ABSTRACT
Escherichia coli is overrepresented in all bloodstream infections (BSIs) series, mostly associated with a few clonal lineages. Its population structure has been analyzed but the dynamics remains to be fully understood. We analyze the dynamics of E. coli-BSIs in a sample of 649 isolates, representing all 7165 E. coli BSI episodes recorded in a tertiary hospital (1996-2016) according to clonal identification (phylogenetic groups/subgroups, STc131 subclades), antibiotic susceptibility (13 antibiotics), and virulence-associated genes (VAGs, 29 genes). Patient data were obtained from the laboratory system and clinical charts. The incidence of BSI-EC doubled from 1996 to 2016 (5.5 to 10.8 BSI episodes/1000 hospitalizations). Intertwined waves of community-acquired (CA) and hospital-acquired isolates (HA) episodes of both B2 and non-B2 phylogroups, occurred until B2 overtook non-B2 BSI episodes. ST131 contributed to increasing the B2 rates, but only transiently altered the population structure. B2 isolates predominates (53%), overrepresented by subgroups B2-I (STc131), B2-II, B2-IX, and B2-VI (25%, 25%, 14%, and 9%). We observed a remarkable increase only for B2-I-STc131 (C1/C2 subclades), a decreasing trend for phylogroup D, and oscillations for other B2 subgroups throughout the years. According to VAG patterns, B2 strains exhibit a population structure compatible with the niche specialization theory. A reservoir of B2 and non-B2 strains represented in human microbiota, flows from the community to the hospital and vice-versa, where they can either be selected or coexist. The increase of BSI is determined by waves of CA that predate the amplification of HA episodes of both B2 and non-B2 phylogroups in various time periods, influenced by FQR and microbiota composition.
IMPORTANCE The gut microbiota is an important reservoir for bacteria that cause extraintestinal infections including sepsis, which is the third cause of mortality in Western countries and one of the Global Health threads recognized by the WHO since 2017. Most of the bloodstream infections (BSI) and UTIs due to Escherichia coli strains originate in the gut microbiota and belong to the phylogenetic group B2. Most B2 strains recovered from BSI infections are clonal lineages predominant in fecal isolates, often associated with outbreaks. Our study analyzes the long-term dynamics of B2 E. coli subtypes and reveals waves of different E.coli lineages including pandemic clones that emerge periodically and are established in the intestinal microbiota afterward. It also reflects that clonal amplifications in the community predates the clonal increases in hospitals which may favor the acquisition of antibiotic resistance in health centers and further dissemination of well adapted clones that become multidrug resistant.
Competing Interest Statement
The authors have declared no competing interest.
