PCR primers designed from malic acid dehydrogenase gene and their use for detection of Escherichia coli in water and milk samples

Antibiotic-Resistant Pathogenic Escherichia Coli Isolated from Rooftop Rainwater-Harvesting Tanks in the Eastern Cape, South Africa

Although many developing countries use harvested rainwater (HRW) for drinking and other household purposes, its quality is seldom monitored. Continuous assessment of the microbial quality of HRW would ensure the safety of users of such water. The current study investigated the prevalence of pathogenic Escherichia coli strains and their antimicrobial resistance patterns in HRW tanks in the Eastern Cape, South Africa. Rainwater samples were collected weekly between June and September 2016 from 11 tanks in various areas of the province. Enumeration of E. coli was performed using the Colilert^®18/Quanti-Tray^® 2000 method. E. coli isolates were obtained and screened for their virulence potentials using polymerase chain reaction (PCR), and subsequently tested for antibiotic resistance using the disc-diffusion method against 11 antibiotics. The pathotype most detected was the neonatal meningitis E. coli (NMEC) (ibeA 28%) while pathotype enteroaggregative E. coli (EAEC) was not detected. The highest resistance of the E. coli isolates was observed against Cephalothin (76%). All tested pathotypes were susceptible to Gentamicin, and 52% demonstrated multiple-antibiotic resistance (MAR). The results of the current study are of public health concern since the use of untreated harvested rainwater for potable purposes may pose a risk of transmission of pathogenic and antimicrobial-resistant E. coli.

Detection of diarrhoeagenic Escherichia coli in clinical and environmental water sources in South Africa using single-step 11-gene m-PCR

Escherichia coli (E. coli) consists of commensal (ComEC) and diarrhoeagenic (DEC) groups. ComEC are detected using traditional culture methods. Conformational steps are performed after culturing if it is required to test for the presence of DEC, increasing cost and time in obtaining the results. The aim of this study was to develop a single-step multiplex polymerase chain reaction (m-PCR) that can simultaneously amplify genes associated with DEC and ComEC, with the inclusion of controls to monitor inhibition. A total of 701 samples, taken from clinical and environmental water sources in South Africa, were analysed with the optimised m-PCR which targeted the eaeA, stx1, stx2, lt, st, ial, eagg, astA and bfp virulence genes. The mdh and gapdh genes were included as an internal and external control, respectively. The presence of the external control gapdh gene in all samples excluded any possible PCR inhibition. The internal control mdh gene was detected in 100 % of the environmental and 85 % of the clinical isolates, confirming the classification of isolates as E. coli PCR positive samples. All DEC types were detected in varying degrees from the mdh positive environmental and clinical isolates. Important gene code combinations were detected for clinical isolates of 0.4 % lt and eagg. However, 2.3 % of eaeA and ial, and 8.7 % of eaeA and eagg were reported for environmental water samples. The E. coli astA toxin was detected as positive at 35 and 17 % in environmental isolates and clinical isolates, respectively. Interestingly, 25 % of the E. coli astA toxin detected in environmental isolates and 17 % in clinical isolates did not contain any of the other virulence genes tested. In conclusion, the optimised single-step 11-gene m-PCR reactions could be successfully used for the identification of pathogenic and non-pathogenic E. coli types. The m-PCR was also successful in showing monitoring for PCR inhibition to ensure correct reporting of the results.

Environmental Escherichia coli occur as natural plant growth-promoting soil bacterium

Currently, it is presumed that Escherichia coli is not a normal inhabitant of the soil. Soilborne E. coli strains were isolated from broad range of 7 geoclimatic zones of India, indicating that E. coli can survive and thrive under different extreme soil conditions. Diversity among E. coli strains from widely separated geographic regions using enterobacterial repetitive intergenic consensus (ERIC)-PCR did not reveal any relationships between the genotypes and the source of isolation. Inoculation of maize (Zea mays cv. Arkil) seeds with E. coli NBRIAR3 (NBRIAR3) significantly enhanced (P < 0.05) plant growth and nutrient uptake, when compared with uninoculated control. Presence or absence of NBRIAR3 did not affect significantly (P < 0.05) diversity indexes, using substrate utilization patterns on the Biolog Eco plates. Clone libraries based on 16S rRNA gene from rhizosphere of maize plants demonstrated rather similar phylotype diversity from the uninoculated control and NBRIAR3-treated rhizosphere soil, which further indicated that NBRIAR3 did not exert a major influence on the overall bacterial diversity. The methodological approach described in this study supports the idea that E. coli should be treated as native soil bacterium instead of as an "indicator" of the possible presence of other fecal coliform bacteria.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (doi:10.1007/s00203-010-0544-1) contains supplementary material, which is available to authorized users.

Optimization of DGGE community fingerprinting for characterizing Escherichia coli communities associated with fecal pollution

We evaluated the use of DGGE fingerprinting to differentiate communities of Escherichia coli from animal and geographic sources. An initial screening of 15 gene candidates revealed the ability of three target genes (mdh, phoE and uidA-4) to effectively differentiate E. coli communities originating in horses, pigs, geese and goats. Cluster and jackknife analyses performed on the communities from a more extensive number of hosts (n=150) including humans (via raw sewage), horses, pigs, geese and cows revealed that the internal accuracy of classification of E. coli community fingerprints to their origin was similar for each of the three genes (85-86%). Each of the three genes were tested for their ability to associate E. coli source- and sink communities in two settings featuring contaminated water; (i) a stream receiving municipal wastewater effluent and (ii) a pond inhabited by geese. For each gene, DGGE fingerprints effectively matched effluent- and downstream E. coli communities (98-100% similarity) and excluded upstream communities, while communities from goose fecal material were 77-79% similar to communities in pond water, indicating fecal inputs from geese. Furthermore, each gene discriminated against E. coli communities from hosts non-indigenous to either setting. DGGE analysis of E. coli communities appears to be a promising tool to augment existing efforts aiming to address the dynamics of bacteria pollution in complex, natural environments.

Use of the tna operon as a new molecular target for Escherichia coli detection

A quantitative real-time PCR targeting the tnaA gene was studied to detect Escherichia coli and distinguish E. coli from Shigella spp. These microorganisms revealed high similarity in the molecular organization of the tna operon.

Application of a pathogenicity marker found in Escherichia coli for the assessment of irrigation water quality

A polymerase chain reaction (PCR)-based method was developed to differentiate between pathogenic and nonpathogenic Escherichia coli (E. coli). A pathogenicity marker, linked to the deletion of the ygfB gene, was identified in 80% of the clinical E. coli isolates tested. This marker, combined with the malic acid dehydrogenase gene, formed the duplex PCR that was subsequently used to screen E. coli isolates recovered from two secondary wastewater treatment plants (STPs) and a river site. All waters samples are used to irrigate dairy farm pasture in the West Gippsland region of Victoria, Australia. Results from three consecutive months of sampling (December 2001 and January and February 2002) indicated that Longwarry STP showed 8, 8, and 0% pathogenic E. coli; Pakenham STP showed 0, 12.5, and 33%; and the Bunyip river site showed 20, 12, and 25% respectively.

Identification of Bacillus spp., Escherichia coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. with 16S ribosomal DNA-based oligonucleotide array hybridization

Rapid identification of the genus and species of bacteria in foods and clinical specimens is important. In this report, DNA sequences of bacterial 16S rDNA were used to develop the oligonucleotide array for the identification of bacterial strains of Bacillus spp., Escherichia coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. Most of these bacterial strains may cause food-borne outbreaks or sporadic cases. A rapid (<4 h) detection method that used universal PCR primers to amplify the variable regions of bacterial 16S rDNA, followed by reverse hybridization of the PCR products, which were biotin labeled, to the oligonucleotides arrayed on the chip was developed. Fifteen oligonucleotide probes were selected and spotted on the nylon strip to determine the array hybridization patterns. It was successful in discriminating Bacillus spp., E. coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. with identification, in general, to the genus level, not species level. As 182 randomly selected strains were assayed, the detection rate was found higher than 98%. Except for 3 strains, the remaining 179 strains were correctly identified and no cross reactions were observed. These 179 strains generated five hybridization patterns. Adding more oligonucleotide probes to the array may allow the detection of more bacterial genera and species without significantly increasing the complexity or cost.

Preparation of milk samples for PCR analysis using a rapid filtration technique

AIMS

To investigate the usefulness of a straightforward filtration method for the isolation of Escherichia coli O157:H7 contaminants from milk for PCR detection.

METHODS AND RESULTS

Escherichia coli O157:H7 is grown in milk and enriched in Luria-Bertani (LB) medium. Samples are filtered through a 0.45-microm pore membrane. The membrane is immersed in 200-microl lysis buffer and incubated at 95 degrees C for 10 min to release bacterial DNA for subsequent PCR detection. Under current conditions, the overall duration from filtration to PCR-ready DNA generation is <20 min, and the detection level for PCR was as low as 10 CFU of bacteria in 1 ml of milk.

CONCLUSION

Bacterial contaminants of milk can be concentrated and isolated by a simple, one-step filtration and their DNA can be released for subsequent PCR detection by heating the filter membrane at 95 degrees C for 10 min.

SIGNIFICANCE AND IMPACT OF THE STUDY

The simplicity of this method allows inexpensive, high throughput automation that meets the demands of modern food hygiene monitoring.

PCR detection of Bacillus and Staphylococcus in various foods

A broad-range PCR assay for the detection of bacteria belonging to Bacillus and Staphylococcus genera was developed. Primers targeting the bacterial 16S rRNA gene were newly designed and used in a PCR assay. To determine the specificity of the assay, 81 different bacterial strains (of 50 genera), 2 fungi, 3 animals, and 4 plants were tested. Results were positive for every tested Bacillus, Staphylococcus, or Aerococcus strain. In addition, the result for Listeria grayi was positive with lower PCR product. For all other bacterial strains and eukaryotes tested, results were negative. Bacterial DNA was prepared with the use of achromopeptidase and Chelex 100 resin from culture after growth in brain heart infusion medium. To test the sensitivity of this PCR assay for Bacillus or Staphylococcus genus, either Bacillus cereus or Staphylococcus aureus was inoculated into various foods with undetectable levels of endogenous microbial contamination as an indicator. Inoculation of bacteria at 10 to 30 CFU/g of food was followed by a 5-h enrichment culture step after which the PCR assay allowed the detection of bacterial cells. When the inoculation (B. cereus or S. aureus) of 10 to 90 CFU/g into noodle foods containing endogenous microflora (10(3) to 10(5) CFU/g) was followed by a 6-h enrichment culture step, the PCR assay detected the bacteria. Including the enrichment culture step, the entire PCR detection process can be completed within 8.5 h.

A PCR assay for detection of acetic acid-tolerant lactic acid bacteria in acidic food products

A PCR assay for the detection of acetic acid-tolerant lactic acid bacteria in the genera of Lactobacillus and Pediococcus was developed in this study. Primers targeting the bacterial 16S rRNA gene were newly designed and used in this PCR assay. To determine the specificity of the assay, 56 different bacterial strains (of 33 genera), 2 fungi, 3 animals, and 4 plants were tested. Results were positive for most tested bacterial members of 16S rRNA gene-based phylogenetic groups (classified in the Lactobacillus casei and Pediococcus group), including Lactobacillus fructivorans, Lactobacillus brevis, Lactobacillus buchneri, Lactobacillus plantarum, and Lactobacillus paracasei. For all other bacterial strains and eukaryote tested, results were negative. Bacterial DNA for PCR was prepared with a simple procedure with the use of Chelex 100 resin from culture after growth in deMan Rogosa Sharpe broth (pH 6.0). To test this PCR assay for the monitoring of the acetic acid-tolerant lactic acid bacteria, L. fructivorans was inoculated into several acidic food as an indicator. Before the PCR, the inoculation of 10 to 50 CFU of bacteria per g of food was followed by a 28-h enrichment culture step, and the PCR assay allowed the detection of bacterial cells. Including the enrichment culture step, the entire PCR detection process can be completed within 30 h.

Development of a PCR assay for detection of Enterobacteriaceae in foods

A broad-range PCR assay for the detection of bacteria belonging to the Enterobacteriaceae family was developed in this study. Primers targeting the bacterial 16S rRNA gene were newly designed and used in this PCR assay. To determine the specificity of the assay, 72 different bacterial species (of 49 genera), 2 fungi, 3 animals, and 4 plants were tested. Results were positive for every tested Vibrioaceae or Enterobacteriaceae strain except Proteus mirabilis. For all other bacterial strains and eukaryotes tested, results were negative. Bacterial DNA for PCR was prepared by a simple procedure with the use of Chelex 100 resin from culture after growth in brain heart infusion medium. To test this PCR assay for the monitoring of the Enterobacteriaceae family, either Escherichia coli or Salmonella Enteritidis was inoculated into various foods as an indicator. Prior to the PCR, the inoculation of 10 to 40 CFU of bacteria per g of food was followed by a 5-h enrichment culture step, and the PCR assay allowed the detection of bacterial cells. When actual examinations of the contamination of 15 noodle foods with Enterobacteriaceae by this PCR assay were conducted, 33% (5 of 15) of the samples tested positive. These results agreed with those of the Petrifilm Enterobacteriaceae Count Plate assay. Including the enrichment culture step, the entire PCR detection process can be completed within 7 h.

PCR-ELISA detection of Escherichia coli in milk

AIMS

The purpose of this study was to develop a reliable molecular procedure for the detection of Escherichia coli in milk.

METHODS AND RESULTS

Robust and expeditious DNA extraction and PCR techniques were evaluated using Enzyme-Linked Immunosorbent Assay (ELISA) detection of biotin-labelled amplicons to facilitate optimal detection of E. coli DNA.

CONCLUSIONS

It was found that 5 E. coli colony-forming units (cfu) could be detected per PCR reaction using the PCR-ELISA system, equating to a sensitivity of detection of 100 E. coli cfu ml(-1) pasteurized milk.

SIGNIFICANCE AND IMPACT OF THE STUDY

This approach should facilitate evaluation of milk contamination and enable rapid detection of E. coli mastitis, leading to correct deployment of relevant antibiotic therapy and improved animal welfare.