Development of PCR assays for detection of Escherichia coli O157:H7 in meat products

Development and Application of Four Foodborne Pathogens by TaqMan Multiplex Real-Time PCR

A TaqMan multiplex real-time PCR (mRT-PCR) was developed to detect simultaneously Salmonella spp., Escherichia coli O157, Staphylococcus aureus, and Listeria monocytogenes in food samples. The method involves four sets of primers and probes tailored to the unique DNA sequences found in the invA, nuc, rfbE, and hly genes of each pathogen. The generated standard curves, correlating gene copy numbers with Ct values, demonstrated high accuracy (R2 > 0.99) and efficiency (92%-104%). Meanwhile, the limit of detection was 100 CFU/mL for the four target bacteria in artificially contaminated food samples after 6-8 h of enrichment. The assay's effectiveness was further verified by testing 80 naturally contaminated food samples, showing results largely in agreement with traditional culture methods. Overall, this newly developed TaqMan mRT-PCR, inclusive of a pre-enrichment step, proves to be a dependable and effective tool for detecting single or multiple pathogens in diverse food items, offering significant potential for in vitro diagnostics.

Characterization of diarrheagenic Escherichia coli from different cattle production systems in Brazil

Diarrheagenic E. coli (DEC) can cause severe diarrhea and is a public health concern worldwide. Cattle are an important reservoir for this group of pathogens, and once introduced into the abattoir environment, these microorganisms can contaminate consumer products. This study aimed to characterize the distribution of DEC [Shiga toxin-producing E. coli (STEC), enteroinvasive E. coli (EIEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), and enteroaggregative E. coli (EAEC)] from extensive and intensive cattle production systems in Brazil. Samples (n = 919) were collected from animal feces (n = 200), carcasses (n = 600), meat cuts (n = 90), employee feces (n = 9), and slaughterhouse water (n = 20). Virulence genes were detected by PCR in 10% of animal samples (94/919), with STEC (n = 81) as the higher prevalence, followed by EIEC (n = 8), and lastly EPEC (n = 5). Animals raised in an extensive system had a higher prevalence of STEC (average 48%, sd = 2.04) when compared to animals raised in an intensive system (23%, sd = 1.95) (Chi-square test, P < 0.001). From these animals, most STEC isolates only harbored stx2 (58%), and 7% were STEC LEE-positive isolates that were further identified as O157:H7. This study provides further evidence that cattle are potential sources of DEC, especially STEC, and that potentially pathogenic E. coli isolates are widely distributed in feces and carcasses during the slaughter process.

Development of triplex assay for simultaneous detection of Escherichia coli, methicillin resistant and sensitive Staphylococcus aureus in raw pork samples of retail markets

Escherichia coli and Staphylococcus aureus are the most important food borne pathogen transmitting from animal meat and meat products. Therefore, it is vital to design an accurate and specific diagnostic tool for identifying those food-borne pathogens in animal meat and meat products. In the current study, E. coli, methicillin-resistant and sensitive S. aureus (MRSA and MSSA) were simultaneously detected using a developed triplex PCR-based technique. To obtain an optimal reaction parameter, the multiplex assay was optimised by changing just one parameter while holding the others constant. Specificity of the assay was assessed using several porcine bacterial template DNA. The plasmid DNA was used to test the multiplex PCR assay's sensitivity and interference in spiked pork samples. E. coli, MRSA, and MSSA each have PCR amplified products with sizes of 335, 533, and 209 bp, respectively. The assay detects a minimum microbial load of 102 CFU/μl for all the three pathogens and can identify bacterial DNA as low as 10-2 ng/µl. The assay was validated employing 210 pork samples obtained from retail meat shops and slaughter houses, with MRSA, E. coli, and MSSA with the occurrence rate of 1.9%, 42.38%, and 18.1%, respectively. The rate of mixed bacterial contamination in pork meat samples examined with the developed method was 6.19%, 1.43%, 1.90%, and 1.43% for MSSA & E. coli, MRSA & E. coli, MSSA & MRSA, and E. coli, MSSA & MRSA, respectively. The developed multiplex PCR assay is quick and efficient, and it can distinguish between different bacterial pathogens in a single reaction tube.

