title: Comparative genomics of unintrogressed Campylobacter coli clades 2 and 3.
abstract: BACKGROUND
  Campylobacter jejuni and C. coli share a multitude of risk factors associated with human gastrointestinal disease, yet their phylogeny differs significantly. C. jejuni is scattered into several lineages, with no apparent linkage, whereas C. coli clusters into three distinct phylogenetic groups (clades) of which clade 1 has shown extensive genome-wide introgression with C. jejuni, yet the other two clades (2 and 3) have less than 2% of C. jejuni ancestry. We characterized a C. coli strain (76339) with four novel multilocus sequence type alleles (ST-5088) and having the capability to express gamma-glutamyltranspeptidase (GGT); an accessory feature in C. jejuni. Our aim was to further characterize unintrogressed C. coli clades 2 and 3, using comparative genomics and with additional genome sequences available, to investigate the impact of horizontal gene transfer in shaping the accessory and core gene pools in unintrogressed C. coli.
  
  
  RESULTS
  Here, we present the first fully closed C. coli clade 3 genome (76339). The phylogenomic analysis of strain 76339, revealed that it belonged to clade 3 of unintrogressed C. coli. A more extensive respiratory metabolism among unintrogressed C. coli strains was found compared to introgressed C. coli (clade 1). We also identified other genes, such as serine proteases and an active sialyltransferase in the lipooligosaccharide locus, not present in C. coli clade 1 and we further propose a unique scenario for the evolution of Campylobacter ggt.
  
  
  CONCLUSIONS
  We propose new insights into the evolution of the accessory genome of C. coli clade 3 and C. jejuni. Also, in silico analysis of the gene content revealed that C. coli clades 2 and 3 have genes associated with infection, suggesting they are a potent human pathogen, and may currently be underreported in human infections due to niche separation.
authors: Department of Food Hygiene and Environmental Health, Helsinki University, Helsinki, Finland. astrid.dehaan@helsinki.fi.
authors: Caroline P A
authors: CP
authors: Skarp-de Haan
authors: Alejandra
authors: A
authors: Culebro
authors: Thomas
authors: T
authors: Schott
authors: Joana
authors: J
authors: Revez
authors: Elke K H
authors: EK
authors: Schweda
authors: Marja-Liisa
authors: ML
authors: Hänninen
authors: Mirko
authors: M
authors: Rossi
mesh_terms: D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D001499:Bayes Theorem; D017000:Campylobacter coli / Q000145:classification* / Q000235:genetics*; D016123:Campylobacter jejuni / Q000145:classification / Q000235:genetics; D016680:Genome, Bacterial; D010802:Phylogeny; D012799:Sialyltransferases / Q000145:classification / Q000235:genetics / Q000378:metabolism; D005723:gamma-Glutamyltransferase / Q000145:classification / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D005723:gamma-Glutamyltransferase; D012799:Sialyltransferases