Evaluation of Repetitive Extragenic Palindromic-PCR for Discrimination of FecalEscherichia colifrom Humans, and Different Domestic- and Wild-Animals

Investigation on the temporal variation and source tracking of faecal bacteria in a forest dominated watershed (Comox Lake), British Columbia, Canada

AIMS

The aims of this study were to investigate the temporal variation in Escherichia coli density and its sources at the drinking water intake of Comox Lake for a period of 3 years (2011-2013).

METHODS AND RESULTS

Density of E. coli was assessed by standard membrane filtration method. Source tracking of E. coli were done by using BOX-A1R-based rep-PCR DNA fingerprinting method. Over the years, the mean E. coli density ranged from nondetectable to 9·8 CFU 100 ml(-1) . The density of E. coli in each of the years did not show any significant difference (P > 0·05); however, a comparatively higher density was observed during the fall. Wildlife was (64·28%, 153/238) identified as the major contributing source of E. coli, followed by human (18·06%, 43/238) and unknown sources (17·64%, 42/238). Although the sources were varied by year and season, over all, the predominant contributing sources were black bear, human, unknown, elk, horse and gull.

CONCLUSIONS

The findings of this investigation identified the multiple animal sources contributing faecal bacteria into the drinking water intake of Comox Lake and their varying temporal occurrence.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this study can reliably inform the authorities about the most vulnerable period (season) of faecal bacterial loading and their potential sources in the lake for improving risk assessment and pollution mitigation.

Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms

The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. However, recent advances have developed many useful techniques taking into account the house-keeping genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and 26S, 28S, β-tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques. In this review, certain aspects of the merits and limitations of different methods for molecular identification and systematics of microorganisms have been discussed. The major advantages of the polyphasic approach have also been described taking into account certain groups of bacteria as case studies to arrive at a consensus approach to microbial identification.

Use of Escherichia coli BOX-PCR fingerprints to identify sources of fecal contamination of water bodies in the State of São Paulo, Brazil

Repetitive element sequence-based polymerase chain reaction (rep-PCR) is one of the commonest methods used to identify sources of fecal contamination of water systems. In this work, BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) was used to discriminate Escherichia coli strains originating from different animals and water sources, and the suitability of the technique for bacterial source tracking (BST) was evaluated. A total of 214 strains from humans, 150 strains from animals, 55 strains from sewage and 77 strains from water bodies were analyzed by the BOX-PCR technique. When maximum similarity between the fingerprints was used, a correct classification rate of 84% was achieved for strains from human and animal sources. Furthermore, 95% of the strains found in sewage were classified as being from human sources by at least one of the four classification tools used. Classification of the strains found in water bodies in the State of São Paulo was based on the fingerprints obtained for human and animal sources. Most of the sampling sites appeared to be affected by mixed sources of fecal contamination. The use of BOX-PCR for BST could be especially valuable in developing countries, where simplicity and cost are important considerations.

Virulence factors and genetic variability of uropathogenic Escherichia coli isolated from dogs and cats in Italy

In this study, the association between virulence genotypes and phylogenetic groups among Escherichia (E.) coli isolates obtained from pet dogs and cats with cystitis was detected, and fingerprinting methods were used to explore the relationship among strains. Forty uropathogenic E. coli (UPEC) isolated from dogs (n = 30) and cats (n = 10) in Italy were analysed by polymerase chain reaction (PCR) for the presence of virulence factors and their classification into phylogenetic groups. The same strains were characterized by repetitive extragenic palindromic (REP)- and enterobacterial repetitive intergenic consensus (ERIC)-PCR techniques. We found a high number of virulence factors such as fimbriae A, S fimbriae (sfa) and cytotoxic necrotizing factor 1 (cnf1) significantly associated with phylogenetic group B2. We demonstrated a high correlation between α-hemolysin A and pyelonephritis C, sfa, and cnf1 operons, confirming the presence of pathogenicity islands in these strains. In addition, UPEC belonging to group B2 harboured a greater number of virulence factors than strains from phylogenetic groups A, B1, and D. REP- and ERIC-PCR grouped the UPEC isolates into two major clusters, the former grouping E. coli strains belonging to phylogenetic group B2 and D, the latter grouping those belonging to groups A and B1. Given the significant genetic variability among the UPEC strains found in our study, it can be hypothesized that no specific genotype is responsible for cystitis in cats or dogs.

