK204, pEK499, and pEK516, Encoding CTX-M Enzymes in Three Major Escherichia coli Lineages from the United Kingdom, All Belonging to the International O25:H4-ST131 Clone

(2009) N. Woodford et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Antimicrobial Resistance-Conferring Plasmids with Similarity to Virulence Plasmids from Avian Pathogenic Escherichia coli Strains in Salmonella enterica Serovar Kentucky Isolates from Poultry

(2009) W. F. Fricke et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype

(2009) R. A. Kingsley et al.   GENOME RESEARCH

Short-Term Signatures of Evolutionary Change in the Salmonella enterica Serovar Typhimurium 14028 Genome

(2009) T. Jarvik et al.   JOURNAL OF BACTERIOLOGY

Drawing explicit phylogenetic networks and their integration into SplitsTree

(2008) Tobias H Kloepper et al.   BMC EVOLUTIONARY BIOLOGY

Complete Genome Sequence and Comparative Analysis of the Wild-type Commensal Escherichia coli Strain SE11 Isolated from a Healthy Adult

(2008) K. Oshima et al.   DNA RESEARCH

Multilocus sequence typing of IncI1 plasmids carrying extended-spectrum β-lactamases in Escherichia coli and Salmonella of human and animal origin

(2008) Aurora García-Fernández et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS