Mark Eppinger

Genomics of Shiga toxin-producing Escherichia coli: Past, present and future

Application of next generation sequencing (NGS) technology for genomic epidemiology outbreak investigation, with its significantly higher throughput and lower cost, is revolutionizing response time and resolution power. Next generation sequencing, informatics and omics technologies permit rapid high-throughput sequencing and comprehensive phylogenomic analysis of large numbers of pathotypes, thus obviating the reliance on archetypical outbreak strains that may not be fully representative of the population of bacteria responsible for the outbreak. In the NGS era we have transitioned from targeted sequencing of prototype isolates or only few loci to sequencing the complete genomes of large numbers of biothreat agents in an effort to understand microbial population structures associated with human health. For this study we have investigated the genome-wide diversity and plasticity in 245 epidemiological diverse enterohemorrhagic Escherichia coli (EHEC) specimens and catalogued mutational and structural polymorphisms using hybrid sequencing, optical mapping and custom tailored whole genome sequence typing (WGST) approaches. While there is no gold standard, and the favored methodologies in achieving short- or long-term resolution power largely depend on the types of scientific enquiries and data sets being analyzed, use of single nucleotide polymorphism discovery allowed us to identify high-resolution phylogenetic markers in genetically highly homogenous EHECs. Identified polymorphic markers are readily available to develop powerful, standardized and automated subtyping tools to support timely and informed countermeasures, such as to detect and backtrack outbreaks to the contaminated source. Sequence-based methods provide the technological foundation for genomic epidemiology investigations to examine outbreaks in near real time and to survey for novel, emergent pathotypes following the concept of a digital immune system, and most importantly to assess the pathogenic potential of individual clones to predict risks associated with human infection.