Large-Scale Population Structure of Human Commensal Escherichia coli Isolates

Abstract

The study of several Escherichia coli intestinal commensal isolates per individual in 265 healthy human subjects belonging to seven populations distributed worldwide showed that the E. coli population is highly structured, with major differences between the tropical and temperate populations.Escherichia coli is a commensal inhabitant of the intestinal tracts of healthy humans and many animal species, but it can also cause a wide range of diseases, ranging from diarrhea to extraintestinal infections (8). As it has been proposed that pathogenic E. coli strains are derived from commensal strains by the acquisition of chromosomal or extrachromosomal virulence operons (19), identifying the factors that shape the genetic structure of commensal strains might help us understand the emergence of virulence. E. coli can be considered to have a clonal genetic structure with a low level of recombination (7, 10). Four main phylogenetic groups, A, B1, B2, and D, constitute the bulk of the species (15). A few authors have examined commensal strains from humans (3-5, 13) using population genetics molecular tools (for a pioneer review, see reference 14). A significant locale-specific distribution among groups A, B1, B2, and D has been observed in human commensal strains in three geographically distinct human populations (French, Croatian, and Malian) (9).To gain insight into the composition of the E. coli human commensal microbiota, we characterized the relative abundance of E. coli phylogenetic groups in a large collection of 1,740 isolates from 265 subjects belonging to seven populations spread over three continents and compared the results to those of previous studies using the same approach.Bacterial isolates. Isolates were collected between 1999 and 2001 from seven human populations composed of healthy adult subjects of both sexes from 15 to 65 years of age, except when otherwise stated. The populations were the following: (i) 27 subjects living in the Paris area (mainland France, Europe), (ii) 21 university students living in Brest (Brittany, mainland France), (iii) 25 bank and insurance workers (BIW) living in seven distinct areas of Brittany (mainland France), (iv) 25 pig farmers (PF) living in the same seven areas as the BIW, (v) 93 ethnically homogeneous Wayampi Amerindians living in three villages of southern French Guyana (South America) with no modern sanitary or hygienic facilities, (vi) 46 women living in Cotonou (Benin, Africa), and (vii) 28 subjects living in Bogotá (Colombia, South America). The individuals in the BIW and PF populations in Brittany were matched for county of residence, age (20 to 60 years), and sex (13 men and 12 women). A subset of 25 Amerindians was also matched for age and sex with the BIW and PF populations. These matched populations had neither been hospitalized nor had taken antibiotics for at least 1 month before stool sampling. In all, 1,740 E. coli isolates were obtained after plating fresh fecal samples on Drigalski agar, with 5 or 10 randomly chosen E. coli isolates per individual.The...

Phylogenetic Grouping of Dominant Fecal Escherichia coli Isolates from Healthy Males and Females in Al-Kut/Wasit Province/Iraq

“…Gender distribution of phylogroups showed insignificant differences between females and males. Similar results were obtained by others [25,26] who found that sex and age factors had no effect on distribution of phylogroups. Whereas Gordon et al [27] found that in males the probability of isolating A or D strains increased with host age, whilst the probability of detecting a group B2 strain declined, while in females the probability of recovering A or B2 strains increased with increasing host age and there was a concomitant decline in the likelihood of isolating B1 or D strains.…”

Phylo-typing of clinicalEscherichia coliisolates originating from bovine mastitis and canine pyometra and urinary tract infection by means of quadruplex PCR

“…Besides this, assignment of the subgroups (A 0 , A 1 , B1, B2 2 , B2 3 , D 1 and D 2 ) in triplex PCR was evaluated according to Escobar-Paramo et al (2004b).…”

Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells

“…coli is primarily a commensal inhabitant of the mammalian colon, colonizing the gut early after birth and remaining resident throughout the life of the host, but commensal strains differ in their colonization efficiency. E. coli strains belonging to phylogenetic group B2 seem to have a superior capacity to colonize and persist in the colonic microbiota (3), and during the last decade the incidence of B2 strains has risen quickly in colonic microflora of human beings living in high-income countries (2). Surveys have shown that the pks island is present in up to 34% of commensal isolates of phylogenetic group B2 from healthy individuals (4)(5)(6).…”