Predominance of phylogenetic group B2 among commensal Escherichia coli in humans from Kandy District, Sri Lanka

Escherichia coli is a commensal bacterial gut inhabitant in vertebrates, while some strains are pathogens. Analysis of the genetic substructure within E. coli has identified nine phylogenetic groups within the species, as group A, B1, B2, C, D, E, F, G and cryptic clade I. These groups vary in attributes such as host characteristics, pathogenicity, antibiotic sensitivity patterns and virulence profiles. The current study was conducted to determine the distribution of phylogenetic groups, commonly encountered sequence types (ST), and group B2 subgroups (SG) of human faecal E. coli in a sample population in the Kandy District, Sri Lanka. A total of 158 faecal swabs, collected from healthy individuals, were cultured on MacConkey agar and presumptive E. coli isolates were confirmed by a negative reaction on Simmons citrate agar. E. coli isolates were characterized according to their phylogenetic group, SG, and ST distribution by a series of PCR protocols. Results revealed a predominance of group B2 (28 %), followed by B1 (23 %), A (17 %), D (14 %), C (5 %), F (4 %), and E (3 %). Within phylogroup B2, SG III was predominant while ST 73, 95, and 131 were detected at low frequencies. ST 69 accounted for 20 % of the group D isolates. Distribution of phylogroups was independent of host gender except group D, which was significantly over-represented by males. As B2 E. coli are strongly associated with extraintestinal infections and a high degree of virulence, characterization of these human faecal E. coli isolates for antibiotic susceptibility and virulence profiles would be of clinical importance.