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Background  Many  Escherichia coli  strains are considered to be a component of the normal flora found in the human and animal intestinal tracts. While most  E. coli  strains are commensal, some strains encode virulence factors that enable the bacteria to cause intestinal and extra-intestinal clinically-relevant infections. Colibactin, encoded by a genomic island ( pks  island), and cytotoxic necrotizing factor (CNF), encoded by the  cnf  gene, are genotoxic and can modulate cellular differentiation, apoptosis and proliferation. Some commensal and pathogenic  pks + and  cnf +  E. coli  strains have been associated with inflammation and cancer in humans and animals.    Results  In the present study,  E. coli  strains encoding colibactin and CNF were identified in macaque samples. We performed bacterial cultures utilizing rectal swabs and extra-intestinal samples from clinically normal macaques. A total of 239  E. coli  strains were isolated from 266 macaques. The strains were identified biochemically and selected isolates were serotyped as O88:H4, O25:H4, O7:H7, OM:H14, and OM:H16. Specific PCR for  pks  and  cnf1  gene amplification, and phylogenetic group identification were performed on all  E. coli  strains. Among the 239 isolates, 41 (17.2%) were  pks + /cnf1 −, 19 (7.9%) were  pks −/ cnf1 +, and 31 (13.0%) were  pks +/ cnf1 +. One hundred forty-eight (61.9%)  E. coli  isolates were negative for both genes ( pks −/ cnf1 −). In total, 72 (30.1%) were positive for  pks  genes, and 50 (20.9%) were positive for  cnf1 . No  cnf2 + isolates were detected. Both  pks + and  cnf1 +  E. coli  strains belonged mainly to phylogenetic group B2, including B2 1 . Colibactin and CNF cytotoxic activities were observed using a HeLa cell cytotoxicity assay in representative isolates. Whole genome sequencing of 10 representative  E. coli  strains confirmed the presence of virulence factors and antibiotic resistance genes in rhesus macaque  E. coli  isolates.    Conclusions  Our findings indicate that colibactin- and CNF-encoding  E. coli  colonize laboratory macaques and can potentially cause clinical and subclinical diseases that impact macaque models.    Electronic supplementary material  The online version of this article (10.1186/s13099-017-0220-y) contains supplementary material, which is available to authorized users.

Cytotoxic Escherichia coli strains encoding colibactin and cytotoxic necrotizing factor (CNF) colonize laboratory macaques