Characterization of intestinal cnf1+ Escherichia coli from weaned pigs

Detection of Cyclomodulin CNF-1 Toxin-Producing Strains of Escherichia coli in Pig Kidneys at a Slaughterhouse

Food is often contaminated with Escherichia coli (E. coli) bacteria strains, which have been associated with different diseases, including urinary tract infections. The consumption of meat by humans is a potential route of transmission of antimicrobial resistance, and food-producing animals have been associated as a major reservoir of resistant bacterial strains. The aim of this study was to determine the presence of the E. coli strains producing the CNF-1 toxin in pig kidneys. Pig kidneys were collected from a Mexican slaughterhouse and classified according to their coloration into reddish kidneys (RK) and yellowish kidneys (YK). A tissue sample from each kidney was processed for histological analysis, the presence of E. coli was determined by conventional PCR assay, and the CNF-1 toxin was detected by both conventional PCR and Western blotting. Herein, an inflammatory cell infiltrate was found in all collected kidneys, regardless of macroscopic differences. Surprisingly, E. coli and the CNF-1 toxin were detected in all kidney samples. We clearly demonstrate contamination by CNF-1 toxin-producing E. coli in pork kidneys from a slaughterhouse, even in those without apparent damage. This suggests that pork may serve as a reservoir for pathogens, representing an important risk to human health.

In Vitro Effect on Piglet Gut Microbiota and In Vivo Assessment of Newly Isolated Bacteriophages against F18 Enterotoxigenic Escherichia coli (ETEC)

Enterotoxigenic Escherichia coli (ETEC) causing post-weaning diarrhea (PWD) in piglets have a detrimental impact on animal health and economy in pig production. ETEC strains can adhere to the host's small intestinal epithelial cells using fimbriae such as F4 and F18. Phage therapy could represent an interesting alternative to antimicrobial resistance against ETEC infections. In this study, four bacteriophages, named vB_EcoS_ULIM2, vB_EcoM_ULIM3, vB_EcoM_ULIM8 and vB_EcoM_ULIM9, were isolated against an O8:F18 E. coli strain (A-I-210) and selected based on their host range. These phages were characterized in vitro, showing a lytic activity over a pH (4-10) and temperature (25-45 °C) range. According to genomic analysis, these bacteriophages belong to the Caudoviricetes class. No gene related to lysogeny was identified. The in vivo Galleria mellonella larvae model suggested the therapeutic potential of one selected phage, vB_EcoS_ULIM2, with a statistically significant increase in survival compared to non-treated larvae. To assess the effect of this phage on the piglet gut microbiota, vB_EcoS_ULIM2 was inoculated in a static model simulating the piglet intestinal microbial ecosystem for 72 h. This study shows that this phage replicates efficiently both in vitro and in vivo in a Galleria mellonella model and reveals the safety of the phage-based treatment on the piglet microbiota.

Prevalence of Virulence Genes and Antimicrobial Resistances in E. coli Associated with Neonatal Diarrhea, Postweaning Diarrhea, and Edema Disease in Pigs from Austria

Increasing numbers of multi-resistant Escherichia (E.) coli from clinical specimens emphasize the importance of monitoring of their resistance profiles for proper treatment. Furthermore, knowledge on the presence of virulence associated genes in E. coli isolates from European swine stocks is scarce. Consequently, a total of 694 E. coli isolated between 2016 and 2018 from diarrheic piglets of Austrian swine herds were investigated. The isolates were tested for their susceptibility to twelve antibiotics using agar disk diffusion test and for the presence of 22 virulence associated genes via PCR. Overall, 71.9, 67.7, and 49.5% of all isolates were resistant to ampicillin, tetracycline, and trimethoprim-sulfamethoxazole, while resistance levels to gentamicin and fosfomycin were 7.7 and 2.0%, respectively. Resistance frequency to ciprofloxacin was higher than in previous studies. Isolates were more likely to be resistant to ampicillin if they were also resistant to ciprofloxacin. No isolate was resistant to meropenem or amikacin. Virulence genes were detected more frequently in isolates expressing hemolytic activity on blood agar plates. The detection rate of faeG was increased in fimH negative isolates. We assume, that hemolytic activity and absence of fimH could be considered as potential indicators for the virulence of E. coli in piglets.

