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List of works by Stephen Baker

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The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome

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

scientific article published on 27 July 2008
Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health

scientific article published on 22 June 2015
Evolutionary history of Salmonella typhi

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

scientific article published on 11 May 2015
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

scientific article published in September 2012
Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray

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

scientific article published on 20 February 2018
Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond

scientific article (publication date: July 2016)
The utility of diagnostic tests for enteric fever in endemic locations

scientific article published on June 2011
Salmonella enterica serovar Typhi and the pathogenesis of typhoid fever

scientific article published on January 2014
Incidence of invasive salmonella disease in sub-Saharan Africa: a multicentre population-based surveillance study

scientific article published on March 2017
Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7.

scientific article
A changing picture of shigellosis in southern Vietnam: shifting species dominance, antimicrobial susceptibility and clinical presentation

scientific article
The role of prophage-like elements in the diversity of Salmonella enterica serovars

scientific article published in May 2004
Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

scientific article published on 22 March 2013
Salmonella chronic carriage: epidemiology, diagnosis, and gallbladder persistence

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

scientific article published on 10 December 2013
Tracking the establishment of local endemic populations of an emergent enteric pathogen

scientific article published on 30 September 2013
Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study

scientific article published on 27 April 2015
Immune profiling with a Salmonella Typhi antigen microarray identifies new diagnostic biomarkers of human typhoid

scientific article published on 9 January 2013
Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid

scientific article published in July 2011
A prospective descriptive study of cryptococcal meningitis in HIV uninfected patients in Vietnam - high prevalence of Cryptococcus neoformans var grubii in the absence of underlying disease

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

scientific article published in October 2011
Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

scientific article
Searching for the elusive typhoid diagnostic

scientific article
Identification of a new cyclovirus in cerebrospinal fluid of patients with acute central nervous system infections

scientific article published on 18 June 2013
Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258.

scientific article published on 10 April 2015
The Rising Dominance of Shigella sonnei: An Intercontinental Shift in the Etiology of Bacillary Dysentery

scientific article
Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes

scientific article
A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae

scientific article published on 20 February 2015
High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children

scientific article published on 31 May 2010
The influence of reduced susceptibility to fluoroquinolones in Salmonella enterica serovar Typhi on the clinical response to ofloxacin therapy

scientific article
The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens

scientific article published on 21 May 2010
The genomic signatures of Shigella evolution, adaptation and geographical spread

scientific article published on 29 February 2016
Gatifloxacin versus chloramphenicol for uncomplicated enteric fever: an open-label, randomised, controlled trial

scientific article published on 29 April 2011
Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri

scientific article published on 4 August 2015
An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

scientific article published on 05 October 2016
The genome of Salmonella enterica serovar Typhi

scientific article published on July 2007
The decline of typhoid and the rise of non-typhoid salmonellae and fungal infections in a changing HIV landscape: bloodstream infection trends over 15 years in southern Vietnam

scientific article
High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia

scientific article published on 5 March 2008
Use of Colistin and Other Critical Antimicrobials on Pig and Chicken Farms in Southern Vietnam and Its Association with Resistance in Commensal Escherichia coli Bacteria

scientific article
Predicting the impact of vaccination on the transmission dynamics of typhoid in South Asia: a mathematical modeling study

scientific article published on 09 January 2014
High prevalence of plasmid-mediated quinolone resistance determinants in commensal members of the Enterobacteriaceae in Ho Chi Minh City, Vietnam

scientific article published on 20 August 2009
Variation at HLA-DRB1 is associated with resistance to enteric fever

scientific article
Gatifloxacin versus ceftriaxone for uncomplicated enteric fever in Nepal: an open-label, two-centre, randomised controlled trial

scientific article published on 19 January 2016
Differential epidemiology of Salmonella Typhi and Paratyphi A in Kathmandu, Nepal: a matched case control investigation in a highly endemic enteric fever setting

scientific article
Suitable disk antimicrobial susceptibility breakpoints defining Salmonella enterica serovar Typhi isolates with reduced susceptibility to fluoroquinolones

scientific article
Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray.

scientific article published on December 2005
The burden and characteristics of enteric fever at a healthcare facility in a densely populated area of Kathmandu

scientific article published on 15 November 2010

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