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

Antimicrobial Resistance in Salmonella enterica Serovar Typhi Isolates from Bangladesh, Indonesia, Taiwan, and Vietnam

(2014) Chien-Shun Chiou et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Genomic Signature of Multidrug-Resistant Salmonella enterica Serovar Typhi Isolates Related to a Massive Outbreak in Zambia between 2010 and 2012

(2014) Rene S. Hendriksen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Evolution and transmission of drug-resistant tuberculosis in a Russian population

(2014) Nicola Casali et al.   NATURE GENETICS

A Randomized Trial of Prolonged Co-trimoxazole in HIV-Infected Children in Africa

(2014) Mutsawashe Bwakura-Dangarembizi et al.   NEW ENGLAND JOURNAL OF MEDICINE

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

(2014) Michael Inouye et al.   Genome Medicine

Burden of typhoid fever in low-income and middle-income countries: a systematic, literature-based update with risk-factor adjustment

(2014) Vittal Mogasale et al.   Lancet Global Health

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

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

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

(2013) Stephen Baker et al.   eLife

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

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

Mutations in 23S rRNA Confer Resistance against Azithromycin in Pseudomonas aeruginosa

(2012) Rasmus Lykke Marvig et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Multidrug-Resistant Typhoid Fever With Neurologic Findings on the Malawi-Mozambique Border

(2012) Emily Lutterloh et al.   CLINICAL INFECTIOUS DISEASES

In Vitro Development and Analysis of Escherichia coli and Shigella boydii Azithromycin–Resistant Mutants

(2012) Cláudia Gomes et al.   Microbial Drug Resistance

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

(2012) Kathryn E Holt et al.   NATURE GENETICS

Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

(2012) Simon R Harris et al.   NATURE GENETICS

Population-Based Incidence of Typhoid Fever in an Urban Informal Settlement and a Rural Area in Kenya: Implications for Typhoid Vaccine Use in Africa

(2012) Robert F. Breiman et al.   PLoS One

High-Resolution Genotyping of the Endemic Salmonella Typhi Population during a Vi (Typhoid) Vaccination Trial in Kolkata

(2012) Kathryn E. Holt et al.   PLoS Neglected Tropical Diseases

Antimicrobial resistance trends in blood culture positive Salmonella Typhi isolates from Pondicherry, India, 2005–2009

(2011) G.A. Menezes et al.   CLINICAL MICROBIOLOGY AND INFECTION

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

PHAST: A Fast Phage Search Tool

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

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission

(2011) S. Baker et al.   Open Biology

Temporal Fluctuation of Multidrug Resistant Salmonella Typhi Haplotypes in the Mekong River Delta Region of Vietnam

(2011) Kathryn E. Holt et al.   PLoS Neglected Tropical Diseases

Emergence of a Globally Dominant IncHI1 Plasmid Type Associated with Multiple Drug Resistant Typhoid

(2011) Kathryn E. Holt et al.   PLoS Neglected Tropical Diseases

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

High-throughput bacterial SNP typing identifies distinct clusters of SalmonellaTyphi causing typhoid in Nepalese children

(2010) Kathryn E Holt et al.   BMC INFECTIOUS DISEASES

Population impact of Vi capsular polysaccharide vaccine

(2010) M Imran Khan et al.   Expert Review of Vaccines

A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A

(2010) Y. Song et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Typhoid in Kenya Is Associated with a Dominant Multidrug-Resistant Salmonella enterica Serovar Typhi Haplotype That Is Also Widespread in Southeast Asia

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

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi

(2009) Kathryn E Holt et al.   BMC GENOMICS

Global Trends in Typhoid and Paratyphoid Fever

(2009) John A. Crump et al.   CLINICAL INFECTIOUS DISEASES

Variation in Salmonella enterica Serovar Typhi IncHI1 Plasmids during the Global Spread of Resistant Typhoid Fever

(2008) M.-D. Phan et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

(2008) Tim Carver et al.   BIOINFORMATICS

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

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

High-Throughput Genotyping of Salmonella enterica Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia

(2008) S. Baker et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2008) Kathryn E Holt et al.   NATURE GENETICS