title: Comparative Analysis of Phylogenetic Assignment of Human and Avian ExPEC and Fecal CommensalEscherichia coliUsing the (Previous and Revised) Clermont Phylogenetic Typing Methods and its Impact on Avian PathogenicEscherichia coli(APEC) Classification.
abstract: The Clermont scheme has been used for subtyping ofEscherichia colisince it was initially described in early 2000. Since then, researchers have used the scheme to type and sub-type commensalE. coliand pathogenicE. coli, such as extraintestinal pathogenicE. coli(ExPEC), and compare their phylogenetic assignment by pathogenicity, serogroup, distribution among ExPEC of different host species and complement of virulence and resistance traits. Here, we compare assignments of human and avian ExPEC and commensalE. coliusing the old and revised Clermont schemes to determine if the new scheme provides a refined snapshot of isolate classification. 1,996E. colifrom human hosts and poultry, including 84 human neonatal meningitisE. coliisolates, 88 human vaginalE. coli, 696 human uropathogenicE. coli, 197 healthy human fecalE. coli, 452 avian pathogenicE. coli(APEC), 200 retail poultryE. coli, 80 crop and gizzardE. colifrom healthy poultry at slaughter and 199 fecalE. colifrom healthy birds at slaughter. All isolates were subject to phylogenetic analysis using the Clermont et al. (2000, 2013) schemes and compared to determine the effect of the new classification on strain designation. Most of the isolates' strain designation remained where they were originally assigned. Greatest designation change occurred in APEC where 53.8% of isolates were reclassified; while classification rates among human strains ranged from 8 to 14%. However, some significant changes were observed for UPEC associated strains with significant (P< 0.05) designation changes observed from A to C and D to E or F phylogenetic types; a similar designation change was noted among NMEC for D to F designation change. Among the APEC significant designation changes were observed from A to C and D to E and F. These studies suggest that the new scheme provides a tighter and more meaningful definition of some ExPEC; while the new typing scheme has a significant impact on APEC classification. A comparison of phylogenetic group assignment by content of virulence, resistance, replicon and pathogenicity island genes in APEC suggests that insertion of pathogenicity islands into the genome appears to correlate closely with revised phylogenetic assignment.
authors.affiliation: Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames IA, USA.
authors.forename: Catherine M
authors.initials: CM
authors.lastname: Logue
authors.affiliation: Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames IA, USA.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Wannemuehler
authors.affiliation: Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames IA, USA.
authors.forename: Bryon A
authors.initials: BA
authors.lastname: Nicholson
authors.affiliation: Department of Statistics, North Dakota State University, Fargo ND, USA.
authors.forename: Curt
authors.initials: C
authors.lastname: Doetkott
authors.affiliation: Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames IA, USA.
authors.forename: Nicolle L
authors.initials: NL
authors.lastname: Barbieri
authors.affiliation: Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames IA, USA.
authors.forename: Lisa K
authors.initials: LK
authors.lastname: Nolan
keywords: Escherichia coli; avian pathogenic E. coli (APEC); classification; extraintestinal pathogenic E. coli (ExPEC); phylogenetic typing