Human Escherichia coli strains of different geographical and time source: bacteriocin types and their gene sequences are population-specific

Antimicrobial efficacy and prevalence of colicinogenic E. coli in faecal matter of human, cow and sheep

Colicinogenic Escherichia coli in the human or animal gut prevent pathogen accumulation, thereby protecting against severe gut infections. This ability of commensal human and animal E. coli to restrain Gram-negative pathogens was evaluated invitro. Approximately 13.2% of E. coli isolates inhibited the growth of target pathogens. The greatest inhibition of 36% was observed against E. coli O157:H7 followed by 35%, 27%, 24% and 13% inhibition against E. coli O26:H11, Pseudomonas aeruginosa, Salmonella enterica and Klebsiella pneumoniae, respectively. Detection of 20 colicin determinants in colicinogenic E. coli revealed that >50% isolates exhibited multiple colicin genes. Among all isolates, 70.4% of E. coli had the col E6 gene followed by col Ib (66.4%), E4 (53.6%), E7 (49.9%), J (35.3%) and M (35.2%) determinants. The frequency of col D (8.8%), Ia (27.9%), S4 (12%), E3 (13.2%) and E9 (2.9%) was greater in human samples compared with samples from cows and sheep, whereas col10 (5.8%) and E5 (4.4%) were produced only by cow-derived E. coli. Colicinogenic E. coli belonging to phylogenetic group B2 (52.8%) were more prevalent followed by D1 (16%), B1 (13.2%), A1 (11.6%) and A0 (5.8%). The 16S rRNA sequencing of all colicinogenic E. coli provided 27 non-clinical variants of E. coli that can be further explored for their probiotic properties to minimize risk of gut diseases.

Non-antibiotic antibacterial peptides and proteins of Escherichia coli: efficacy and potency of bacteriocins

INTRODUCTION

The emergence and spread of antibiotic resistance among pathogenic bacteria drives the search for alternative antimicrobial therapies. Bacteriocins represent a potential alternative to antibiotic treatment. In contrast to antibiotics, bacteriocins are peptides or proteins that have relatively narrow spectra of antibacterial activities and are produced by a wide range of bacterial species. Bacteriocins of Escherichia coli are historically classified as microcins and colicins, and, until now, more than 30 different bacteriocin types have been identified and characterized.

AREAS COVERED

We performed bibliographical searches of online databases to review the literature regarding bacteriocins produced by E. coli with respect to their occurrence, bacteriocin role in bacterial colonization and pathogenicity, and application of their antimicrobial effect.

EXPERT OPINION

The potential use of bacteriocins for applications in human and animal medicine and the food industry includes (i) the use of bacteriocin-producing probiotic strains, (ii) recombinant production in plants and application in food, and (iii) application of purified bacteriocins.

Antibacterial Activity of Bacteriocinogenic Commensal Escherichia coli against Zoonotic Strains Resistant and Sensitive to Antibiotics

Antibiotic resistance concerns various areas with high consumption of antibiotics, including husbandry. Resistant strains are transmitted to humans from livestock and agricultural products via the food chain and may pose a health risk. The commensal microbiota protects against the invasion of environmental strains by secretion of bacteriocins, among other mechanisms. The present study aims to characterize the bactericidal potential of bacteriocinogenic Escherichia coli from healthy humans against multidrug-resistant and antibiotic-sensitive strains from pigs and cattle. Bacteriocin production was tested by the double-layer plate method, and bacteriocin genes were identified by the PCR method. At least one bacteriocinogenic E. coli was detected in the fecal samples of 55% of tested individuals, adults and children. Among all isolates (n = 210), 37.1% were bacteriocinogenic and contained genes of colicin (Col) Ib, ColE1, microcin (Mcc) H47, ColIa, ColM, MccV, ColK, ColB, and single ColE2 and ColE7. Twenty-five E. coli carrying various sets of bacteriocin genes were further characterized and tested for their activity against zoonotic strains (n = 60). Strains with ColE7 (88%), ColE1-ColIa-ColK-MccH47 (85%), MccH47-MccV (85%), ColE1-ColIa-ColM (82%), ColE1 (75%), ColM (67%), and ColK (65%) were most active against zoonotic strains. Statistically significant differences in activity toward antibiotic-resistant strains were shown by commensal E. coli carrying MccV, ColK-MccV, and ColIb-ColK. The study demonstrates that bacteriocinogenic commensal E. coli exerts antagonistic activity against zoonotic strains and may constitute a defense line against multidrug-resistant strains.

Identifying geographic origins of the Escherichia coli isolates from food by a method based on single-nucleotide polymorphisms

BACKGROUND

E.coli is an important foodborne pathogen. Rapid and robust tracking of the source of E. coli is the key step to control foodborne infections.

