A 21-year survey ofEscherichia colifrom bloodstream infections (BSIs) in a tertiary hospital reveals how community-hospital dynamics of the B2 phylogroup clones influence local BSI rates
Authors: Rodríguez Irene , Figueiredo Ana Sofia , Sousa Melissa , Aracil-Gisbert Sonia , Fernández de Bobadilla Miguel Díez , Lanza Val F. , Rodríguez Concepción , Zamora Javier , Loza Elena , Mingo Patricia , Brooks Claire J. , Cantón Rafael , Baquero Fernando , Coque Teresa M 
Published: April 2020

This is a longitudinal study comprising 649Escherichia coli(EC) isolates representing all 7165 EC-BSI episodes recorded in a hospital (1996-2016). Strains analysis included clonal identification (phylogenetic groups/subgroups, STc131 subclades, PFGE, and WGS), antibiotic susceptibility (13 antibiotics), and virulence-associated genes (VAGs, 29 genes). The incidence of BSI-EC increased from 1996 to 2016 (5.5 to 10.8 BSI episodes/1000 hospitalizations, average 7-8/1000). B2 isolates predominate (53%), subgroups B2-I (STc131), B2-II, B2-IX, and B2-VI representing 25%, 25%, 14%, and 9%, respectively. Intertwined waves of community-acquired (CA) + healthcare-associated and community-onset healthcare-associated (HCA), and hospital-acquired (HA) episodes of both B2 and non-B2 phylogroups occurred. A remarkable increase was only observed for B2-I-STc131 (C1/C2 subclades), with oscillations for other B2 subgroups and phylogroups throughout the years. Epidemic and persistent clones (comprising isolates with highly similar/identical-PFGE types and genomes differing in 18-97 SNPs) of B2-I (STc131), B2-II (STc73), B2-III (STc127), B2-IX (STc95), and B2-VI (STc12) were recovered from different patients, most at hospital admission, for long periods (2-17 years), ESBL producers or resistance to ciprofloxacin in B2 isolates were almost restricted to B2-I (STc131) subclade C. STc131 contributed to increasing the B2 rates but only transiently altered the EC-population structure.

The increase of EC-BSI was determined by waves of CA+HCA-BSI episodes that predate the waves of HA-BSI. Besides the risk of hospital transmission that led to temporal increases in BSIs, this study suggests that EC-populations/clones from community-based healthy individuals may occasionally have an epidemic structure and provide a source of transmissible strains influencing the HA-BSIs incidence.

IMPORTANCE

Sepsis is the third cause of mortality in Western countries and one of the Global Health threads recognized by the WHO since 2017. DespiteEscherichia coliconstitutes the most common cause of bloodstream infections (BSI), its epidemiology is not fully understood, in part due to the scarcity of local and longitudinal studies. Our work analyzes the long-term dynamics ofE. colicausing bacteremia in a single institution and reveals waves of different clonal lineages that emerge periodically and successfully spread afterward in both the community and hospitals. Because the origin of BSI-E. coliinfections is the gut, the microbiota of healthy individuals might occasionally have an epidemic structure, providing a source ofE. colistrains to influence the incidence of hospital BSIs. The study complements previous fractionated observations focusing on specificE. colilineages or antibiotic-resistant isolates in the last decades and helps to understand the epidemiology ofE. coliBSIs and the dynamics of pandemic clones.