Evaluation of DNA preparation techniques for detection of the SLT-1 gene of Escherichia coli O157: H7 in bovine faeces using the polymerase chain reaction

Optimized microbial DNA extraction from diarrheic stools

BACKGROUND

The detection of enteropathogens in stool specimens increasingly relies on the detection of specific nucleic acid sequences. We observed that such detection was hampered in diarrheic stool specimens and we set-up an improved protocol combining lyophilization of stools prior to a semi-automated DNA extraction.

FINDINGS

A total of 41 human diarrheic stool specimens comprising of 35 specimens negative for enteropathogens and six specimens positive for Salmonella enterica in culture, were prospectively studied. One 1-mL aliquot of each specimen was lyophilised and total DNA was extracted from lyophilised and non-lyophilised aliquots by combining automatic and phenol-chloroform DNA extraction. DNA was incorporated into real-time PCRs targeting the 16S rRNA gene of Bacteria and the archaea Methanobrevibacter smithii and the chorismate synthase gene of S. enterica. Whereas negative controls consisting in DNA-free water remained negative, M. smithii was detected in 26/41 (63.4%) non-lyophilised (Ct value 28.78 ± 9.1) versus 39/41 (95.1%) lyophilised aliquots (Ct value 22.04 ± 5.5); bacterial 16S rRNA was detected in 33/41 (80.5%) non-lyophilised (Ct value 28.11 ± 5.9) versus 40/41 (97.6%) lyophilised aliquots (Ct value 24.94 ± 6.6); and S. enterica was detected in 6/6 (100%) non-lyophilized and lyophilized aliquots (Ct value 26.98 ± 4.55 and 26.16 ± 4.97, respectively). S. enterica was not detected in the 35 remaining diarrheal-stool specimens. The proportion of positive specimens was significantly higher after lyophilization for the detection of M. smithii (p = 0.00043) and Bacteria (p = 0.015).

CONCLUSION

Lyophilization of diarrheic stool specimens significantly increases the PCR-based detection of microorganisms. The semi-automated protocol described here could be routinely used for the molecular diagnosis of infectious diarrhea.

Lyophilization prior to direct DNA extraction from bovine feces improves the quantification of Escherichia coli O157:H7 and Campylobacter jejuni

Lyophilization was used to concentrate bovine feces prior to DNA extraction and analysis using real-time PCR. Lyophilization significantly improved the sensitivity of detection compared to that in fresh feces and was associated with reliable quantification of both Escherichia coli O157:H7 and Campylobacter jejuni bacteria present in feces at concentrations ranging between 2 log(10) and 6 log(10) CFU g(-)(1).

DNA extraction from bovine faeces: current status and future trends

There is an increasing interest in the detection and enumeration of micro-organisms pathogenic for human and present in bovine faeces. This interest is because pollution of the environment by animal faeces may affect the safety of food and of drinking or recreational water. Detection and quantification of microbial pathogens carried out using DNA extracted from the faecal matrix are affected by the quality and the quantity of the DNA extracts, which are critical factors that limit the accuracy and sensitivity of molecular studies. This review compares published methods on DNA extraction from bovine faeces, focusing on the extent to which the success of DNA amplification is affected by issues related to the faeces. Following a general discussion on the DNA extraction methods used for faeces, we focus particularly on issues related to the faecal environment itself. The objective is to identify information that can be used to improve the sensitivity of those PCR methods used after direct DNA extraction.

Comparison of methods of extracting Salmonella enterica serovar Enteritidis DNA from environmental substrates and quantification of organisms by using a general internal procedural control

