Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study, Lancet, vol.382, pp.209-222, 2013. ,
Estimates of global, regional, and national morbidity, mortality, and aetiologies of diarrhoeal diseases: a systematic analysis for the Global Burden of Disease Study, Lancet Infect. Dis, vol.3099, pp.1-40, 2015. ,
A changing picture of shigellosis in southern Vietnam: shifting species dominance, antimicrobial susceptibility and clinical presentation, BMC Infect. Dis, vol.9, p.204, 2009. ,
The rising dominance of shigella sonnei: an intercontinental shift in the etiology of bacillary dysentery, PLoS Negl. Trop. Dis, vol.9, pp.1-13, 2015. ,
Molecular pathogenesis of Shigella spp.: controlling host cell signaling, invasion, and death by type III secretion, Clin. Microbiol. Rev, vol.21, pp.134-156, 2008. ,
Guidelines for the control of shigellosis, including epidemics due to Shigella dysenteriae type 1. World Health Organisation, 2005. ,
Out of Asia: the independent rise and global spread of fluoroquinolone-resistant, Shigella. Microb. Genom, vol.4, p.171, 2018. ,
Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics, World Health Organization, pp.1-7, 2017. ,
South Asia as a reservoir for the global spread of ciprofloxacin resistant Shigella sonnei, PLoS Med, vol.13, pp.1-12, 2016. ,
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe, Nat. Genet, vol.44, pp.1056-1059, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01117702
Introduction and establishment of fluoroquinolone resistant Shigella sonnei into, Bhutan. Microb. Genom, vol.1, pp.1-11, 2015. ,
Tracking the establishment of local endemic populations of an emergent enteric pathogen, Proc. Natl Acad. Sci. USA, vol.110, pp.17522-17527, 2013. ,
Ciprofloxacin facilitates the transfer of XDR plasmids from commensal E. coli into epidemic fluoroquinolone-resistant Shigella sonnei, 2019. ,
Activity spectrum of colicins produced by shigella sonnei and genetic mechanism of colicin resistance in conspecific S. sonnei strains and Escherichia coli, Antimicrob. Agents Chemother, vol.59, pp.152-158, 2015. ,
Shedding of genes that interfere with the pathogenic lifestyle: the Shigella model, Res. Microbiol, vol.163, pp.399-406, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-00947763
Oxygen-insensitive nitroreductases: analysis of the roles of nfsA and nfsB in development of resistance to 5-nitrofuran derivatives in Escherichia coli, J. Bacteriol, vol.180, pp.5529-5539, 1998. ,
Homologous trans-editing factors with broad tRNA specificity prevent mistranslation caused by serine/threonine misactivation, Proc. Natl Acad. Sci. USA, vol.112, pp.6027-6032, 2015. ,
Protein mistranslation protects bacteria against oxidative stress, Nucleic Acids Res, vol.43, pp.1740-1748, 2015. ,
Preferential transposition of an IS630-associated composite transposon to TA in the 5?-CTAG-3? sequence, J. Bacteriol, vol.173, pp.6207-6212, 1991. ,
Ja Expression of flagella and motility by Shigella, Mol. Microbiol, vol.18, pp.63-75, 1995. ,
Mutations in two global regulators lower individual mortality in Escherichia coli, Mol. Microbiol, vol.67, pp.2-14, 2008. ,
The metabolic cost of flagellar motion in Pseudomonas putidaKT2440, Environ. Microbiol, vol.16, pp.291-303, 2014. ,
Practical approaches for detecting selection in microbial genomes, PLOS Comput. Biol, vol.12, p.1004739, 2016. ,
The rpoS gene is predominantly inactivated during laboratory storage and undergoes source-sink evolution in Escherichia coli species, J. Bacteriol, vol.196, pp.4276-4284, 2014. ,
Enhancement of glutathione production with a tripeptidase-deficient recombinant Escherichia coli, J. Ind. Microbiol. Biotechnol, vol.36, pp.1447-1452, 2009. ,
A new piece of the shigella pathogenicity puzzle: Spermidine accumulationby silencing of the speg gene, PLoS One, vol.6, p.27226, 2011. ,
Shigella reroutes host cell central metabolism to obtain highflux nutrient supply for vigorous intracellular growth, Proc. Natl Acad. Sci. USA, vol.111, pp.9929-9934, 2014. ,
No clinical benefit of empirical antimicrobial therapy for pediatric diarrhea in a high-usage, high-resistance setting, Clin. Infect. Dis, vol.66, pp.504-511, 2018. ,
EmrR is a negative regulator of the Escherichia coli multidrug resistance pump EmrAB, J. Bacteriol, vol.177, pp.2328-2334, 1995. ,
The role of reactive oxygen species in antibioticmediated killing of bacteria, Trends Microbiol, vol.25, pp.456-466, 2017. ,
Role of CysE in production of an extracellular signaling molecule in providencia stuartii and Escherichia coli: loss of cysE enhances biofilm formation in Escherichia coli, J. Bacteriol, vol.186, pp.7610-7617, 2004. ,
Measurement of biofilm formation by clinical isolates of Escherichia coli is method-dependent, J. Appl. Microbiol, vol.105, pp.585-590, 2008. ,
Transcriptional cross talk within the Mar-Sox-Rob regulon in Escherichia coli is limited to the rob and marRAB operons, J. Bacteriol, vol.194, pp.4867-4875, 2012. ,
Two functions of the C-terminal domain of Escherichia coli rob: mediating 'sequestrationdispersal' as a novel off-on switch for regulating rob's activity as a transcription activator and preventing degradation of rob by lon protease, J. Mol. Biol, vol.388, pp.415-430, 2009. ,
Activation of multiple antibiotic resistance and binding of stress-inducible promoters by Escherichia coli Rob protein, J. Bacteriol, vol.177, pp.1655-1661, 1995. ,
Defining a rob regulon in Escherichia coli by using transposon mutagenesis, J. Bacteriol, vol.182, pp.3794-3801, 2000. ,
SoxS and Rob of Escherichia coli -global regulators of multidrug resistance, virulence and stress response, Int. J. Biotechnol. Wellness Ind, vol.2, pp.101-124, 2014. ,
Structure of the bacterial RNA polymerase promoter specificity ? subunit, Mol. Cell, vol.9, pp.527-539, 2002. ,
Interactions between the 2.4 and 4.2 regions of ?S, the stress-specific ? factor of Escherichia coli, and the ?10 and ?35 promoter elements, Nucleic Acids Res, vol.32, pp.45-53, 2004. ,
a major player in the response to environmental stresses in Escherichia coli: role, regulation and mechanisms of promoter recognition, Environ. Microbiol. Rep, vol.6, pp.1-13, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-00926634
Antibiotic resistance in india: drivers and opportunities for action, PLoS Med, vol.13, pp.1-7, 2016. ,
Recent outbreaks of shigellosis in california caused by two distinct populations of shigella sonnei with either increased virulence or fluoroquinolone resistance, vol.1, pp.1-18, 2016. ,
The worldwide spread of ciprofloxacin-resistant Shigella sonnei among HIV-infected men who have sex with men, Clin. Microbiol. Infect, vol.22, 2016. ,
Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study, Lancet Infect. Dis, vol.3099, pp.1-9, 2015. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02042957
What is the overlap between HIV and shigellosis epidemics in England: further evidence of MSM transmission?, Sex. Transm. Infect, vol.94, pp.67-71, 2017. ,
Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species, Nat. Commun, vol.9, p.1462, 2018. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02005961
Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Shigella sonnei isolated from cases of diarrhoeal disease in England and Wales, J. Antimicrob. Chemother, vol.72, pp.2496-2502, 2015. ,
The emergence of quinolone resistant Shigella sonnei, PLoS One, vol.11, p.160290, 2016. ,
Co-circulation of multidrug-resistant shigella among men who have sex with men in Australia, Clin. Infect. Dis, 2019. ,
The population genetics of dN/dS, PLoS Genet, vol.4, p.1000304, 2008. ,
Non-target gene mutations in the development of fluoroquinolone resistance in Escherichia coli, Antimicrob. Agents Chemother, vol.44, pp.814-820, 2000. ,
Interplay in the selection of fluoroquinolone resistance and bacterial fitness, PLoS Pathog, vol.5, p.1000541, 2009. ,
Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure, vol.2, pp.1229-01229, 2013. ,
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins, Nucleic Acids Res, vol.44, pp.1-13, 2014. ,
RAxML version 8: a tool for phylogenetic analysis and postanalysis of large phylogenies, Bioinformatics, vol.30, pp.1312-1313, 2014. ,
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res, vol.44, pp.242-245, 2016. ,
Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations, BMC Bioinform, vol.9, p.539, 2008. ,
Hierarchical and spatially explicit clustering of DNA sequences with BAPS software, Mol. Biol. Evol, vol.30, pp.1224-1228, 2013. ,
ModelFinder: fast model selection for accurate phylogenetic estimates, Nat. Methods, vol.14, pp.587-589, 2017. ,
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol. Biol. Evol, vol.32, pp.268-274, 2015. ,
BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evol. Biol, vol.7, p.214, 2007. ,
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty, Mol. Biol. Evol, vol.29, pp.2157-2167, 2012. ,
Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics, Mol. Biol. Evol, vol.30, pp.239-243, 2013. ,
The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography, Mol. Biol. Evol, vol.33, pp.1711-1725, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374966
Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics, Mol. Biol. Evol, vol.25, pp.1459-1471, 2008. ,
Bayesian coalescent inference of past population dynamics from molecular sequences, Mol. Biol. Evol, vol.22, pp.1185-1192, 2005. ,
Global and regional dissemination and evolution of Burkholderia pseudomallei, Nat. Microbiol, vol.2, p.16263, 2017. ,
SIMMAP: stochastic character mapping of discrete traits on phylogenies, BMC Bioinform, vol.7, p.88, 2006. ,
phytools: an R package for phylogenetic comparative biology (and other things), Methods Ecol. Evol, vol.3, pp.217-223, 2012. ,
Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res, vol.18, pp.821-829, 2008. ,
Prokka: rapid prokaryotic genome annotation, Bioinformatics, vol.30, pp.2068-2069, 2014. ,
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads, Microb. Genom, vol.3, p.131, 2017. ,
Identification of acquired antimicrobial resistance genes, J. Antimicrob. Chemother, vol.67, pp.2640-2644, 2012. ,
In Silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing, Antimicrob. Agents Chemother, vol.58, pp.3895-3903, 2014. ,
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database, Bioinformatics, vol.24, pp.2672-2676, 2008. ,
Roary: rapid large-scale prokaryote pan genome analysis, Bioinformatics, vol.31, pp.3691-3693, 2015. ,
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly, vol.6, pp.80-92, 2012. ,
Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes, Nat. Genet, vol.43, pp.1275-1280, 2011. ,
PAML 4: phylogenetic analysis by maximum likelihood, Mol. Biol. Evol, vol.24, pp.1586-1591, 2007. ,
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene, Genetics, vol.148, pp.929-936, 1998. ,
Evaluation of luminex xTAG gastrointestinal pathogen panel assay for detection of multiple diarrheal pathogens in fecal samples in Vietnam, J. Clin. Microbiol, vol.54, pp.1094-1100, 2016. ,
Nutritional requirements of shigellae for growth in a minimal medium, Infect. Immun, vol.56, pp.1007-1009, 1988. ,
Antibiotic treatment enhances the genome-wide mutation rate of target cells, Proc. Natl Acad. Sci. USA, vol.113, pp.2498-2505, 2016. ,
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, 2013. ,
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, vol.20, pp.1297-1303, 2010. ,
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J. Comput. Biol, vol.19, pp.455-477, 2012. ,