title: Whole genome multilocus sequence typing as an epidemiologic tool for Yersinia pestis.
abstract: Human plague is a severe and often fatal zoonotic disease caused by Yersinia pestis. For public health investigations of human cases, nonintensive whole genome molecular typing tools, capable of defining epidemiologic relationships, are advantageous. Whole genome multilocus sequence typing (wgMLST) is a recently developed methodology that simplifies genomic analyses by transforming millions of base pairs of sequence into character data for each gene. We sequenced 13 US Y. pestis isolates with known epidemiologic relationships. Sequences were assembled de novo, and multilocus sequence typing alleles were assigned by comparison against 3979 open reading frames from the reference strain CO92. Allele-based cluster analysis accurately grouped the 13 isolates, as well as 9 publicly available Y. pestis isolates, by their epidemiologic relationships. Our findings indicate wgMLST is a simplified, sensitive, and scalable tool for epidemiologic analysis of Y. pestis strains.
authors.affiliation: Division of Vector-Borne Diseases, Bacterial Diseases Branch, Centers for Disease Control and Prevention, Fort Collins, CO 80523.
authors.forename: Luke C
authors.initials: LC
authors.lastname: Kingry
authors.affiliation: Division of Scientific Resources, Biotechnology Core Facility Branch, Centers for Disease Prevention and Control, Atlanta, GA 30329.
authors.forename: Lori A
authors.initials: LA
authors.lastname: Rowe
authors.affiliation: Division of Vector-Borne Diseases, Bacterial Diseases Branch, Centers for Disease Control and Prevention, Fort Collins, CO 80523.
authors.forename: Laurel B
authors.initials: LB
authors.lastname: Respicio-Kingry
authors.affiliation: Division of Vector-Borne Diseases, Bacterial Diseases Branch, Centers for Disease Control and Prevention, Fort Collins, CO 80523.
authors.forename: Charles B
authors.initials: CB
authors.lastname: Beard
authors.affiliation: Division of Vector-Borne Diseases, Bacterial Diseases Branch, Centers for Disease Control and Prevention, Fort Collins, CO 80523.
authors.forename: Martin E
authors.initials: ME
authors.lastname: Schriefer
authors.affiliation: Division of Vector-Borne Diseases, Bacterial Diseases Branch, Centers for Disease Control and Prevention, Fort Collins, CO 80523. Electronic address: nzp0@cdc.gov.
authors.forename: Jeannine M
authors.initials: JM
authors.lastname: Petersen
mesh_terms: D000818:Animals; D016680:Genome, Bacterial; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods; D058885:Multilocus Sequence Typing / Q000379:methods*; D010930:Plague / Q000453:epidemiology* / Q000382:microbiology*; D014481:United States / Q000453:epidemiology; D015010:Yersinia pestis / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification
keywords: Molecular epidemiology; Plague; Whole genome sequencing; Yersinia pestis; wgMLST