Whole genome sequencing (WGS) of bacterial isolates is a powerful tool for advancing characterization of pathogens, as well as bolstering outbreak detection. As the repertoire of available equipment and reagents to achieve this goal expands or are replaced, it is imperative for laboratories to continuously compare current methods to alternate options. 

This webinar compares the extraction and library preparation protocols currently employed by the Colorado Department of Public Health and Environment (CDPHE) to sequence enteric bacterial pathogens for the PulseNet surveillance laboratory network using the EZ1 Advanced XL and Illumina DNA Library Prep Kit, with extraction on the newly available EZ2 Connect platform and library preparation using the QIASeq FX DNA Prep Kit.

The results of these comparisons present the pros and cons to each extraction and library preparation option based on key quality metrics described in the methods. They also assess the compatibility of the alternative approaches described in this evaluation to the current protocol used at CDPHE for sequencing of PulseNet organisms.

Enterohemorrhagic Escherichia coli (EHEC) are strains of E. coli that can cause severe infections in humans with symptoms ranging from bloody diarrhea to hemolytic uremic syndrome (HUS), kidney failure, and, in some cases, death. The Shiga toxin (stx) and intimin (eae) genes are the two key virulence factors that determine the severity of the infection. 

In addition to E. coli O157:H7, the most common EHEC serotype, other E. coli serogroups can also harbor stx and eae, and cause infections of equal severity. Federal agencies worldwide mandate EHEC testing for a wide range of food products, such as red meat and fresh produce for other EHEC serogroups, including O26, O45, O103, O111, O121, and O145. Therefore, it is critically important to develop one innovative and robust EHEC diagnostic method that can be used for detecting all EHEC strains spread across a large number of E. coli serogroups. 

This webinar will present data on the validation of dPCR Microbial DNA Detection Assay (QIAGEN) for characterizing E. coli strains and to develop a dPCR assay for detecting a broad range of EHEC strains.