title: Integrated whole-genome sequencing and temporospatial analysis of a continuing Group A Streptococcus epidemic.
abstract: Analysis of microbial epidemics has been revolutionized by whole-genome sequencing. We recently sequenced the genomes of 601 type emm59 Group A Streptococcus (GAS) organisms responsible for an ongoing epidemic of invasive infections in Canada and some of the United States. The epidemic has been caused by the emergence of a genetically distinct, hypervirulent clone that has genetically diversified. The ease of obtaining genomic data contrasts with the relatively difficult task of translating them into insightful epidemiological information. Here, we sequenced the genomes of 90 additional invasive Canadian emm59 GAS organisms, including 80 isolated recently in 2010-2011. We used an improved bioinformatics pipeline designed to rapidly process and analyze whole-genome data and integrate strain metadata. We discovered that emm59 GAS organisms are undergoing continued multiclonal evolutionary expansion. Previously identified geographic patterns of strain dissemination are being diluted as mixing of subclones over time and space occurs. Our integrated data analysis strategy permits prompt and accurate mapping of the dissemination of bacterial organisms in an epidemic wave, permitting rapid generation of hypotheses that inform public health and virulence studies.
authors.affiliation: Department of Pathology and Genomic Medicine, The Methodist Hospital, and Center for Molecular and Translational Human Infectious Disease Research, The Methodist Hospital Research Institute , Houston, TX 77030, USA.
authors.forename: Nahuel
authors.initials: N
authors.lastname: Fittipaldi
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Alberta, and Provincial Laboratory for Public Health (Microbiology) , Edmonton, Alberta T6G 2J2, Canada.
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Tyrrell
authors.affiliation: Department of Laboratory Medicine and Pathobiology, University of Toronto and Department of Microbiology, Mount Sinai Hospital , Toronto, Ontario M5G 1X5, Canada.
authors.forename: Donald E
authors.initials: DE
authors.lastname: Low
authors.affiliation: National Microbiology Laboratory, Public Health Agency of Canada , Winnipeg, Manitoba R3E 3R2, Canada.
authors.forename: Irene
authors.initials: I
authors.lastname: Martin
authors.affiliation: cBio Inc. , Fremont, CA 94536, USA.
authors.forename: David
authors.initials: D
authors.lastname: Lin
authors.affiliation: cBio Inc. , Fremont, CA 94536, USA.
authors.forename: Kumar L
authors.initials: KL
authors.lastname: Hari
authors.affiliation: Department of Pathology and Genomic Medicine, The Methodist Hospital, and Center for Molecular and Translational Human Infectious Disease Research, The Methodist Hospital Research Institute , Houston, TX 77030, USA.
authors.forename: James M
authors.initials: JM
authors.lastname: Musser
keywords: Canada; United States; bacterial epidemics; group A Streptococcus; invasive disease; whole-genome sequencing