Epidemiology and Antimicrobial Susceptibility Pattern of E. coli O157:H7 Along Dairy Milk Supply Chain in Central Ethiopia

Background

Enterohemorrhagic Escherichia coli (O157:H7) is the primary cause of bloody diarrhea or hemorrhagic colitis. The study was carried out with to determine the epidemiology and antimicrobial resistance pattern of E. coli O157:H7 along the dairy supply chains in Akaki Kaliti sub-city of Addis Ababa, Bishoftu and Sululta towns of central Ethiopia.

Methods

A cross-sectional study design with random sampling methods was employed. Thus, a total of 450 raw cow milk (294), milker hand swab (65) and water (91) samples were collected from dairy farms, milk collection centers and Cafeterias and processed according to the standards to isolate and identify E. coli O157:H7. The samples were initially enriched in buffered peptone water, then plated onto Sorbitol MacConkey agar. Consequently, the suspected non-sorbitol fermenting colonies were confirmed as E. coli biochemically and serological test using latex agglutination tests.

Results

Out of the total 450 samples examined, 6.0% were found to be contaminated by E. coli O157:H7. Accordingly, 9.89% of water, 9.23% of milker hand swab and 4.08% of raw milk samples were contaminated by the pathogen. Furthermore, the prevalence of E. coli O157:H7 was 7.79%, 6.21% and 3.97% in Akaki kaliti sub-city, Sululta and Bishoftu towns, respectively. The result of Fisher exact analysis revealed a significant difference observed (p < 0.05) between the occurrence of the pathogen and the source of sample, sources of water used, sampled material and type of containers. The study also revealed that varying level of resistance of E. coli O157:H7 isolates against nine antimicrobial discs tested and 100% (n = 27) of the isolates showed multidrug-resistance comprising from two up to seven antimicrobial drugs.

Conclusion

In conclusion, this study has indicated the occurrence of E. coli O157:H7 and its multiple drug-resistant profiles in milk samples along the dairy supply chains and its risk to public health and food safety. Therefore, proper hygienic practices from dairy farms to fork and rational drug usage are recommended.

'Evidence for waterborne origin of an extended mixed gastroenteritis outbreak in a town in Northern Greece, 2019'

We investigated a large gastroenteritis outbreak that occurred in Northern Greece in 2019. A case was defined as anyone presenting with diarrhoea and/or vomiting from 24 January 2019 to 04 February 2019. We conducted a case-control study (CCS) using random selection of participants >16 years of age, residents of town X, who visited the health care centre between 25 and 28 January 2019. Moreover, we conducted a retrospective cohort study (CS) at the four elementary schools of the town. We collected clinical and water samples and the water supply system was inspected. In total, we recorded 638 cases (53% female; median age was 44 years (range 0-93)). Forty-eight cases and 52 controls participated in the CCS and 236 students in the CS. Both CCS and CS indicated tap water as the most likely source (OR 10, 95% CI 2.09-93.4, explaining 95.7% of cases; RR = 2.22, 95% CI 1.42-3.46, respectively). More than one pathogen was detected from stool samples of 6 of the 11 cases tested (norovirus, Campylobacter jejuni, Enterohemorrhagic E. coli (EHEC) and Enteropathogenic E. coli (EPEC)). Water samples, collected after ad-hoc chlorination, tested negative. Technical failures of the water tanks' status were identified. Our results suggested a waterborne outbreak. We recommended regular monitoring of the water supply system and immediate repair of technical failures.

The Development of a Portable SPR Bioanalyzer for Sensitive Detection of Escherichia coli O157:H7

The purpose of this study was to develop a portable surface plasmon resonance (SPR) bioanalyzer for the sensitive detection of Escherichia coli O157:H7 in comparison with an enzyme-linked immunosorbent assay (ELISA). The experimental setup mainly consisted of an integrated biosensor and a homemade microfluidic cell with a three-way solenoid valve. In order to detect Escherichia coli O157:H7 using the SPR immunoassay, 3-mercaptopropionic acid (3-MPA) was chemisorbed onto a gold surface via covalent bond for the immobilization of biological species. 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) were used as crosslinker reagents to enable the reaction between 3-MPA and Escherichia coli O157:H7 antibodies by covalent –CO–NH– amide bonding. The experimental results were obtained from the Escherichia coli O157:H7 positive samples prepared by 10-, 20-, 40-, 80-, and 160-fold dilution respectively, which show that a good linear relationship with the correlation coefficient R of 0.982 existed between the response units from the portable SPR bioanalyzer and the concentration of Escherichia coli O157:H7 positive samples. Moreover, the theoretical detection limit of 1.87 × 10³ cfu/mL was calculated from the positive control samples. Compared with the Escherichia coli O157:H7 ELISA kit, the sensitivity of this portable SPR bioanalyzer is four orders of magnitude higher than the ELISA kit. The results demonstrate that the portable SPR bioanalyzer could provide an alternative method for the quantitative and sensitive determination of Escherichia coli O157:H7 in field.