RESULTS

In this study, a genotyping and tracing method based on highly discriminatory single nucleotide polymorphisms (SNPs) was developed to investigate the geographical origin of E. coli in food. A highly informative set of 12 SNPs was derived from 4 housekeeping genes in E. coli multilocus sequence typing (MLST) database. A collection of 253 E. coli isolates from food in 12 countries and regions were screened, resulting in a total of 61 profiles, 35 geographically specific SNP profiles were revealed and further verified by blind sample test. Also, the evolutionary relationship of 61 SNP profiles with different geographical origins was established by the enhanced analysis Based Upon Related Sequence Types (eBURST) analysis, which provided evidence that strains of different geographical origins owned the same ancestor strain.

CONCLUSIONS

Our study established a powerful method based on a set of 12 SNPs for identifying geographical origins. The blind sample analysis proved that this SNPs panel had a high traceability of E. coli in food. Furthermore, this method based on SNPs combined with eBURST analysis revealed the potential evolutionary relationship between E.coli strains of different geographical origins.

Molecular investigation of the colicinogenic Escherichia coli strains that are capable of inhibiting E. coli O157:H7 in vitro

Background

Escherichia coli O157:H7 is a highly virulent human pathogen with severe consequences following infection, which claims many lives worldwide. A suggested method for controlling this bacterium is the competitive elimination through using probiotic bacteria that prevent its colonization. Some nonpathogenic E. coli strains that produce antibacterial colicins are among these probiotic bacteria. We aimed to isolate and characterize the colicinogenic E. coli strains from diarrheic and healthy sheep that inhibit E. coli O157:H7, which could be used as possible probiotic sources. A total of 292 E. coli isolates (146 from each diarrheic and healthy sheep) were screened for the presence of colicin and virulence genes. The phylogenetic group/subgroup determination was performed by PCR. In vitro evaluation of inhibitory effect of colicinogenic isolates on E. coli O157:H7 was done phenotypically.

Results

The frequency of diarrhea associated colicinogenic E. coli isolates was significantly higher than those isolated from healthy sheep. An association between ETEC and the genes coding for colicin-V & colicin-Iab in diarrheic E. coli isolates was observed. Moreover, there was an association between ipaH and Colicin-V encoding genes. Furthermore, E. coli isolates showing bacteriocinogeny while possessing no virulence genes had a frequency of 97.67 and 11.94% in healthy and diarrheic isolates, respectively. Of these strains, five isolates (3.42%) from diarrheic and twenty-five isolates (17.12%) from healthy sheep inhibited O157:H7 strain. Additionally, colicin E1 and colicin Iab genes were more prevalent in B1 phylogroup.

Conclusions

These results signified that healthy sheep could be considered as a potential source for anti-O175:H7 bacterial isolates.

Escherichia coli isolates from patients with inflammatory bowel disease: ExPEC virulence- and colicin-determinants are more frequent compared to healthy controls

A set of 178 Escherichia coli isolates taken from patients with inflammatory bowel disease (IBD) was analyzed for bacteriocin production and tested for the prevalence of 30 bacteriocin and 22 virulence factor determinants. Additionally, E. coli phylogenetic groups were also determined. Pulsed-field gel electrophoresis (PFGE) was used for exclusion of clonal character of isolates. Results were compared to data from a previously published analysis of 1283 fecal commensal E. coli isolates. The frequency of bacteriocinogenic isolates (66.9%) was significantly higher in IBD E. coli compared to fecal commensal E. coli isolates (54.2%, p < 0.01). In the group of IBD E. coli isolates, a higher prevalence of determinants for group B colicins (i.e., colicins B, D, Ia, Ib, M, and 5/10) (p < 0.01), including a higher prevalence of the colicin B determinant (p < 0.01) was found. Virulence factor determinants encoding fimbriae (fimA, 91.0%; pap, 27.5%), cytotoxic necrotizing factor (cnf1, 11.2%), aerobactin synthesis (aer, 43.3%), and the locus associated with invasivity (ial, 9.0%) were more prevalent in IBD E. coli (p < 0.05 for all five determinants). E. coli isolates from IBD mucosal biopsies were more frequently bacteriocinogenic (84.6%, p < 0.01) compared to fecal IBD isolates and fecal commensal E. coli. PFGE analysis revealed clusters specific for IBD E. coli isolates (n = 11), for fecal isolates (n = 13), and clusters containing both IBD and fecal isolates (n = 10). ExPEC (Extraintestinal Pathogenic E. coli) virulence and colicin determinants appear to be important characteristics of IBD E. coli isolates, especially the E. coli isolates obtained directly from biopsy samples.

