Comparative genomics of Australian and international isolates of Salmonella Typhimurium: correlation of core genome evolution with CRISPR and prophage profiles

The driving force of prophages and CRISPR-Cas system in the evolution of Cronobacter sakazakii

(2017) Haiyan Zeng et al.   Scientific Reports

Genomic Analysis of Salmonella enterica Serovar Typhimurium from Wild Passerines in England and Wales

(2016) Alison E. Mather et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomic Analysis of Salmonella enterica Serovar Typhimurium Characterizes Strain Diversity for Recent U.S. Salmonellosis Cases and Identifies Mutations Linked to Loss of Fitness under Nitrosative and Oxidative Stress

(2016) Hillary S. Hayden et al.   mBio

Delineating Community Outbreaks of Salmonella enterica Serovar Typhimurium by Use of Whole-Genome Sequencing: Insights into Genomic Variability within an Outbreak

(2015) Sophie Octavia et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Defining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing

(2015) Songzhe Fu et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Characterization and evolution of Salmonella CRISPR-Cas systems

(2015)   MICROBIOLOGY-SGM

Comparative Analysis of Subtyping Methods against a Whole-Genome-Sequencing Standard for Salmonella enterica Serotype Enteritidis

(2014) Xiangyu Deng et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Distribution of Gifsy-3 and of Variants of ST64B and Gifsy-1 Prophages amongst Salmonella enterica Serovar Typhimurium Isolates: Evidence that Combinations of Prophages Promote Clonality

(2014) Lester Hiley et al.   PLoS One

The evolutionary history and diagnostic utility of the CRISPR-Cas system withinSalmonella entericassp.enterica

(2014) James B. Pettengill et al.   PeerJ

Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types

(2013) Stanley Pang et al.   BMC GENOMICS

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

(2013) Jane Hawkey et al.   BMC GENOMICS

NleB, a Bacterial Effector with Glycosyltransferase Activity, Targets GAPDH Function to Inhibit NF-κB Activation

(2013) Xiaofei Gao et al.   Cell Host & Microbe

CRISPR Typing and Subtyping for Improved Laboratory Surveillance of Salmonella Infections

(2012) Laëtitia Fabre et al.   PLoS One

Phage-Mediated Acquisition of a Type III Secreted Effector Protein Boosts Growth of Salmonella by Nitrate Respiration

(2012) C. A. Lopez et al.   mBio

Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

(2012) Mark Achtman et al.   PLoS Pathogens

CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation

(2011) Devaki Bhaya et al.   Annual Review of Genetics

Novel Virulence Gene and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Multilocus Sequence Typing Scheme for Subtyping of the Major Serovars ofSalmonella entericasubsp.enterica

(2011) Fenyun Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Subtyping Salmonella enterica Serovar Enteritidis Isolates from Different Sources by Using Sequence Typing Based on Virulence Genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

(2011) Fenyun Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genetic Relationships of Phage Types and Single Nucleotide Polymorphism Typing of Salmonella enterica Serovar Typhimurium

(2011) S. Pang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

PHAST: A Fast Phage Search Tool

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

Salmonella Phage ST64B Encodes a Member of the SseK/NleB Effector Family

(2011) Nat F. Brown et al.   PLoS One

Single Nucleotide Polymorphism Typing of Global Salmonella enterica Serovar Typhi Isolates by Use of a Hairpin Primer Real-Time PCR Assay

(2010) S. Octavia et al.   JOURNAL OF CLINICAL MICROBIOLOGY

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Genomic analysis of bacteriophage epsilon34 of Salmonella enterica serovar Anatum (15+)

(2008) Robert Villafane et al.   BMC MICROBIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Insertion Hot Spot for Horizontally Acquired DNA within a Bidirectional Small-RNA Locus in Salmonella enterica

(2008) R. Balbontin et al.   JOURNAL OF BACTERIOLOGY