An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

Utility of Whole-Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance

(2015) Anne Holmes et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2015) Vanessa K Wong et al.   NATURE GENETICS

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

(2014) Nicola Casali et al.   NATURE GENETICS

Antimicrobial Resistance, Virulence Profiles and Molecular Subtypes of Salmonella enterica Serovars Typhi and Paratyphi A Blood Isolates from Kolkata, India during 2009-2013

(2014) Shanta Dutta et al.   PLoS One

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

(2014) Francesc Coll et al.   Nature Communications

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

Identification of Salmonella enterica Serovar Typhi Genotypes by Use of Rapid Multiplex Ligation-Dependent Probe Amplification

(2013) D. Pham Thanh et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak

(2011) Jennifer L. Gardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

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

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

(2010) Giovanna Morelli et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Global Trends in Typhoid and Paratyphoid Fever

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

Clustering Analysis of Salmonella enterica Serovar Typhi Isolates in Korea by PFGE, Ribotyping, and Phage Typing

(2009) Shukho Kim et al.   Foodborne Pathogens and Disease

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

(2008) Jukka Corander et al.   BMC BIOINFORMATICS

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