Analysis of persistent and antibiotic resistant commensal Escherichia coli from healthy adults

Abstract

Human commensal strains can infect anatomical sites outside the colon, particularly the urinary tract. This is further complicated by the fact many commensal E. coli are resistant to antibiotics. It was hypothesized that strains which can persist in the human colon for a long time, are more likely than others, to share the properties of E. coli that cause extraintestinal infections. Thirteen persistent strains were found, and the group II capsule [kpsMT II] and the yersiniabactin receptor [fyuA] correlated well with strain persistence. Nine of the 13 strains belonged to ST95, ST69, ST405 or ST131, the clones that are often found in UTI and other non-intestinal infections. In contrast, a group of 36 strains found here that were not detected in multiple samples included only 12 with kpsMT II and 14 with fyuA, and a single ST95 and one ST131 strain. The 73 strains and few additional commensal strains were characterised for their resistance to 11 antibiotics and 46 resistant strains were found. Seven of the persistent strains were resistant to at least one antibiotic, showing that resistant strains can persist in the absence of antibiotic selection. One of the resistant strains was found to carry a 6.8 kb plasmid that had a dfrA14 gene cassette, which confers resistance to trimethoprim, in the strA streptomycin resistance gene. This plasmid, named pCERC1, was completely sequenced and its replication region was identified. A large plasmid carrying a large resistance island that contained a class 1 integron, appeared to be present in 3 ST69 strains that were found here. Variants of this island were present in 2 further ST69. Hence, plasmids appeared to be the main agent in the dissemination of antibiotic resistance genes amongst the commensal strains. The resemblance shared between persistent strains and those that cause extraintesintal infections indicated that persistent strains, which are successful commensals, are the subset of commensal strains that are most likely to cause non-intestinal infections. Moreover, the acquisition and accumulation of resistance genes by persistent strains could explain the emergence of multiply antibiotic resistant clones like ST131 and ST69.