This paper compares five commercially available DNA extraction methods with respect to DNA extraction efficiency of Salmonella enterica serovar Enteritidis from soil, manure, and compost and uses an Escherichia coli strain harboring a plasmid expressing green fluorescent protein as a general internal procedural control. Inclusion of this general internal procedural control permitted more accurate quantification of extraction and amplification of S. enterica serovar Enteritidis in these samples and reduced the possibility of false negatives. With this protocol it was found that the optimal extraction method differed for soil (Mobio soil DNA extraction kit), manure (Bio101 soil DNA extraction kit), and compost (Mobio fecal DNA extraction kit). With each method, as little as 1.2 x 10(3) to 1.8 x 10(3) CFU of added serovar Enteritidis per 100 mg of substrate could be detected by direct DNA extraction and subsequent S. enterica-specific TaqMan PCR. After bacterial enrichment, as little as 1 CFU/100 mg of original substrate was detected. Finally, the study presents a more accurate molecular analysis for quantification of serovar Enteritidis initially present in soil or manure using DNA extraction and TaqMan PCR.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the discrimination of food-borne microorganisms

A methodology based on matrix-assisted laser desorption ionization-time of flight mass spectrometry of intact bacterial cells was used for rapid discrimination of 24 bacterial species, and detailed analyses to identify Escherichia coli O157:H7 were carried out. Highly specific mass spectrometric profiles of pathogenic and nonpathogenic bacteria that are well-known major food contaminants were obtained, uploaded in a specific database, and made available on the Web. In order to standardize the analytical protocol, several experimental, sample preparation, and mass spectrometry parameters that can affect the reproducibility and accuracy of data were evaluated. Our results confirm the conclusion that this strategy is a powerful tool for rapid and accurate identification of bacterial species and that mass spectrometric methodologies could play an essential role in polyphasic approaches to the identification of pathogenic bacteria.

Characterization of Shiga toxin-producingEscherichia coliisolated from aquatic environments

This study reports the phenotypic and genotypic characterization of 144 Shiga toxin-producing Escherichia coli (STEC) strains isolated from urban sewage and animal wastewaters using a Shiga toxin 2 gene variant (stx(2))-specific DNA colony hybridization method. All the strains were classified as E. coli and belonged to 34 different serotypes, some of which had not been previously reported to carry the stx(2) genes (O8:H31, O89:H19, O166:H21 and O181:H20). Five stx(2) subtypes (stx(2), stx(2c), stx(2d), stx(2e) and stx(2g)) were detected. The stx(2), stx(2c), stx(2d) and stx(2e) subtypes were present in urban sewage and stx(2e) was the only stx(2) subtype found in pig wastewater samples. The stx(2c) and stx(2g) were more associated with cattle wastewater. One strain was positive for the intimin gene (eae) and five strains of serotypes were positive for the adhesin encoded by the saa gene. A total of 41 different seropathotypes were found. On the basis of occurrence of virulence genes, most non-O157 STEC strains are assumed to be low-virulence serotypes.

Rapid detection of Escherichia coli O157:H7 by immunomagnetic separation and real-time PCR

A method combining immunomagnetic separation (IMS) and real-time (5'-nuclease) PCR was developed to detect Escherichia coli O157:H7. Monoclonal antibody specific for the E. coli O157 antigen was added to protein A-coated magnetic particles to create antibody-coated beads. The beads specifically captured E. coli O157:H7 from bacterial suspensions. The cells were eluted from the beads and lysed by heating; the eluate was then assayed by real-time PCR, using primers and probe specifically targeting the eaeA gene of E. coli O157:H7. Approximately 50% of the cells in suspension were captured by the beads and detected by real-time PCR. No cross-reactivity was detected when other strains of E. coli were tested. This method was applied to detect E. coli O157:H7 from ground beef. Both cell capture efficiency and real-time PCR efficiency were reduced by meat-associated inhibitors. However, we were still able to detect up to 8% of E. coli O157:H7 from inoculated ground beef samples. The detection sensitivity varied among ground beef samples. The minimum detection limit was <5x10(2) cells ml(-1) for suspensions of E. coli O157:H7 in buffer and 1.3x10(4) cells g(-1) for E. coli O157:H7 in ground beef. The combination of IMS and real-time PCR results in rapid, specific and quantitative detection of E. coli O157:H7 without the need for an enrichment culture step.

Diversity of stx2 converting bacteriophages induced from Shiga-toxin-producing Escherichia coli strains isolated from cattle

The presence of bacteriophages encoding Shiga toxin 2 (stx(2) phages) was analysed in 168 strains of Shiga-toxin-producing Escherichia coli (STEC) isolated from cattle. Following mitomycin C induction, strains carrying stx(2) phages were screened by plaque blot and hybridization with an stx(2)A-probe. In the stx(2)-phage-carrying strains, the amounts of phage production, phage DNA extracted and Stx(2) produced after induction were assessed. The induced stx(2) phages were characterized morphologically and genetically. Assays to obtain lysogens from different strains were also carried out and phages induced from the lysogens were compared with those induced from the STEC isolates. Results indicated that 18 % of the strains carried an inducible stx(2) phage. Most of them showed a direct relationship between phage induction and toxin production. Each strain carried only one inducible stx(2) phage, although a few strains had two copies of the stx(2) in the chromosome. The stx(2) phages showed diverse morphology and a wide variability in their genome. Assays to obtain lysogens showed that not all the phages were transduced with the same frequency and only six lysogens were obtained. Phages in the lysogens were the same as those induced from their respective initial STEC host strains, although the induction and relative toxin production of the lysogens varied. Most phages carried the stx(2) gene, while a few carried stx(2) variants. Infectivity of the phages depended on the different hosts, although O157 : H7 was preferentially infected by phages induced from O157 strains. The results show that inducible stx(2) phages are common among STEC of animal origin and that they may enhance the spread of stx(2).

Comparison of real-time PCR methods for detection of Salmonella enterica and Escherichia coli O157:H7, and introduction of a general internal amplification control

The objectives of this study were to compare different real-time PCR-based methods for detection of either Salmonella spp. or E. coli O157:H7 with respect to sensitivity, precision and accuracy. In addition, a general internal amplification control (IAC) is presented, allowing prevention of false negative results. The IAC allows insight in amplification efficiency and enables a more accurate quantification with the evaluated real-time PCR methods. Implementation of the IAC with the different PCR methods did not affect the precision of the methods, but the sensitivity was reduced 10-fold. Introduction of an IAC with the Salmonella enterica specific detection method showed a shift in Ct-value (increase of target Ct-value with 0.45+/-0.17 cycles), while with the method to detect E. coli O157:H7 no influence of IAC co-amplification was observed. The quantification threshold of the methods in which the IAC was included was determined at 1 pg of target DNA (equal to 200 CFU) per reaction. Qualitative detection was feasible down to 10 fg of target DNA per reaction using both methods in which the IAC was incorporated. The adjusted methods have the potential to provide fast and sensitive detection of Salmonella spp. or E. coli O157:H7, enabling accurate quantification and preventing false negative results by using the general IAC.

Animal host associated differences in Shiga toxin-producing Escherichia coli isolated from sheep and cattle on the same farm

AIMS

To investigate if cattle on the same farm as sheep are a possible risk factor for stx in sheep and to determine whether or not sheep and cattle on the same farm share the same stx pool.

METHODS AND RESULTS

Faecal samples from sheep and cattle were screened for stx by polymerase chain reaction (PCR). Of these samples, 87.6 and 64.6% were stx positive in sheep and cattle, respectively. There was no difference in stx occurrence in sheep from farms with or without cattle. From stx positive samples, 118 Shiga toxin-producing Escherichia coli (STEC) isolates were recovered by a filter-hybridization method. Serotyping, PCR and pulsed-field gel electrophoresis (PFGE) showed that there was a distinct association between serotypes, stx profiles and animal species.

CONCLUSIONS

Keeping animals together in pens, which enhances faecal-oral contact, is suggested as a possible explanation for the differences seen in stx occurrence. Sheep and cattle isolates are distinctly different in serotype and stx profile although isolated from the same farm, and are more related to isolates within the same serotype with the same stx profile than to isolates with different serotype from the same farm.

SIGNIFICANCE AND IMPACT OF STUDY

The study supports the animal-host relationship hypothesis suggested in other studies and indicates that the STEC sheep reservoir in Norway may not pose a serious public health risk.

A comparison of DNA extraction and purification methods to detect Escherichia coli O157:H7 in cattle manure

The extraction of DNA from manure and the subsequent polymerase chain reaction (PCR) amplification of virulence genes to detect pathogens require an effective method of purification. Four different methods were assessed for their effectiveness in extracting and purifying Escherichia coli O157:H7 DNA from cattle manure: phenol/chloroform purification, phenol/chloroform/Sepharose B4 spin columns, phenol/chloroform/polyvinylpolypyrrolidone (PVPP) spun columns, and Mo Bio UltraClean kit. A PCR assay targeting the shiga-like toxin I gene (sltI) was carried out to determine the effectiveness of the four methods in removing PCR inhibitors from the manure samples. All methods were used to extract a manure slurry and the cleanliness of the samples was tested by the PCR with varying concentrations of spiked E. coli O157:H7 target DNA. The PVPP spun columns and the UltraClean kit had the best detection limit, detecting 20 pg of E. coli DNA (about 2x10(3) cells) per 100 mg of manure. The UltraClean kit and the PVPP spun columns also had the best and similar detection limits of 3x10(4) CFU/100 mg manure when E. coli O157:H7 cells were spiked into the manure sample and purified by all four methods. The enrichment of cells after inoculation into manure was performed using tryptic soy broth at 37 degrees C for 5 h. Both the PVPP spun columns and the UltraClean kit methods were used to purify the enriched samples and were able to detect initial inocula of 6 CFU/100 mg manure, indicating that the two methods were highly efficient in purifying DNA from manure samples.

Shiga toxin 2-converting bacteriophages associated with clonal variability in Escherichia coli O157:H7 strains of human origin isolated from a single outbreak

Shiga toxin 2 (Stx2)-converting bacteriophages induced from 49 strains of Escherichia coli O157:H7 isolated during a recent outbreak of enterocolitis in Spain were examined in an attempt to identify the variability due to the stx(2)-converting phages. The bacterial isolates were divided into low-, medium-, and high-phage-production groups on the basis of the number of phages released after mitomycin C induction. Low- and medium-phage-production isolates harbored two kinds of phages but released only one of them, whereas high-phage-production isolates harbored only one of the two phages. One of the phages, phi SC370, which was detected only in the isolates with two phages, showed similarities with phage 933W. The second phage, phi LC159, differed from phi SC370 in morphology and DNA structure. When both phages were present in the same bacterial chromosome, as occurred in most of the isolates, only phi SC370 was detected in the supernatants of the induced cultures. If phi LC159 was released, its presence was masked by phi SC370. When phi SC370 was absent, large amounts of phi LC159 were released, suggesting that there was some regulation of phage expression between the two phages. To our knowledge, this is the first description of clonal variability due to phage loss. The higher level of phage production was reflected in the larger amounts of Stx2 toxin produced by the cultures. Some relationship between phage production and the severity of symptoms was observed, and consequently these observations suggest that the virulence of the isolates studied could be related to the variability of the induced stx(2)-converting phages.

PCR detection of Escherichia coli O157:H7 directly from stools: evaluation of commercial extraction methods for purifying fecal DNA

Rapid identification of Escherichia coli O157:H7 is important for patient management and for prompt epidemiological investigations. We evaluated one in-house method and three commercially available kits for their ability to extract E. coli O157:H7 DNA directly from stool specimens for PCR. Of the 153 stool specimens tested, 107 were culture positive and 46 were culture negative. The sensitivities and specificities of the in-house enrichment method, IsoQuick kit, NucliSens kit, and QIAamp kit were comparable, as follows: 83 and 98%, 85 and 100%, 74 and 98%, and 86 and 100%, respectively. False-negative PCR results may be due to the presence of either inherent inhibitors or small numbers of organisms. The presence of large amounts of bacteria relative to the amount of the E. coli O157:H7 target may result in the lower sensitivities of the assays. All commercial kits were rapid and easy to use, although DNA extracted with the QIAamp kit did not require further dilution of the DNA template prior to PCR.