Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

• Published in: Genome research Vol. 27; no. 8; pp. 1437 - 1449
• Main Authors: Kallonen, Teemu, Brodrick, Hayley J, Harris, Simon R, Corander, Jukka, Brown, Nicholas M, Martin, Veronique, Peacock, Sharon J, Parkhill, Julian
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01-08-2017
• Subjects: Anti-Bacterial Agents - pharmacology; Anti-Bacterial Agents - therapeutic use; Bacteremia - epidemiology; Bacteremia - microbiology; Drug Resistance, Multiple, Bacterial - genetics; England - epidemiology; Escherichia coli - genetics; Escherichia coli - pathogenicity; Escherichia coli Infections - epidemiology; Escherichia coli Infections - microbiology; Humans; Longitudinal Studies; Phylogeny; England
• ISSN: 1088-9051; 1549-5469; 1549-5469
• DOI: 10.1101/gr.216606.116

associated with urinary tract infections and bacteremia has been intensively investigated, including recent work focusing on the virulent, globally disseminated, multidrug-resistant lineage ST131. To contextualize ST131 within the broader
population associated with disease, we used genomics to analyze a systematic 11-yr hospital-based survey of
associated with bacteremia using isolates collected from across England by the British Society for Antimicrobial Chemotherapy and from the Cambridge University Hospitals NHS Foundation Trust. Population dynamics analysis of the most successful lineages identified the emergence of ST131 and ST69 and their establishment as two of the five most common lineages along with ST73, ST95, and ST12. The most frequently identified lineage was ST73. Compared to ST131, ST73 was susceptible to most antibiotics, indicating that multidrug resistance was not the dominant reason for prevalence of
lineages in this population
Temporal phylogenetic analysis of the emergence of ST69 and ST131 identified differences in the dynamics of emergence and showed that expansion of ST131 in this population was not driven by sequential emergence of increasingly resistant subclades. We showed that over time, the
population was only transiently disturbed by the introduction of new lineages before a new equilibrium was rapidly achieved. Together, these findings suggest that the frequency of
lineages in invasive disease is driven by negative frequency-dependent selection occurring outside of the hospital, most probably in the commensal niche, and that drug resistance is not a primary determinant of success in this niche.