Low density macro-array targeting non-LEE effectors (nle genes) and main virulence factors of Shiga toxin-encoding Escherichia coli (STEC) as a new approach for the molecular risk assessment of STEC isolates

Rapid and specific detection of Shiga toxin-producing Escherichia coli (STEC) strains with high virulence for human has become a priority for public health authorities. This study reports on the development of a low density macro-array for simultaneously testing the genes stx1, stx2, eae, ehxA, and six different nle genes issued from genomic islands OI#122 (ent, nleB, nleE) and OI#71 (nleF, nleH1-2, nleA). Various strains of E. coli isolated from the environment, food, animals and healthy children have been compared with clinical isolates of various seropathotypes. The eae gene was detected in all enteropathogenic E. coli (EPEC) strains as well as in enterohaemorrhagic E. coli (EHEC) strains, excepted in EHEC O91:H21 and EHEC O113:H21. The gene ehxA was more prevalent (90%) in EHEC than in STEC (42.66%) strains in which it was unequally distributed. The nle genes were detected only in some EPEC and EHEC strains but with various distributions, showing that nle are either strain and/or serotype specific, probably reflecting adaptation of the strains to different host or environmental niche. One characteristic nle gene distribution in EHEC O157:[H7], O111:[H8], O26:[H11], O103:H25, O118:[H16], O121:[H19], O112:H19, O5:HNM, O55:H7, O123:H11, O172:H25 and O165:H25 was [ent/espL2, nleB, nleE, nleF, nleH1-2, nleA]. A second nle pattern [ent/espL2, nleB, nleE, nleH1-2] was characteristic of EHEC O103:H2, O145:[H28], O45:H2 and O15:H2. The presence of eae, ent/espL2, nleB, nleE, and nleH1-2 genes is a clear signature of STEC strains with high virulence for humans.