Distribution, Functional Expression, and Genetic Organization of Cif, a Phage-Encoded Type III-Secreted Effector from Enteropathogenic and EnterohemorrhagicEscherichia coli

EnteropathogenicEscherichia coli(EPEC) and enterohemorrhagicE. coli(EHEC) inject effector proteins into host cells via a type III secretion system encoded by the locus of enterocyte effacement (LEE). One of these effectors is Cif, encoded outside the LEE by a lambdoid prophage. In this study, we demonstrated that the Cif-encoding prophage of EPEC strain E22 is inducible and produces infectious phage particles. We investigated the distribution and functional expression of Cif in 5,049E. colistrains of human, animal, and environmental origins. A total of 115E. coliisolates from diverse origins and geographic locations carriedcif. The presence ofcifwas tightly associated with the LEE, since all thecif-positive isolates were positive for the LEE. These results suggested that the Cif-encoding prophages have been widely disseminated within the natural population ofE. colibut positively selected within the population of LEE-positive strains. Nonetheless, 66% ofcif-positiveE. colistrains did not induce a typical Cif-related phenotype in eukaryotic cells due to frameshift mutations or insertion of an IS element in thecifgene. The passenger region of the prophages carryingcifwas highly variable and showed various combinations of IS elements and genes coding for other effectors such asnleB,nleC,nleH,nleG,espJ, andnleA/espI(some of which were also truncated). This diversity and the presence of nonfunctional effectors should be taken into account to assess EPEC and EHEC pathogenicity and tropism.