Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters

Genome Biology and Evolution
Ruth E TimmeEric W Brown

Abstract

The enteric pathogen Salmonella enterica is one of the leading causes of foodborne illness in the world. The species is extremely diverse, containing more than 2,500 named serovars that are designated for their unique antigen characters and pathogenicity profiles-some are known to be virulent pathogens, while others are not. Questions regarding the evolution of pathogenicity, significance of antigen characters, diversity of clustered regularly interspaced short palindromic repeat (CRISPR) loci, among others, will remain elusive until a strong evolutionary framework is established. We present the first large-scale S. enterica subsp. enterica phylogeny inferred from a new reference-free k-mer approach of gathering single nucleotide polymorphisms (SNPs) from whole genomes. The phylogeny of 156 isolates representing 78 serovars (102 were newly sequenced) reveals two major lineages, each with many strongly supported sublineages. One of these lineages is the S. Typhi group; well nested within the phylogeny. Lineage-through-time analyses suggest there have been two instances of accelerated rates of diversification within the subspecies. We also found that antigen characters and CRISPR loci reveal different evolutionary patterns than t...Continue Reading

References

Jun 3, 2014·BMC Genomics·Nathan L BachmannScott A Beatson
Apr 12, 2014·Gut Pathogens·Sathyaseelan SathyabamaJaved N Agrewala
Sep 5, 2014·Foodborne Pathogens and Disease·Guojie CaoJianghong Meng
Jan 17, 2016·Annual Review of Food Science and Technology·Rodolphe Barrangou, Edward G Dudley
Jan 17, 2016·Annual Review of Food Science and Technology·Xiangyu DengRene S Hendriksen
Dec 7, 2014·Microbiology·Nikki W ShariatEdward G Dudley
Apr 18, 2015·Genome Announcements·Marie BugarelGuy H Loneragan
Mar 5, 2015·PeerJ·Eduardo Castro-NallarKeith A Crandall
Jul 25, 2015·Gut Pathogens·Lorraine D Rodriguez-RiveraMartin Wiedmann
Feb 24, 2017·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Laure FonteneauSimon Le Hello
Mar 1, 2017·Annual Review of Food Science and Technology·Emily StoutRodolphe Barrangou
Aug 26, 2016·Clinical Microbiology Reviews·J RonholmFranco Pagotto
Jan 28, 2014·Applied and Environmental Microbiology·Narjol Gonzalez-EscalonaShashi K Sharma
Jan 13, 2018·Pathogens and Disease·Liliana Medina-AparicioIsmael Hernández-Lucas
Aug 14, 2020·Journal of the South African Veterinary Association·Tsepo A RamatlaMichelo Syakalima
Sep 2, 2018·Applied and Environmental Microbiology·Cameron P ThompsonNikki W Shariat
Jun 20, 2017·Frontiers in Microbiology·Jean-Guillaume Emond-RheaultRoger C Levesque

Citations

Aug 1, 1988·Journal of Medical Microbiology·R M BarkerP B Crichton
Sep 1, 1996·Endocrinology and Metabolism Clinics of North America·W A Horton
Mar 1, 1996·Applied and Environmental Microbiology·E F BoydR K Selander
Aug 6, 1998·Epidemiology and Infection·S RubinoP Cappuccinelli
Sep 24, 1998·Infection and Immunity·A J BäumlerL G Adams
Jun 9, 2000·Molecular Microbiology·R A Kingsley, A J Bäumler
Jul 20, 2002·Molecular Phylogenetics and Evolution·Eric W BrownThomas A Cebula
Jan 22, 2004·Bioinformatics·Emmanuel ParadisKorbinian Strimmer
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Oct 26, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Daniel FalushMark Achtman
May 19, 2007·Journal of Medical Microbiology·Francine GrimontPatrick A D Grimont
Jun 6, 2007·Genome Biology·Georgios S VernikosJulian Parkhill
Jul 27, 2007·Microbial Drug Resistance : MDR : Mechanisms, Epidemiology, and Disease·Svetlana EgorovaFrançois-Xavier Weill
Nov 17, 2007·Bioinformatics·Luke J HarmonWendell Challenger
Dec 11, 2007·Journal of Bacteriology·Philippe HorvathRodolphe Barrangou
Jun 20, 2008·Evolution; International Journal of Organic Evolution·Michael P CummingsKerry L Shaw
Sep 12, 2008·Molecular Ecology Notes·Daniel FalushJonathan K Pritchard
Oct 15, 2008·Systematic Biology·Alexandros StamatakisJacques Rougemont
Oct 12, 2010·Journal of Bacteriology·Vartul SangalMark Achtman
Oct 21, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Sébastien BoisvertJacques Corbeil
Oct 21, 2010·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Socrates TrujilloEric W Brown
Jan 5, 2011·Emerging Infectious Diseases·Elaine ScallanPatricia M Griffin
Jun 7, 2011·Microbial Ecology·Annika JacobsenCarsten Friis
Aug 11, 2011·PLoS Genetics·Xavier DidelotPeter Donnelly
Nov 9, 2011·Annual Review of Genetics·Devaki BhayaRodolphe Barrangou
Jan 10, 2012·Annual Review of Food Science and Technology·Rodolphe Barrangou, Philippe Horvath
Mar 14, 2012·BMC Genomics·Pimlapas LeekitcharoenphonDavid W Ussery
May 25, 2012·PloS One·Laetitia FabreFrançois-Xavier Weill
Jun 28, 2012·PLoS Pathogens·Mark AchtmanS. Enterica MLST Study Group
Aug 24, 2012·Science Translational Medicine·Evan S SnitkinJulia A Segre
Oct 12, 2012·Journal of Clinical Microbiology·Wenting JuJianghong Meng
Jan 10, 2013·MBio·M E PalmerC D Bayliss
Mar 7, 2013·MBio·Prerak T DesaiMichael McClelland

Related Concepts

Genome
Pathogenic Organism
Salmonella enterica
Phylogeny
Gene Transfer, Horizontal
Clone
Antigens
Clustered Regularly Interspaced Short Palindromic Repeats
Salmonella enterica subsp. enterica
Recombination, Interspecies

Related Feeds

CRISPR (general)

Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). CRISPR-Cas system enables the editing of genes to create or correct mutations. Discover the latest research on CRISPR here.

CRISPR Ribonucleases Deactivation

CRISPR-Cas system enables the editing of genes to create or correct mutations. This feed focuses on mechanisms that underlie deactivation of CRISPR ribonucleases. Here is the latest research.

CRISPR for Genome Editing

Genome editing technologies enable the editing of genes to create or correct mutations. Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). Here is the latest research on the use of CRISPR-Cas system in gene editing.

CRISPR & Staphylococcus

CRISPR-Cas system enables the editing of genes to create or correct mutations. Staphylococci are associated with life-threatening infections in hospitals, as well as the community. Here is the latest research on how CRISPR-Cas system can be used for treatment of Staphylococcal infections.