Infectious Diseases and Internal Medicine,
Department of Medicine, University of Minnesota
1 Veterans Dr.
Minneapolis, MN 55417
Serotyping and other typing methods for studying extraintestinal pathogenic E. coli (ExPEC)
Diverse methods can be used for sub-specific typing of E. coli clinical and surveillance isolates. Such typing is relevant both for determining strain relatedness within a given sample set (for example, to detect transmission events or clonal prevalence trends) and for cross-referencing to external databases, which allows inferences regarding strain characteristics. Sub-specific typing is particularly relevant to studies of ExPEC, which cause most E. coli infections of the urinary tract and other extraintestinal sites in humans, other mammals, and poultry, and for which the main reservoir is the host's intestinal tract. Traditional serotypes, which involve various combinations of O, K, and H antigens or their molecular surrogates, correspond roughly with specific defined clonal lineages, as can be resolved more definitively by multilocus enzyme electrophoresis (MLEE), multilocus sequence typing (MLST), or whole-genome sequencing (WGS), and various short-cut surrogates. Certain such lineages have come to be recognized as "virulent clones" because of their over-representation among clinical (i.e., disease) isolates compared with fecal isolates, and/or their enhanced ability to cause disease in various experimental animal models. Different ExPEC lineages have variably distinctive and predictable epidemiological associations (e.g., with host group and clinical syndrome) and accessory trait content (e.g., for antimicrobial resistance and virulence genes). Which typing method or combination thereof is optimal for characterizing E. coli isolates depends on the context, study question, and available resources. This is a rapidly evolving area due to emerging technologies and progressively more refined understandings of the underlying evolutionary and biological relationships.