Culture-independent Sequence-based Approaches for Diagnostics and Food Safety Testing
Susan R. Leonard and Christopher A. Elkins
from: Pathogenic Escherichia coli: Evolution, Omics, Detection and Control (Edited by: Pina M. Fratamico, Yanhong Liu and Christopher H. Sommers). Caister Academic Press, U.K. (2018) Pages: 185-206.
Technological advances in genome sequencing have been leveraged to determine microbial compositions of sample matrices without culturing for individual bacterial species. Such metagenomics approaches have only recently been effectively utilized in pathogenic Escherichia coli research. This chapter provides an overview of current metagenomics research and applications, bioinformatic analysis tools, and considerations for detection sensitivity as it relates to E. coli pathogens in diagnostics and food safety testing. By bioinformatically mining the metagenomic dataset, E. coli serotype, virulence determinants, and antimicrobial susceptibility can be determined. Strain-level discrimination is complex and may be complicated by indigenous E. coli strains in the sample microbiota. Nevertheless, the application of metagenomics has the potential benefit of rapid diagnosis or characterisation of a contaminating E. coli pathogen in food products. This would be particularly valuable for epidemiological efforts and source attribution during outbreak investigations. Furthermore, as the entire microbial community and relative abundances are defined, the effect of perturbations in the microbial community on the growth or survival of E. coli pathogens can be elucidated. Bioinformatic analysis tools yielding reliably accurate results presented with a straightforward interpretation will enhance the practicality of metagenomics as a surveillance method in the future read more ...