Extensive gene diversity in septicemic Escherichia coli strains

Abstract

Extraintestinal pathogenic Escherichia coli strains (ExPEC) are the cause of a diverse spectrum of invasive infections in humans and animals, and these infections often lead to septicemia. Strains of serogroups O2 and O78 of E. coli are involved in human urinary tract infections and newborn meningitis and also constitute the major serotypes involved in avian colisepticemia. In the present study we compared the unique genomic sequences of two such septicemic strains, strains O2-1772 and O78-9, obtained by suppression subtractive hybridization. Evaluation of the degree of similarity between these two strains, which cause the same disease, revealed a high degree of diversity, with only a few shared genes. Subsequently, additional strains of each serogroup of human and animal origin were screened by PCR, and the results provided further evidence for the existence of a high degree of genome plasticity. These results were unexpected, in view of data showing that the two O157:H7 strains that have been sequenced are nearly identical in terms of virulence factors. Furthermore, the data obtained for the septicemic strains suggest that each step in the infection can be mediated by a number of alternative virulence factors, indicating the existence of a mix-and-match combinatorial system. Although whole-genome comparisons of E. coli strains causing different diseases have shown great differences in gene contents, we show that such differences exist even within strains that cause the same disease and that target the same host tissues. Moreover, in addition to the high level of genome plasticity, we show that the large pool of virulence genes in the septicemic strains is independent of the host, implying a high degree of zoonotic risk.

FIG. 1.

Breakdown of the specific sequences of each library into categories according to their homologies.

FIG. 2.

Results of PCRs of specific sequences, performed with 14 septicemic strains and nonpathogenic strain K-12. Lanes 1 to 16, 1-kb DNA marker, O2-1772, O2-YN, O2-MAN, O2-SA, O2-U33, O2-B18, O2-BEN, O78-9, O78-285, O78-286, O78-287, O78-6, O78-7, O78-63-1, and K-12, respectively. (a) Multiplex PCR with primers specific for the sequences of O2-210, O2-334, O78-18, and O78-55; (b) PCR with primers specific for the putative autotransporter (O78-95 sequence).