Real-Time PCR for Quantitative Analysis of Human Commensal Escherichia coli Populations Reveals a High Frequency of Subdominant Phylogroups

Abstract

e Escherichia coli is divided into four main phylogenetic groups, which each exhibit ecological specialization. To understand the population structure of E. coli in its primary habitat, we directly assessed the relative proportions of these phylogroups from the stools of 100 healthy human subjects using a new real-time PCR method, which allows a large number of samples to be studied. The detection threshold for our technique was 0.1% of the E. coli population, i.e., 10 5 CFU/g of feces; in other methods based on individual colony analysis, the threshold is 10%. One, two, three, or four phylogenetic groups were simultaneously found in 21%, 48%, 21%, and 8% of the subjects, respectively. Phylogroups present at a threshold of less than 10% of the population were found in 40% of the subjects, revealing high within-individual diversity. Phylogroups A and B2 were detected in 74% and 70% of the subjects, respectively; phylogroups B1 and D were detected in 36% and 32%, respectively. When phylogroup B2 was dominant, it tended not to cooccur with other phylogroups. In contrast, other phylogroups were present when phylogroup A was dominant. These data indicate a complex pattern of interactions between the members of a single species within the human gut and identify a reservoir of clones that are present at a low frequency. The presence of these minor clones could explain the fluctuation in the composition of the E. coli microbiota within single individuals that may be seen over time. They could also constitute reservoirs of virulent and/or resistant strains. Escherichia coli is the most common commensal aerobic bacterium in the human gut microbiota (1); it is also the Gramnegative bacillus most frequently implicated in human extraintestinal infections (2). This apparent paradox, which characterizes opportunistic pathogens, is classically associated with host deficiencies (for example, as a result of immune-compromising illness, surgery, or catheterization). However, there are still questions concerning the role of the intrinsic properties of the parasite and the conditions that may cause commensal intestinal E. coli strains to become extraintestinal pathogens.Four main phylogenetic groups named A, B1, B2, and D have been distinguished among E. coli strains (3, 4), and distribution within these groups appears to correlate with the origin of the strains. Phylogroup B2 has been shown to include extraintestinal virulent strains (extraintestinal pathogenic E. coli [ExPEC]), which express numerous virulence factors (5, 6), whereas phylogroups A and B1 contain mostly human and animal commensal strains, respectively (7,8,9). However, more recently, an increase in B2 phylogroup strains was observed in human commensal strains originating from industrialized countries (10,11,12,13).Little is known about the diversity, transmission, and persistence of E. coli commensal strains within human populations (1). An individual can be colonized by more than one distinct strain at any given time (14,15,16). However, the few available studies ...

Escherichia coli Population Structure and Antibiotic Resistance at a Buffalo/Cattle Interface in Southern Africa

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“…Then, one yellow colony was randomly picked and confirmed by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analysis (MALDI Biotyper Microflex; Bruker) to belong to E. coli/Escherichia clade species. This colony was considered to represent the dominant E. coli/Escherichia clade clone as it has been recently shown (33,34). The strain was tested for antibiotic susceptibility, phylotyped, and stored at Ϫ80°C.…”

VIM‐1 carbapenemase‐producing Escherichia coli in gulls from southern France

“…The association between some phylogroups and antimicrobial resistance patterns is for now poorly understood. Nevertheless, several studies have already highlighted that phylogroup A E. coli are over‐represented within resistant strains isolated in France (Smati et al., 2013), including chromosomal AmpC β‐lactamase overproducers carried by humans (Corvec et al., 2007) as well as ESBL E. coli detected in cattle (Valat et al., 2012) and ampicillin‐resistant isolates from pigs (Bibbal, Dupouy, Prère, Toutain, & Bousquet‐Mélou, 2009). Further studies are still needed to determine if E. coli belonging to phylogroup A are more likely to acquire antimicrobial resistances and why.…”

Prospective Cohort Study of the Relative Abundance of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli in the Gut of Patients Admitted to Hospitals

“…The ESBL RA was calculated as the ratio of the ESBL E. coli counts divided by the total E. coli number, expressed as a percentage. E. coli clones were considered dominant if they represented 50% or more of the E. coli population (11).…”