Genotoxic Escherichia coli Strains Encoding Colibactin, Cytolethal Distending Toxin, and Cytotoxic Necrotizing Factor in Laboratory Rats

Although many Escherichia coli strains are considered commensals in mammals, strains encoding the cyclomodulin genotoxins are associated with clinical and subclinical disease in the urogenital and gastrointestinal tracts, meningitis, and inflammatory disorders. These genotoxins include the polyketide synthase (pks) pathogenicity island, cytolethal distending toxin (cdt), and hemolysin-associated cytotoxic necrotizing factor (cnf). E. coli strains are not excluded from rodents housed under SPF conditions in academic or vendor facilities. This study isolated and characterized genotoxin-encoding E. coli from laboratory rats obtained from 4 academic institutions and 3 vendors. A total of 69 distinct E. coli isolates were cultured from feces, rectal swab, nares, or vaginal swab of 52 rats and characterized biochemically. PCR analysis for cyclomodulin genes and phylogroup was performed on all 69 isolates. Of the 69 isolates, 45 (65%) were positive for pks, 20/69 (29%) were positive for cdt, and 4 (6%) were positive for cnf. Colibactin was the sole genotoxin identified in 21 of 45 pks+ isolates (47%), whereas cdt or cnf was also present in the remaining 24 isolates (53%); cdt and cnf were never present together or without pks. All genotoxin-associated strains were members of pathogen-associated phylogroup B2. Fisher exact and χ² tests demonstrated significant differences in genotoxin prevalence and API code distribution with regard to vendor. Select E. coli isolates were characterized by HeLa cell in vitro cytotoxicity assays, serotyped, and whole-genome sequenced. All isolates encoding cyclomodulins induced megalocytosis. Serotypes corresponded with vendor origin and cyclomodulin composition, with the cnf+ serotype representing a known human uropathogen. Whole-genome sequencing confirmed the presence of complete pks, cdt, and hemolysin-cnf pathogenicity islands. These findings indicate that genotoxin-encoding E. coli colonize laboratory rats from multiple commercial vendors and academic institutions and suggest the potential to contribute to clinical disease and introduce confounding variables into experimental rat models.

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

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 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.

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.

Biology and Diseases of Swine

Swine are used in biomedical research as models for biomedical research and for teaching. This chapter covers normative biology and behavior along with common and emerging swine diseases. Xenotransplantation is discussed along with similarities and differences of swine immunology.

Characterization of cytotoxic necrotizing factor 1-producing Escherichia coli strains from faeces of healthy macaques

Twenty-five (27 %) of 92 clinically normal macaques were found to have beta-haemolytic Escherichia coli isolated from their faeces. Five of six isolates chosen for further characterization had multiple antibiotic resistance and were PCR-positive for cytotoxic necrotizing factor 1 (cnf1) with a demonstrated cytopathic effect in vitro. By repetitive element sequence-based PCR genotyping, genetic similarity was established for selected isolates. We believe this to be the first report of E. coli strains producing CNF1 in non-human primates.

Predominance of afr2 and ral fimbrial genes related to those encoding the K88 and CS31A fimbrial adhesins in enteropathogenic Escherichia coli isolates from rabbits with postweaning diarrhea in Central Europe

PCR tests designed in these studies identified three rabbit adhesive factor genes among 43 enteropathogenic E. coli (EPEC) strains: afr1 (2 strains), the F4(K88)/CS31A-related afr2 (10 strains), and ral (15 strains). Several EPEC strains (i.e., O153:H7 and O157:H2) lacked these genes but did adhere to HeLa cells and produced attaching and effacing lesions in rabbits.

Chapter 8 Adhesins and receptors for colonization by different pathotypes of Escherichia coli in calves and young pigs

This chapter provides an overview of the virulence factors and their genetic regulators in Escherichia coli. The most important adhesins and their receptors playing a role in the pathogenesis of different pathotypes of enteric E. coli are also described. The main pathotypes involved in enteric colibacillosis of pigs and calves are the enterotoxigenic E. coli (ETEC), verotoxigenic E. coli (VTEC), enteropathogenic E. coli (EPEC), and necrotoxigenic E. coli (NTEC). Adhesion and colonization are the first (but not the only) functional prerequisites for a mucosal bacterium to be pathogenic. The adhesins represent surface proteins, governed by specific operons and constructed in ways according to the particular adhesin. Besides their structure, the adhesins can also be grouped according to their receptors present on the intestinal mucosal epithelium and on the urinary epithelium. Apart from direct practical applications, there are further significant scientific developments and applications expected in the area of neonatal biology and comparative human pathobacteriology.

The molecular basis of infectious diseases: pathogenicity islands and other mobile genetic elements. A review

Bacterial genomes generally consist of stable regions termed core genome, and variable regions that form the so-called flexible gene pool. The flexible part is composed of bacteriophages, plasmids, transposons as well as unstable large regions that have been termed genomic islands. Genomic islands encoding virulence factors of pathogenic bacteria have been designated "pathogenicity islands". Pathogenicity islands were first discovered in uropathogenic Escherichia coli and presently more than 30 bacterial species carrying pathogenicity islands have been described. This review summarises the current knowledge on bacterial genomic islands and their general features, and discusses their putative role in the evolution of microbes in the light of genomics of pathogenic bacteria.

