Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Draft genome sequence of blaTEM-1-mediated cephalosporin-resistant Salmonella enterica serovar Typhi from bloodstream infection

(2016) Naveen Kumar Devanga Ragupathi et al.   Journal of Global Antimicrobial Resistance

Typhoid fever vaccination strategies

(2015) Kashmira A. Date et al.   VACCINE

A Large-Scale Community-Based Outbreak of Paratyphoid Fever Caused by Hospital-Derived Transmission in Southern China

(2015) Meiying Yan et al.   PLoS Neglected Tropical Diseases

Systematic review of the global epidemiology, clinical and laboratory profile of enteric fever

(2015) Asma Azmatullah et al.   Journal of Global Health

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Z. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

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

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

Development of the EUCAST disk diffusion antimicrobial susceptibility testing method and its implementation in routine microbiology laboratories

(2013) E. Matuschek et al.   CLINICAL MICROBIOLOGY AND INFECTION

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

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

Bloodstream Infection among Children Presenting to a General Hospital Outpatient Clinic in Urban Nepal

(2012) Rahul Pradhan et al.   PLoS One

Typhoid fever and paratyphoid fever: Systematic review to estimate global morbidity and mortality for 2010

(2012) Geoffrey C. Buckle et al.   Journal of Global Health

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

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

Genetic Diversity of Salmonella enteric serovar Typhi and Paratyphi in Shenzhen, China from 2002 through 2007

(2010) Weiyuan Wu et al.   BMC MICROBIOLOGY

The burden of vaccine-preventable invasive bacterial infections and pneumonia in children admitted to hospital in urban Nepal

(2010) Dominic F. Kelly et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses

(2010) C. Firth et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Hospital‐Based Surveillance of Invasive Pneumococcal Disease among Young Children in Urban Nepal

(2009) Eleri J. Williams et al.   CLINICAL INFECTIOUS DISEASES