USDA Agricultural Research Service,
Eastern Regional Research Center (ARS-ERRC)
Wyndmoor, PA 19038 USA
Application of genomic technologies for characterization, typing, and detection of E. coli
Serotyping using polyclonal antibodies raised in rabbits has been the gold standard for classification of E. coli based on the O- (somatic) and H- (flagellar) antigens; however, problems associated with serotyping are that the procedure is time consuming and labor intensive, cross reactions among different serogroups often occurs, many strains are non-typeable, among other issues. Thus, various approaches for molecular determination of O- and H-antigens, for characterization of E. coli to determine the pathotype, and for subtyping are being developed. DNA sequencing of specific regions or whole genomes of E. coli is providing information on the evolution and virulence of E. coli and is facilitating the development of molecular methods for typing and detection. Certain O-serogroups of Shiga toxin-producing E. coli (STEC), including O26, O45, O103, O111, O121, O145, and O157 cause the majority of severe STEC infections in humans, and DNA sequence information has been used to develop PCR-based methods targeting specific virulence genes and O-group-specific sequences to detect these pathogens. These methods are being employed by regulatory agencies to test for the presence of these STEC in food. STEC are zoonotic pathogens, and cattle and other animals, including swine are reservoirs for STEC belonging to various serotypes. In the U.S. and other countries, pigs have been found to harbor STEC, including strains that can potentially cause human illness, at prevalence rates similar to those reported in cattle, and pork has been linked to outbreaks caused by STEC. However, there is a paucity of studies evaluating the risk of zoonotic transmission of swine STEC. A descriptive longitudinal study was conducted to investigate the fecal shedding of STEC in finishing swine and to characterize the isolates that were recovered by determining their serotypes and the presence of a number of virulence genes. The findings provided insights into the epidemiology of fecal STEC shedding in finishing swine. In 2011, whole genome sequencing facilitated the investigation of an outbreak caused by enteroaggregative hemorrhagic E. coli (EAHEC) O104:H4 in Europe and provided information for an evolutionary model for the emergence of the outbreak strain. PCR-based methods targeting O-group-specific and virulence genes carried by STEC O104 and EAHEC O104 strains were developed to detect these pathogens in food. In a subsequent study, whole genome sequencing and comparative genomics of E. coli O104 strains showed that genetic variation among the strains was due to the presence of plasmids, prophages, and genomic island regions. Whole genome sequencing and the use of genetic-based methods can by utilized to discern among E. coli pathotypes and genotypes and will increase the understanding of pathways for the emergence of new strains with human illness causing potential.