Production of cytolethal distending toxins by pathogenic Escherichia coli strains isolated from human and animal sources: establishment of the existence of a new cdt variant (Type IV)

Three types of cytolethal distending toxin (CDT), namely, CDT-I, CDT-II, and CDT-III, have been described in Escherichia coli. Using primers designed for the detection of sequences common to the cdtB genes, we analyzed by PCR a set of 21 CDT-producing E. coli strains of intestinal and extraintestinal origins isolated from human and different animal species in several European countries and in the United States. On the basis of the existing differences in the cdtB genes, cdt-I-, cdt-II-, and cdt-III-specific primer pairs were designed and used for cdt typing. These new primers successfully differentiated all of the previously described cdt genes. Six strains proved to be cdt-I; eight strains proved to be cdt-III. However, none of the type I-, II-, and III-specific primers generated amplicons from six CDT(+) strains, suggesting the existence of a new cdt variant. Sequence analysis of the amplicons from two untypeable genes confirmed the existence of a new cdt variant that we called cdt-IV. Using the new specific primers, cdt-IV was detected in human, porcine, and poultry strains of intestinal and extraintestinal origins. To validate all sets of cdt specific primers, a group of 353 human E. coli strains isolated in Hungary was then investigated for the presence of cdt genes. This included 190 strains isolated from patients with urinary tract infections (UTI), 51 strains isolated from other (nonurinary) extraintestinal infections, and 112 intestinal strains isolated from healthy individuals. Of 190 UTI strains, 15 (7.9%) had cdt genes. Of 51 non-UTI extraintestinal strains 3 (5.9%) contained the cdt gene, and 1 (0.9%) of 112 healthy intestinal strains was PCR positive. Five strains proved to be cdt-I, and fourteen strains proved to be cdt-IV. The CDT-producing extraintestinal strains belonged to a wide variety of serogroups, including O2, O6, O75, and O170. In conclusion, we have developed a new PCR typing system for CDT able to detect a new CDT variant present in pathogenic E. coli strains obtained from animals and humans.

Prevalence and identity of cdt-related sequences in necrotoxigenic Escherichia coli

The cytolethal distending toxins (CDT) are responsible for the mitosis block at G2/M and the cycle arrest of cells in culture. Escherichia coli isolated from humans and animals with intestinal and extra-intestinal diseases can be positive for the production of a CDT-like cytopathic effect or for the presence of cdt-related genes. The purpose of this study was to compare the prevalence and the identity of cdt-related sequences in necrotoxigenic E. coli (NTEC). A collection of 98 bovine type 2 NTEC (NTEC2) and 45 bovine, 20 canine, 3 feline, 65 human and 129 porcine type 1 NTEC (NTEC1) isolates was studied by colony hybridisation and PCR assays specific for the cdtB genes encoding the B sub-unit of the CDT-I, CDT-II, CDT-III and CDT-IV toxins produced by E. coli. cdtB-III sequences were frequent amongst bovine NTEC2, since 83% of these isolates were positive by colony hybridisation and/or PCR, whereas cdtB-related sequences were rare amongst NTEC1, since only 2 bovine (4%), 3 canine (15%), 10 human (15%) and 13 porcine (10%) of these isolates were positive. The 28 probe-positive NTEC1 harboured cdtB-IV sequences (13 isolates), cdtB-I sequences (10 isolates), or still unidentified cdt-related sequences (5 isolates). After comparison with previously published and unpublished results of phenotypic assay on cell cultures, existence of other cdt-related sequences is suggested amongst NTEC1. The differences between NTEC1 and NTEC2 in their CDT profiles may have implication for the pathogenesis of those two classes of pathogenic E. coli.

Investigation of putative CDT gene in Escherichia coli isolates from pigs with diarrhea

In this study, 98 Escherichia coli isolates from 42 diarrheic neonatal piglets were screened for the presence of cytolethal distending toxin coding gene by polymerase chain reaction (PCR). PCR yielded a single product which was specifically generated for E. coli cdt(+) control strain and not for other control strains. Twenty two (22.4%) of the isolates tested were cdtB positive, and 50% of the cdtB(+) isolates were also estII positive. The most prevalent pathotype was O32 cdtB(+) estII(+), which accounted for 59% of the cdtB positive strains. These results indicate an association between the presence of the cdtB gene and diarrhea, and support the need for further studies to determine the role of this toxin in diarrhea.