Escherichia coli Genome sequencing and assembly

Current outbreak investigation routines typically involve whole genome sequencing (WGS) of clinical isolates by public health laboratories, making it possible for partner agencies (e.g., food inspection laboratories) to rapidly acquire WGS data which may offer important clues about the particular characteristics of the causative organism to aid in its detection in food samples.For example, it may be possible to determine a priori the presence of antibiotic resistance markers and strain-specific DNA sequences enabling the application of customized selective recovery and identification methods (e.g., polymerase chain reaction) enhancing their detection against a background of non-target bacteria.