Genomics and pathotypes of the many faces of Escherichia coli

• Published in: FEMS microbiology reviews Vol. 46; no. 6; pp. 1 - 30
• Main Authors: Geurtsen, Jeroen, de Been, Mark, Weerdenburg, Eveline, Zomer, Aldert, McNally, Alan, Poolman, Jan
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-11-2022
• Subjects: Antibiotic resistance; Commensalism; Drug resistance in microorganisms; E coli; Escherichia coli; Escherichia coli - genetics; Escherichia coli Infections - microbiology; Escherichia coli Proteins - genetics; Extraintestinal Pathogenic Escherichia coli - genetics; Gastrointestinal diseases; Genes; Genomes; Genomics; Humans; Microorganisms; Phylogeny; Population biology; Population structure; Streamlining; Vaccine development; Virulence; Virulence (Microbiology); Virulence Factors - genetics; United Kingdom; Netherlands; Japan; bacterial species; pathotypes; accessory genome, antibiotic resistance; population dynamics; virulence factors; Escherichia coli pathotypes
• ISSN: 1574-6976; 0168-6445; 1574-6976
• DOI: 10.1093/femsre/fuac031

Abstract
Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli’s infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.
A schematic characterization of the disease manifestations, genomic flexibility, population dynamics, and vaccine targets of Escherichia coli, a multi-faceted bacterium with pathogenic potential throughout the entire species.