Genomic Epidemiology of Salmonella enterica Serotype Enteritidis based on Population Structure of Prevalent Lineages

Major lineages emerged during the 17th–18th centuries and diversified during the 1920s and 1950s.

[1]  Bart C. Weimer,et al.  Intraspecies Variation in the Emergence of Hyperinfectious Bacterial Strains in Nature , 2012, PLoS pathogens.

[2]  Mark R. Wilson,et al.  The forensic analysis of foodborne bacterial pathogens in the age of whole‐genome sequencing , 2013, Cladistics : the international journal of the Willi Hennig Society.

[3]  J. Corander,et al.  Detection of recombination events in bacterial genomes from large population samples , 2011, Nucleic acids research.

[4]  M. Achtman,et al.  Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona , 2013, PLoS genetics.

[5]  Pushkala Jayaraman,et al.  A computational genomics pipeline for prokaryotic sequencing projects , 2010, Bioinform..

[6]  B. Birren,et al.  Short-term genome evolution of Listeria monocytogenes in a non-controlled environment , 2008, BMC Genomics.

[7]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[8]  Craig W. Hedberg,et al.  Foodborne Illness Acquired in the United States , 2011, Emerging infectious diseases.

[9]  Ruth Timme,et al.  On the Evolutionary History, Population Genetics and Diversity among Isolates of Salmonella Enteritidis PFGE Pattern JEGX01.0004 , 2013, PloS one.

[10]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[11]  Mandev S. Gill,et al.  Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. , 2013, Molecular biology and evolution.

[12]  Rodolphe Barrangou,et al.  Novel Virulence Gene and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Multilocus Sequence Typing Scheme for Subtyping of the Major Serovars of Salmonella enterica subsp. enterica , 2011, Applied and Environmental Microbiology.

[13]  Shaohua Zhao,et al.  Enhanced Subtyping Scheme for Salmonella Enteritidis , 2007, Emerging infectious diseases.

[14]  Henrik C Wegener,et al.  Global monitoring of Salmonella serovar distribution from the World Health Organization Global Foodborne Infections Network Country Data Bank: results of quality assured laboratories from 2001 to 2007. , 2011, Foodborne pathogens and disease.

[15]  Paolo Piazza,et al.  Microevolutionary analysis of Clostridium difficile genomes to investigate transmission , 2012, Genome Biology.

[16]  M. Kaufmann,et al.  Pulsed-field gel electrophoresis. , 1998, Methods in molecular medicine.

[17]  F. Aarestrup,et al.  Risk factors and epidemiology of the ten most common Salmonella serovars from patients in Thailand: 2002-2007. , 2009, Foodborne pathogens and disease.

[18]  B. Hargis,et al.  Tracing the Origins of Salmonella Outbreaks , 2000, Science.

[19]  L. Florea,et al.  Characterization of Salmonella enterica Subspecies I Genovars by Use of Microarrays , 2004, Journal of bacteriology.

[20]  Errol Strain,et al.  Identification of a salmonellosis outbreak by means of molecular sequencing. , 2011, The New England journal of medicine.

[21]  F. Gulland,et al.  Prevalence and characterization of Salmonella spp. among marine animals in the Channel Islands, California. , 2008, Diseases of aquatic organisms.

[22]  Wai Lok Sibon Li,et al.  Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. , 2012, Molecular biology and evolution.

[23]  D. Bryant,et al.  A Simple and Robust Statistical Test for Detecting the Presence of Recombination , 2006, Genetics.

[24]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[25]  Giovanna Morelli,et al.  Microevolution of Helicobacter pylori during Prolonged Infection of Single Hosts and within Families , 2010, PLoS genetics.

[26]  B. Swaminathan,et al.  Second generation subtyping: a proposed PulseNet protocol for multiple-locus variable-number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 (STEC O157). , 2006, Foodborne pathogens and disease.

[27]  S. Ho,et al.  Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.

[28]  A. Rambaut,et al.  BEAST: Bayesian evolutionary analysis by sampling trees , 2007, BMC Evolutionary Biology.

[29]  J. Besser,et al.  Comparison of Multiple-Locus Variable-Number Tandem Repeat Analysis, Pulsed-Field Gel Electrophoresis, and Phage Typing for Subtype Analysis of Salmonella enterica Serotype Enteritidis , 2006, Journal of Clinical Microbiology.

[30]  James H. Bullard,et al.  Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. , 2011, The New England journal of medicine.

[31]  C. Braden,et al.  Salmonella enterica serotype Enteritidis and eggs: a national epidemic in the United States. , 2006, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[32]  James H. Bullard,et al.  The origin of the Haitian cholera outbreak strain. , 2011, The New England journal of medicine.

[33]  M. Bissell.  Multiplex, Bead-Based Suspension Array for Molecular Determination of Common Salmonella Serogroups , 2009 .

[34]  Julian Parkhill,et al.  Evolution of MRSA During Hospital Transmission and Intercontinental Spread , 2010, Science.

[35]  T. Cebula,et al.  Genomic anatomy of Escherichia coli O157:H7 outbreaks , 2011, Proceedings of the National Academy of Sciences.

[36]  P. Fields,et al.  Multiplex, Bead-Based Suspension Array for Molecular Determination of Common Salmonella Serogroups , 2007, Journal of Clinical Microbiology.

[37]  M. Gilmour,et al.  Limited genetic diversity in Salmonella enterica Serovar Enteritidis PT13 , 2007, BMC Microbiology.

[38]  Georgios S. Vernikos,et al.  Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. , 2008, Genome research.

[39]  Stephen M. Graham,et al.  Nontyphoidal salmonellosis in Africa , 2010, Current opinion in infectious diseases.

[40]  E. Holmes,et al.  Out of Africa: A Molecular Perspective on the Introduction of Yellow Fever Virus into the Americas , 2007, PLoS pathogens.

[41]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[42]  M. Wiedmann,et al.  A Whole-Genome Single Nucleotide Polymorphism-Based Approach To Trace and Identify Outbreaks Linked to a Common Salmonella enterica subsp. enterica Serovar Montevideo Pulsed-Field Gel Electrophoresis Type , 2011, Applied and Environmental Microbiology.

[43]  A. Wollam,et al.  Evolutionary Genomics of Salmonella enterica Subspecies , 2013, mBio.

[44]  M. Suchard,et al.  Bayesian selection of continuous-time Markov chain evolutionary models. , 2001, Molecular biology and evolution.

[45]  M. Mikoleit,et al.  Characterization of Salmonella enterica serovar Enteritidis isolates recovered from blood and stool specimens in Thailand , 2012, BMC Microbiology.