Integrated whole-genome sequencing and temporospatial analysis of a continuing Group A Streptococcus epidemic

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.