Population structure of rumen Escherichia coli associated with subacute ruminal acidosis (SARA) in dairy cattle

Previous studies indicated that only subacute ruminal acidosis (SARA), induced by feeding a high-grain diet, is associated with an inflammatory response and increased abundance of Escherichia coli in the rumen. We hypothesized that ruminal E. coli in grain pellet-induced SARA carried virulence factors that potentially contribute to the immune activation during SARA. One hundred twenty-nine E. coli isolates were cultured from the rumens of 8 cows (4 animals per treatment) in which SARA had been nutritionally induced by feeding a high-grain diet (GPI-SARA) or a diet containing alfalfa pellets (API-SARA). The population structure of the E. coli was evaluated with the ABD genotyping system and repetitive sequence-based (rep)-PCR fingerprinting. Twenty-five virulence factors were evaluated with PCR. Escherichia coli numbers were higher in the GPI-SARA treatment than in the API-SARA treatment. The genetic structure of the E. coli was significantly different between SARA challenge models. Isolates from GPI-control (46%), API-control (70%), and API-SARA (53%) were closely related and fell into one cluster, whereas isolates from GPI-SARA (54%) grouped separately. The ABD typing indicated a shift from an A-type E. coli population to a B1-type population only due to GPI-SARA. Of the 25 virulence factors tested, curli fiber genes were highly associated with GPI. Curli fibers were first identified in E. coli mastitis isolates and are potent virulence factors that induce a range of immune responses. Results suggest that under low rumen pH conditions induced by a grain diet, there is a burst in the number of E. coli with virulence genes that can take advantage of these rumen conditions to trigger an inflammatory response.

Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination

BACKGROUND

Escherichia coli strains are commonly found in the gut microflora of warm-blooded animals. These strains can be assigned to one of the four main phylogenetic groups, A, B1, B2 and D, which can be divided into seven subgroups (A0, A1, B1, B22, B23, D1 and D2), according to the combination of the three genetic markers chuA, yjaA and DNA fragment TspE4.C2. Distinct studies have demonstrated that these phylo-groups differ in the presence of virulence factors, ecological niches and life-history. Therefore, the aim of this work was to analyze the distribution of these E. coli phylo-groups in 94 human strains, 13 chicken strains, 50 cow strains, 16 goat strains, 39 pig strains and 29 sheep strains and to verify the potential of this analysis to investigate the source of fecal contamination.

RESULTS

The results indicated that the distribution of phylogenetic groups, subgroups and genetic markers is non-random in the hosts analyzed. Strains from group B1 were present in all hosts analyzed but were more prevalent in cow, goat and sheep samples. Subgroup B23 was only found in human samples. The diversity and the similarity indexes have indicated a similarity between the E. coli population structure of human and pig samples and among cow, goat and sheep samples. Correspondence analysis using contingence tables of subgroups, groups and genetic markers frequencies allowed the visualization of the differences among animal samples and the identification of the animal source of an external validation set. The classifier tools Binary logistic regression and Partial least square--discriminant analysis, using the genetic markers profile of the strains, differentiated the herbivorous from the omnivorous strains, with an average error rate of 17%.

CONCLUSIONS

This is the first work, as far as we are aware, that identifies the major source of fecal contamination of a pool of strains instead of a unique strain. We concluded that the analysis of the E. coli population structure can be useful as a supplementary bacterial source tracking tool.

Isolation of faecal coliform bacteria from the American alligator (Alligator mississippiensis)

AIMS

To determine whether American alligators (Alligator mississippiensis) are an unrecognized poikilothermic source of faecal coliform and/or potential pathogenic bacteria in South Carolina's coastal waters.

METHODS AND RESULTS

Bacteria from the cloaca of American alligators, as well as bacteria from surface water samples from their aquatic habitat, were isolated and identified. The predominant enteric bacteria identified from alligator samples using biochemical tests included Aeromonas hydrophila, Citrobacter braakii, Edwardsiella tarda, Escherichia coli, Enterobacter cloacae, Plesiomonas shigelloides and putative Salmonella, and these were similar to bacteria isolated from the surface waters in which the alligators inhabited. Based on most-probable-number enumeration estimates from captive alligator faeces, faecal coliform bacteria numbered 8.0x10(9) g(-1) (wet weight) of alligator faecal material, a much higher concentration than many other documented endothermic animal sources.

CONCLUSIONS

A prevalence of enteric bacteria, both faecal coliforms and potential pathogens, was observed in American alligators. The high faecal coliform bacterial density of alligator faeces may suggest that alligators are a potential source of bacterial contamination in South Carolina coastal waters.

SIGNIFICANCE AND IMPACT OF THE STUDY

These findings help to increase our understanding of faecal coliform and potential pathogenic bacteria from poikilothermic reptilian sources, as there is the potential for these sources to raise bacterial water quality levels above regulatory thresholds.