Molecular Typing Methods for Analysis of Extraintestinal PathogenicEscherichia coli

Abstract

Escherichia coli, although perhaps best known as a cause of diarrheal disease, is actually responsible for more morbidity, mortality, and increased health care costs in the developed world as an extraintestinal pathogen. Two main categories of typing methods are relevant for studies involving extraintestinal pathogenic E. coli (ExPEC), including methods that define the strain’s phylogenetic and clonal background (at varying levels of resolution) and those that detect virulence-associated accessory traits. Alternative methods for resolving phylogenetic relationships at the clonal group level that are simpler and cheaper than multilocus sequence typing (MLST) include PCR-based genomic profiling methods, e.g., random amplified polymorphic DNA (RAPD) analysis and repetitive-element (REP) PCR, as performed using the ERIC, BOX, or REP primers. Methods for molecular typing of ExPEC find application in various kinds of studies, including between-population comparisons, assessments of individual isolates for their virulence potential or clonal similarity to other individual isolates, and assessments of colonization and transmission dynamics. The approaches used for statistical analysis of molecular typing data are an important consideration in population level studies involving ExPEC. Molecular typing of ExPEC for phylogenetic and clonal background, as well as accessory traits (e.g., virulence factors) can lead to important new insights into the origins, reservoirs, clinical and commensal behavior, and host group associations of this important group of E. coli. Attention to study design, population selection, specific molecular methods, and appropriate statistical analysis approaches can enhance the quality of typing studies involving ExPEC, which may lead to improvements in human or animal health.