Characterization of four Escherichia albertii isolates collected from animals living in Antarctica and Patagonia

Escherichia albertii is a recently discovered species with a limited number of well characterized strains. The aim of this study was to characterize four of the E. albertii strains, which were among 41 identified Escherichia strains isolated from the feces of living animals on James Ross Island, Antarctica, and Isla Magdalena, Patagonia. Sequencing of 16S rDNA, automated ribotyping, and rep-PCR were used to identify the four E. albertii isolates. Phylogenetic analyses based on multi-locus sequence typing showed these isolates to be genetically most similar to the members of E. albertii phylogroup G3. These isolates encoded several virulence factors including those, which are characteristic of E. albertii (cytolethal distending toxin and intimin) as well as bacteriocin determinants that typically have a very low prevalence in E. coli strains (D, E7). Moreover, E. albertii protein extracts caused cell cycle arrest in human cell line A375, probably because of cytolethal distending toxin activity.

Microcin determinants are associated with B2 phylogroup of human fecal Escherichia coli isolates

Escherichia coli strains are classified into four main phylogenetic groups (A, B1, B2, and D) and strains of these phylogroups differ in a number of characteristics. This study tested whether human fecal E. coli isolates belonging to different phylogroups differ in prevalence of bacteriocinogenic isolates and prevalence of individual bacteriocinogenic determinants. A set of 1283 fecal E. coli isolates from patients with different diseases was tested for the presence of DNA regions allowing classification into E. coli phylogroups and for the ability to produce bacteriocins (23 colicins and 7 microcins). Of the isolates tested, the most common was phylogroup B2 (38.3%) followed by phylogroups A (28.3%), D (26.3%) and B1 (7.2%). Altogether, 695 bacteriocin producers were identified representing 54.2% of all tested isolates. The highest prevalence of bacteriocin producers was found in group B2 (60.3%) and the lowest in group B1 (44.6%). Determinants encoding colicins E1, Ia, and microcin mV were most common in phylogroup A, determinants encoding microcins mM and mH47 were most common in phylogroup B2, and determinant encoding mB17 was most common in phylogroup D. The highest prevalence of bacteriocinogeny was found in phylogroup B2, suggesting that bacteriocinogeny and especially the synthesis of microcins was associated with virulent and resident E. coli strains.

Determinants encoding fimbriae type 1 in fecal Escherichia coli are associated with increased frequency of bacteriocinogeny

Background

To screen whether E. coli strains encoding type 1 fimbriae, isolated from fecal microflora, produce bacteriocins more often relative to fimA-negative E. coli strains of similar origin.

Methods

PCR assays were used to detect presence of genes encoding 30 bacteriocin determinants (23 colicin- and 7 microcin-encoding genes) and 18 virulence determinants in 579 E. coli strains of human and animal origin isolated from hospitals and animal facilities in the Czech and Slovak Republic. E. coli strains were also classified into phylogroups (A, B1, B2 and D).

Results

fimA-negative E. coli strains (defined as those possessing none of the 18 tested virulence determinants) were compared to fimA-positive E. coli strains (possessing fimA as the only detected virulence determinant). Strains with identified bacteriocin genes were more commonly found among fimA-positive E. coli strains (35.6 %) compared to fimA-negative E. coli strains (21.9 %, p < 0.01) and this was true for both colicin and microcin determinants (p = 0.02 and p < 0.01, respectively). In addition, an increased number of strains encoding colicin E1 were found among fimA-positive E. coli strains (p < 0.01).

Conclusions

fimA-positive E. coli strains produced bacteriocins (colicins and microcins) more often compared to fimA-negative strains of similar origin. Since type 1 fimbriae of E. coli have been shown to mediate adhesion to epithelial host cells and help colonize the intestines, bacteriocin synthesis appears to be an additional feature of colonizing E. coli strains.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0530-5) contains supplementary material, which is available to authorized users.

Bacteriocin-encoding genes and ExPEC virulence determinants are associated in human fecal Escherichia coli strains

Background

A set of 1181 E. coli strains of human fecal origin isolated in the South Moravia region of the Czech Republic was collected during the years 2007–2010. Altogether, 17 virulence determinants and 31 bacteriocin-encoding genes were tested in each of them.

Results

The occurrence of bacteriocin-encoding genes was found to be positively correlated with the occurrence of E. coli virulence factors. Based on the presence of virulence factors and their combinations, E. coli strains were classified as non-pathogenic E. coli (n = 399), diarrhea-associated E. coli (n = 179) and ExPEC strains (n = 603). Non-pathogenic and diarrhea-associated E. coli strains had a low frequency of bacteriocinogeny (32.6% and 36.9%, respectively). ExPEC strains encoding S-fimbriae (sfa), P-fimbriae (pap) and having genes for aerobactin biosynthesis (aer, iucC), α-hemolysis (α-hly) and cytotoxic necrosis factor (cnf1) were often bacteriocinogenic (73.8%), had a high prevalence of bacteriocin multi-producers and showed a higher frequency of genes encoding microcins H47, M, V, B17 and colicins E1, Ia and S4.

Conclusions

The occurrence of bacteriocin-encoding genes and ExPEC virulence determinants correlate positively in E. coli strains of human fecal origin. Bacteriocin synthesis appears to modulate the ability of E. coli strains to reside in the human intestine and/or the virulence of the corresponding strains.