Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Predictors of blaCTX-M-15 in varieties of Escherichia coli genotypes from humans in community settings in Mwanza, Tanzania

(2016) Stephen E. Mshana et al.   BMC INFECTIOUS DISEASES

Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae

(2016) Marjolein F. Q. Kluytmans-van den Bergh et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2016) Vanessa K. Wong et al.   Nature Communications

The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia

(2016) Duy Pham Thanh et al.   PLoS Neglected Tropical Diseases

A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure

(2016) Duy Pham Thanh et al.   eLife

Predominance of CTX-M-15 among ESBL Producers from Environment and Fish Gut from the Shores of Lake Victoria in Mwanza, Tanzania

(2016) Nyambura Moremi et al.   Frontiers in Microbiology

Epidemiology, Clinical Presentation, Laboratory Diagnosis, Antimicrobial Resistance, and Antimicrobial Management of Invasive Salmonella Infections

(2015) John A. Crump et al.   CLINICAL MICROBIOLOGY REVIEWS

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

Rapid Emergence of Multidrug Resistant, H58-Lineage Salmonella Typhi in Blantyre, Malawi

(2015) Nicholas A. Feasey et al.   PLoS Neglected Tropical Diseases

A novel plasmid carrying blaCTX-M-15 identified in commensal Escherichia coli from healthy pregnant women in Ibadan, Nigeria

(2015) Daniela Fortini et al.   Journal of Global Antimicrobial Resistance

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

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   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

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

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

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

A three-year review of antimicrobial resistance of Salmonella enterica serovars Typhi and Paratyphi A in Pakistan

(2014) Farah Naz Qamar et al.   Journal of Infection in Developing Countries

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Plasmids and the spread of resistance

(2013) Alessandra Carattoli   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Salmonella enterica serovar Typhi strain producing extended-spectrum  -lactamases in Dhaka, Bangladesh

(2012) D. Ahmed et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance

(2011) A.-P. Magiorakos et al.   CLINICAL MICROBIOLOGY AND INFECTION

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS