A genomic appraisal of invasive Salmonella Typhimurium and associated antibiotic resistance in sub-Saharan Africa
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Jean Pierre Rutanga | K. Otieno | L. Otieno | Anima M. Sarfo | T. Mvalo | C. MacLennan | S. Van Puyvelde | N. Feasey | D. Affolabi | C. Msefula | F. Marks | D. Martiny | P. Ceyssens | M. Beale | O. Lunguya | B. Barbé | P. Lompo | S. Sridhar | B. Ingelbeen | D. Falay | S. Deborggraeve | M. Tahita | J. Lusingu | T. de Block | Wim L. Cuypers | H. Jeon | Se Eun Park | F. Hassan-Hanga | Lisette Mbuyi-Kalonji | J. Mbwana | S. O. Agyei | Matt Bawn | K. Asante | Tessa de Block | Marie-France Phoba | Robert A Kingsley | Olivier Vandenberg | Wesley Mattheus | Marianne A B van der Sande | Simon Kariuki | Samuel Adjei | Walter Otieno | Irving F. Hoffman | S. Obaro | Grant Mackenzie | N. R. Thomson | Jan Jacobs | Gordon Dougan | Samuel Kariuki | Samuel Adjei | Irving F Hoffman | G. Dougan | Nicholas R. Thomson | Simon K Kariuki | Robert A. Kingsley
[1] G. Dougan,et al. Genetic and Structural Variation in the O-Antigen of Salmonella enterica Serovar Typhimurium Isolates Causing Bloodstream Infections in the Democratic Republic of the Congo , 2022, mBio.
[2] N. Shariat,et al. Evidence for common ancestry and microevolution of passerine-adapted Salmonella enterica serovar Typhimurium in the UK and USA , 2022, Microbial genomics.
[3] G. Dougan,et al. The genomic epidemiology of multi-drug resistant invasive non-typhoidal Salmonella in selected sub-Saharan African countries , 2021, BMJ Global Health.
[4] R. Adegbola,et al. Impact of the introduction of pneumococcal conjugate vaccination on invasive pneumococcal disease and pneumonia in The Gambia: 10 years of population-based surveillance , 2021, The Lancet. Infectious diseases.
[5] J. Crump,et al. Incidence of non-typhoidal Salmonella invasive disease: A systematic review and meta-analysis , 2021, The Journal of infection.
[6] Emiliano Cohen,et al. Pathoadaptation of the passerine-associated Salmonella enterica serovar Typhimurium lineage to the avian host , 2021, PLoS pathogens.
[7] R. Bennett,et al. Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa , 2020, Nature Microbiology.
[8] G. Dougan,et al. High relatedness of invasive multi-drug resistant non-typhoidal Salmonella genotypes among patients and asymptomatic carriers in endemic informal settlements in Kenya , 2020, PLoS neglected tropical diseases.
[9] J. Jacobs,et al. Invasive non-typhoidal Salmonella infections in sub-Saharan Africa: a systematic review on antimicrobial resistance and treatment , 2020, BMC Medicine.
[10] M. Wiedmann,et al. The Salmonella enterica Plasmidome as a Reservoir of Antibiotic Resistance , 2020, Microorganisms.
[11] J. Jacobs,et al. Non-typhoidal Salmonella bloodstream infections in Kisantu, DR Congo: Emergence of O5-negative Salmonella Typhimurium and extensive drug resistance , 2020, PLoS neglected tropical diseases.
[12] T. Dallman,et al. Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation , 2019, bioRxiv.
[13] H. Tinto,et al. Supporting evidence for a human reservoir of invasive non-Typhoidal Salmonella from household samples in Burkina Faso , 2019, PLoS neglected tropical diseases.
[14] Jan Jacobs,et al. An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation , 2019, Nature Communications.
[15] C. MacLennan,et al. Invasive Nontyphoidal Salmonella Disease in Africa , 2019, EcoSal Plus.
[16] Jukka Corander,et al. Fast hierarchical Bayesian analysis of population structure , 2018, bioRxiv.
[17] F. Ceccherini‐Silberstein,et al. The Food Additive Maltodextrin Promotes Endoplasmic Reticulum Stress–Driven Mucus Depletion and Exacerbates Intestinal Inflammation , 2018, Cellular and molecular gastroenterology and hepatology.
[18] R. Kingsley,et al. Genome Variation and Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Pathovariants , 2018, Infection and Immunity.
[19] M. Suchard,et al. Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 , 2018, Systematic biology.
[20] Denise N. Bronner,et al. Genetic Ablation of Butyrate Utilization Attenuates Gastrointestinal Salmonella Disease. , 2018, Cell host & microbe.
[21] G. Dougan,et al. Genomic history of the seventh pandemic of cholera in Africa , 2017, Science.
[22] P. Ashton,et al. Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa , 2017, Genome Medicine.
[23] Jacqueline A. Keane,et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads , 2017, bioRxiv.
[24] J. Crump,et al. Incidence of invasive salmonella disease in sub-Saharan Africa: a multicentre population-based surveillance study , 2017, The Lancet. Global health.
[25] C. MacLennan,et al. A Systematic Review of the Incidence, Risk Factors and Case Fatality Rates of Invasive Nontyphoidal Salmonella (iNTS) Disease in Africa (1966 to 2014) , 2017, PLoS neglected tropical diseases.
[26] Ryan R. Wick,et al. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads , 2016, bioRxiv.
[27] Jacqueline A. Keane,et al. An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid , 2016, Nature Communications.
[28] C. MacLennan,et al. Nontyphoidal salmonella disease: Current status of vaccine research and development. , 2016, Vaccine.
[29] Julian Parkhill,et al. Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data , 2016, bioRxiv.
[30] Paul P. Gardner,et al. A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes , 2016, bioRxiv.
[31] Peer Bork,et al. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..
[32] Simon R. Harris,et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments , 2016, bioRxiv.
[33] Andrew Rambaut,et al. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) , 2016, Virus evolution.
[34] J. Muyembe,et al. Invasive Salmonella Infections at Multiple Surveillance Sites in the Democratic Republic of the Congo, 2011-2014. , 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[35] Samuel Kariuki,et al. Epidemiology and Genomics of Invasive Nontyphoidal Salmonella Infections in Kenya. , 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[36] E. Faragher,et al. Three Epidemics of Invasive Multidrug-Resistant Salmonella Bloodstream Infection in Blantyre, Malawi, 1998–2014 , 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[37] Paul Turner,et al. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events , 2015, Nature Genetics.
[38] Mark B. Schultz,et al. Bandage: interactive visualization of de novo genome assemblies , 2015, bioRxiv.
[39] Gemma C. Langridge,et al. Ceftriaxone-Resistant Salmonella enterica Serotype Typhimurium Sequence Type 313 from Kenyan Patients Is Associated with the blaCTX-M-15 Gene on a Novel IncHI2 Plasmid , 2015, Antimicrobial Agents and Chemotherapy.
[40] S. Clare,et al. Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa , 2015, PLoS neglected tropical diseases.
[41] P. Stogios,et al. Multiple histidines in the periplasmic domain of the Salmonella enterica sensor kinase SsrA enhance signaling in response to extracellular acidification , 2015, Molecular microbiology.
[42] Jacqueline A. Keane,et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins , 2014, Nucleic acids research.
[43] Shenghao Xu,et al. Supplementary Information , 2014, States at War, Volume 3.
[44] Amy K. Cain,et al. Drug Resistance in Salmonella enterica ser. Typhimurium Bloodstream Infection, Malawi , 2014, Emerging infectious diseases.
[45] Justin Zobel,et al. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs , 2014, bioRxiv.
[46] Torsten Seemann. Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..
[47] O. Lund,et al. In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing , 2014, Antimicrobial Agents and Chemotherapy.
[48] F. Weill,et al. Invasive Salmonella enterica Serotype Typhimurium Infections, Democratic Republic of the Congo, 2007–2011 , 2014, Emerging infectious diseases.
[49] Derrick E. Wood,et al. Kraken: ultrafast metagenomic sequence classification using exact alignments , 2014, Genome Biology.
[50] Alexandros Stamatakis,et al. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..
[51] Andrew C. Pawlowski,et al. The Comprehensive Antibiotic Resistance Database , 2013, Antimicrobial Agents and Chemotherapy.
[52] J. Jacobs,et al. Antimicrobial Resistance in Invasive Non-typhoid Salmonella from the Democratic Republic of the Congo: Emergence of Decreased Fluoroquinolone Susceptibility and Extended-spectrum Beta Lactamases , 2013, PLoS neglected tropical diseases.
[53] Wai Lok Sibon Li,et al. Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. , 2012, Molecular biology and evolution.
[54] J. Wain,et al. Intra-continental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa , 2012, Nature Genetics.
[55] M. Suchard,et al. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. , 2012, Molecular biology and evolution.
[56] G. Dougan,et al. Genotypic Homogeneity of Multidrug Resistant S. Typhimurium Infecting Distinct Adult and Childhood Susceptibility Groups in Blantyre, Malawi , 2012, PloS one.
[57] G. Dougan,et al. Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa , 2012, The Lancet.
[58] M. Suchard,et al. Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.
[59] D. Maskell,et al. Genomic Comparison of the Closely Related Salmonella enterica Serovars Enteritidis and Dublin , 2012, The open microbiology journal.
[60] Nicola K. Petty,et al. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons , 2011, BMC Genomics.
[61] J. Burton,et al. Rapid Pneumococcal Evolution in Response to Clinical Interventions , 2011, Science.
[62] F. Aarestrup,et al. Microbiologic and Clinical Features of Salmonella Species Isolated From Bacteremic Children in Eastern Democratic Republic of Congo , 2010, The Pediatric infectious disease journal.
[63] G. Dougan,et al. Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. , 2009, Genome research.
[64] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[65] Jukka Corander,et al. Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations , 2008, BMC Bioinformatics.
[66] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.
[67] H. Favoreel,et al. A limited role for SsrA/B in persistent Salmonella Typhimurium infections in pigs. , 2008, Veterinary microbiology.
[68] Alexandros Stamatakis,et al. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..
[69] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[70] F. Blattner,et al. Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.
[71] J. W. Campbell,et al. A new Escherichia coli metabolic competency: growth on fatty acids by a novel anaerobic β‐oxidation pathway , 2003, Molecular microbiology.
[72] D. M. Heithoff,et al. ssrA (tmRNA) Plays a Role inSalmonella enterica Serovar Typhimurium Pathogenesis , 2000, Journal of bacteriology.
[73] F. Mooi,et al. Characterization of a Bordetella pertussis fimbrial gene cluster which is located directly downstream of the filamentous haemagglutinin gene , 1992, Molecular microbiology.
[74] W. Boos,et al. The malZ gene of Escherichia coli, a member of the maltose regulon, encodes a maltodextrin glucosidase. , 1991, The Journal of biological chemistry.
[75] J. Bogaerts,et al. COMMUNITY-ACQUIRED BACTERAEMIA IN AFRICAN CHILDREN , 1987, The Lancet.
[76] J. Bogaerts,et al. Metastatic focal infections due to multiresistant Salmonella typhimurium in children: A 34 month experience in Rwanda , 1986, European Journal of Epidemiology.
[77] E. Kahn. On crises , 2005, Psychiatric Quarterly.
[78] N. Nsibu,et al. [Salmonella infections in Kinshasa: the species involved and sensitivity to antibiotics]. , 1991, Pediatrie.
[79] J. Bogaerts,et al. Severe multiresistant Salmonella typhimurium systemic infections in Central Africa--clinical features and treatment in a paediatric department. , 1984, Journal of Antimicrobial Chemotherapy.