BackgroundMany 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.ResultsIn 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 B21. 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.ConclusionsOur 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 materialThe online version of this article (10.1186/s13099-017-0220-y) contains supplementary material, which is available to authorized users.

BackgroundThe genus Helicobacter are gram-negative, microaerobic, flagellated, mucus-inhabiting bacteria associated with gastrointestinal inflammation and classified as gastric or enterohepatic Helicobacter species (EHS) according to host species and colonization niche. While there are over 30 official species, little is known about the physiology and pathogenic mechanisms of EHS, which account for most in the genus, as well as what genetic factors differentiate gastric versus EHS, given they inhabit different hosts and colonization niches. The objective of this study was to perform a whole-genus comparative analysis of over 100 gastric versus EHS genomes in order to identify genetic determinants that distinguish these Helicobacter species and provide insights about their evolution/adaptation to different hosts, colonization niches, and mechanisms of virulence.ResultsWhole-genome phylogeny organized Helicobacter species according to their presumed gastric or EHS classification. Analysis of orthologs revealed substantial heterogeneity in physiological and virulence-related genes between gastric and EHS genomes. Metabolic reconstruction predicted that unlike gastric species, EHS appear asaccharolytic and dependent on amino/organic acids to fuel metabolism. Additionally, gastric species lack de novo biosynthetic pathways for several amino acids and purines found in EHS and instead rely on environmental uptake/salvage pathways. Comparison of virulence factor genes between gastric and EHS genomes identified overlapping yet distinct profiles and included canonical cytotoxins, outer membrane proteins, secretion systems, and survival factors.ConclusionsThe major differences in predicted metabolic function suggest gastric species and EHS may have evolved for survival in the nutrient-rich stomach versus the nutrient-devoid environments, respectively. Contrasting virulence factor gene profiles indicate gastric species and EHS may utilize different pathogenic mechanisms to chronically infect hosts and cause inflammation and tissue damage. The findings from this study provide new insights into the genetic differences underlying gastric versus EHS and support the need for future experimental studies to characterize these pathogens.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5171-2) contains supplementary material, which is available to authorized users.

Escherichia coli is a gram-negative bacillus that colonizes the gastrointestinal tract of humans and animals. 46 Although some strains are considered commensals, various intestinal and extraintestinal pathogenic E. coli pathotypes are associated with a wide range of clinical disease states in the host; 16,41 these strains are responsible for the deaths of more than 2 million humans annually. 65 Specific pathotypes often harbor similar virulence factors and correspond to distinct clinical and histologic lesions. Intestinal pathotypes include enteropathogenic E. coli, enterohemorrhagic E. coli, enteroinvasive E. coli, enterotoxigenic E. coli, enteroaggregative E. coli, diffusely adhering E. coli, and adherent-invasive E. coli. 65 Extraintestinal pathotypes include uropathogenic E. coli and neonatal meningitis E. coli, both of which have an enhanced ability to translocate through the intestinal epithelium and cause severe clinical disease.E. coli strains typically are classified into 1 of the 4 major phylogenetic groups: A, B1, B2, and D. 10,14,60 Groups B2 and D are often associated with pathogenicity, whereas fecal strains belonging to groups A and B1 generally lack virulence factors. 22,60 Strains belonging to pathogroup B2 have been isolated from the feces of persons from developed countries with increasing frequency. 52,70 These pathogenic strains encode various combinations of virulence genes and pathogenicity islands which promote invasion and colonization, evasion of host defenses, and damage to host tissues. Associated virulence factors include cytotoxins such as genotoxic cyclomodulins, cytotoxic necrotizing factors (cnf), cytolethal distending toxin (cdt), and the genotoxin colibactin (pks). These virulence factors modulate host cellular differentiation, proliferation, and apoptosis and promote cytopathic effects. 7,21,69 CNF is a 115-kDa cyclomodulin protein that induces cell-cycle alterations and cytoskeletal changes by activating rho GTPases, which leads to a variety of aberrant phenotypic effects including micropinocytosis, megalocytosis, and multinucleation. 62 cnf1 is chromosomally encoded, 23 whereas cnf2 is plasmid-encoded. 20 cnf-producing E. coli are considered necrotoxigenic and are associated with intestinal, urinary, 23 and meningeal infection of humans. 41 cnf + E. coli have previously been isolated from clinically

C57BL/6 (B6) mice from Taconic Sciences (Tac) and the Jackson Laboratory (Jax) were infected with H. pylori PMSS1 (Hp) for 16 week; there was no significant difference in the gastric histologic activity index between Hp infected Tac and Jax B6. However, the degree of gastric mucous metaplasia and Th1-associated IgG2c levels in response to Hp infection were increased in Tac mice over Jax mice, whereas the colonization levels of gastric Hp were higher by 8-fold in Jax B6 compared with Tac B6. Additionally, mRNA expression of gastric Il-1β, Il-17A and RegIIIγ were significantly lower in the infected Tac compared to the infected Jax mice. There were significant differences in the microbial community structures in stomach, colon, and feces between Jax and Tac B6 females. Differences in gastric microbial communities between Jax and Tac B6 females are predicted to affect the metagenome. Moreover, Hp infection perturbed the microbial community structures in the stomach, colon and feces of Jax mice, but only altered the colonic microbial composition of Tac mice. Our data indicate that the GI microbiome of Tac B6 mice is compositionally distinct from Jax B6 mice, which likely resulted in different pathological, immunological, and microbial responses to Hp infection.

Escherichia coli strains have not been fully characterized in laboratory mice and are not currently excluded from mouse colonies. Colibactin (Clb), a cytotoxin, has been associated with inflammation and cancer in humans and animals. We performed bacterial cultures utilizing rectal swab, fecal, and extra intestinal samples from clinically unaffected or affected laboratory mice. Fifty-one E. coli were isolated from 45 laboratory mice, identified biochemically, and selected isolates were serotyped. The 16S rRNA gene was amplified and sequenced for specific isolates, PCR used for clbA and clbQ gene amplification, and phylogenetic group identification was performed on all 51 E. coli strains. Clb genes were sequenced and selected E. coli isolates were characterized using a HeLa cell cytotoxicity assay. Forty-five of the 51 E. coli isolates (88 %) encoded clbA and clbQ and belonged to phylogenetic group B2. Mouse E. coli serotypes included: O2:H6, O−:H−, OM:H+, and O22:H−. Clb-encoding O2:H6 mouse E. coli isolates were cytotoxic in vitro. A Clb-encoding E. coli was isolated from a clinically affected genetically modified mouse with cystic endometrial hyperplasia. Our findings suggest that Clb-encoding E. coli colonize laboratory mice and may induce clinical and subclinical diseases that may impact experimental mouse models.