Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

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Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

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Drug-resistant Salmonella enterica serotype Kentucky in Europe

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Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica

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Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever

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Movement of IS26-Associated Antibiotic Resistance Genes Occurs via a Translocatable Unit That Includes a Single IS26 and Preferentially Inserts Adjacent to Another IS26

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The Master Activator of IncA/C Conjugative Plasmids Stimulates Genomic Islands and Multidrug Resistance Dissemination

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ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

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Highly drug-resistant Salmonella enterica serotype Kentucky ST198-X1: a microbiological study

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Clinically Relevant Mutant DNA Gyrase Alters Supercoiling, Changes the Transcriptome, and Confers Multidrug Resistance

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

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Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure

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ramR mutations affecting fluoroquinolone susceptibility in epidemic multidrug-resistant Salmonella enterica serovar Kentucky ST198

(2013) Sylvie Baucheron et al.   Frontiers in Microbiology

The global establishment of a highly-fluoroquinolone resistant Salmonella enterica serotype Kentucky ST198 strain

(2013) Simon Le Hello et al.   Frontiers in Microbiology

Genome sequences of 65Helicobacter pyloristrains isolated from asymptomatic individuals and patients with gastric cancer, peptic ulcer disease, or gastritis

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Early Strains of Multidrug-Resistant Salmonella enterica Serovar Kentucky Sequence Type 198 from Southeast Asia Harbor Salmonella Genomic Island 1-J Variants with a Novel Insertion Sequence

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

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

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

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Fast gapped-read alignment with Bowtie 2

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Toward almost closed genomes with GapFiller

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International Spread of an Epidemic Population of Salmonella enterica Serotype Kentucky ST198 Resistant to Ciprofloxacin

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Scaffolding pre-assembled contigs using SSPACE

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Salmonellagenomic islands and antibiotic resistance inSalmonella enterica

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The Salmonella Genomic Island 1 Is Specifically Mobilized In Trans by the IncA/C Multidrug Resistance Plasmid Family

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ABACAS: algorithm-based automatic contiguation of assembled sequences

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The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

SGI2, a Relative of Salmonella Genomic Island SGI1 with an Independent Origin

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Novel Insertion Sequence- and Transposon-Mediated Genetic Rearrangements in Genomic Island SGI1 of Salmonella enterica Serovar Kentucky

(2008) B. Doublet et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Association of IS26-composite transposons and complex In4-type integrons generates novel multidrug resistance loci in Salmonella genomic island 1

(2008) B. Doublet 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