Real-time PCR vs NGS for serotyping and characterizing E. coli isolates
Results from a recent survey sponsored by groups from the USDA, Penn State and ThermoFisher showed there was strong interest in the use of molecular methods for serotyping as well as extended genetic characterization of E. coli. Responders to the survey (N=59) indicated PCR and next-generation sequencing (NGS) were the top 2 methods of choice for performing molecular tests. A number of PCR approaches have been published for identifying specific E. coli serotypes. More serogroups can be identified within a single reaction using real-time arrays such as the TaqMan® Low Density Array (TLDA) and OpenArray® Real-Time PCR platforms. NGS can be used for whole genome sequencing (WGS) or targeted sequencing (e.g. Ion AmpliSeq™). Ion AmpliSeq technology allows users to sequence specific amplicons thereby allowing for higher throughput than WGS. More samples can be run together on a single run and the workflow is simplified compared to WGS. Gene targets could be identified for E. coli O-typing, and other targets could be used for additional information such strain ID (e.g. MLST), detecting virulence genes and drug resistance genes. There are tradeoffs between platforms and the technology used must be balanced for ease of use, cost, and depth of information.