title: Evaluation of two multi-locus sequence typing schemes for commensal Escherichia coli from dairy cattle in Washington State.
abstract: Multi-locus sequence typing (MLST) is a useful system for phylogenetic and epidemiological studies of multidrug-resistant Escherichiacoli. Most studies utilize a seven-locus MLST, but an alternate two-locus typing method (fumC and fimH; CH typing) has been proposed that may offer a similar degree of discrimination at lower cost. Herein, we compare CH typing to the standard seven-locus method for typing commensal E. coli isolates from dairy cattle. In addition, we evaluated alternative combinations of eight loci to identify combinations that maximize discrimination and congruence with standard seven-locus MLST among commensal E. coli while minimizing the cost. We also compared both methods when used for typing uropathogenic E. coli (UPEC). CH typing was less discriminatory for commensal E. coli than the standard seven-locus method (Simpson's Index of Diversity=0.933 [0.902-0.964] and 0.97 [0.96-0.979], respectively). Combining fimH with housekeeping gene loci improved discriminatory power for commensal E. coli from cattle but resulted in poor congruence with MLST. We found that a four-locus typing method including the housekeeping genes adk, purA, gyrB and recA could be used to minimize cost without sacrificing discriminatory power or congruence with Achtman seven-locus MLST when typing commensal E. coli.
authors.affiliation: Paul G. Allen School for Global Animal Health, WSU, Pullman, WA, USA.
authors.forename: Sara
authors.initials: S
authors.lastname: Ahmed
authors.affiliation: Veterinary Microbiology and Pathology, College of Veterinary Medicine, WSU, Pullman, WA, USA.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Besser
authors.affiliation: Paul G. Allen School for Global Animal Health, WSU, Pullman, WA, USA.
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Call
authors.affiliation: Seattle Children's Research Institute, Seattle, WA, USA.
authors.forename: Scott J
authors.initials: SJ
authors.lastname: Weissman
authors.affiliation: Paul G. Allen School for Global Animal Health, WSU, Pullman, WA, USA.
authors.forename: Lisa P
authors.initials: LP
authors.lastname: Jones
authors.affiliation: Paul G. Allen School for Global Animal Health, WSU, Pullman, WA, USA. Electronic address: madavis@vetmed.wsu.edu.
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Davis
mesh_terms: D000818:Animals; D002417:Cattle / Q000382:microbiology*; D002418:Cattle Diseases / Q000175:diagnosis / Q000382:microbiology*; D004926:Escherichia coli / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D004927:Escherichia coli Infections / Q000175:diagnosis / Q000382:microbiology / Q000662:veterinary*; D029968:Escherichia coli Proteins / Q000235:genetics; D036781:Fimbriae Proteins / Q000235:genetics; D058885:Multilocus Sequence Typing / Q000379:methods*; D014861:Washington
chemical_list: D029968:Escherichia coli Proteins; D036781:Fimbriae Proteins
keywords: CH typing; E. coli; Housekeeping genes; MLST; fimH