Visual Detection of Enterohemorrhagic Escherichia coli O157:H7 Using Loop-Mediated Isothermal Amplification

INTRODUCTION

Escherichia coli O157:H7, an important foodborne pathogen, can cause serious renal damage, which can also lead to mortality. Since a rapid and sensitive method is needed to identify this pathogenic agent, we evaluated Loop-Mediated Isothermal Amplification Assay (LAMP) to detect Escherichia coli O157:H7.

METHODS

We used six primers that specifically identified the rfbE gene. To examine the sensitivity of the method, different dilutions were subjected to the LAMP reaction. Other bacterial strains also were investigated to determine the specificity of the test. The turbidity of the amplified products was assayed by visual detection. The amplified products were detected by addition of SYBR Green II to the reaction tubes.

RESULTS

Amplification products were observed as a ladder-like pattern on the agarose gel. A white turbidity emerged in the positive tubes. Under UV light, the positive samples were green, whereas the negative samples were orange. The detection limit of the LAMP was 78 pg/tube, and this indicated that it was 100 times more sensitive than PCR for the detection of EHEC. No LAMP products were detected when template DNA of non-EHEC strains were used, suggesting high specificity of the LAMP assay.

CONCLUSION

The results indicated that the LAMP assay is a valuable diagnostic assay to identify EHEC O157:H7. In addition, the simplicity, sensitivity, specificity, and rapidity of this assay make it a useful method to diagnose pathogens in primary labs without any need for expensive equipment or specialized techniques.

Estimation of Listeria monocytogenes and Escherichia coli O157:H7 prevalence and levels in naturally contaminated rocket and cucumber samples by deterministic and stochastic approaches

The aims of the present study were to determine the prevalence and levels of Listeria monocytogenes and Escherichia coli O157:H7 in rocket and cucumber samples by deterministic (estimation of a single value) and stochastic (estimation of a range of values) approaches. In parallel, the chromogenic media commonly used for the recovery of these microorganisms were evaluated and compared, and the efficiency of an enzyme-linked immunosorbent assay (ELISA)-based protocol was validated. L. monocytogenes and E. coli O157:H7 were detected and enumerated using agar Listeria according to Ottaviani and Agosti plus RAPID' L. mono medium and Fluorocult plus sorbitol MacConkey medium with cefixime and tellurite in parallel, respectively. Identity was confirmed with biochemical and molecular tests and the ELISA. Performance indices of the media and the prevalence of both pathogens were estimated using Bayesian inference. In rocket, prevalence of both L. monocytogenes and E. coli O157:H7 was estimated at 7% (7 of 100 samples). In cucumber, prevalence was 6% (6 of 100 samples) and 3% (3 of 100 samples) for L. monocytogenes and E. coli O157:H7, respectively. The levels derived from the presence-absence data using Bayesian modeling were estimated at 0.12 CFU/25 g (0.06 to 0.20) and 0.09 CFU/25 g (0.04 to 0.170) for L. monocytogenes in rocket and cucumber samples, respectively. The corresponding values for E. coli O157:H7 were 0.59 CFU/25 g (0.43 to 0.78) and 1.78 CFU/25 g (1.38 to 2.24), respectively. The sensitivity and specificity of the culture media differed for rocket and cucumber samples. The ELISA technique had a high level of cross-reactivity. Parallel testing with at least two culture media was required to achieve a reliable result for L. monocytogenes or E. coli O157:H7 prevalence in rocket and cucumber samples.

Application of multiplex PCR assay based on uidR and fliCH7 genes for detection of Escherichia coli O157:H7 in milk

A highly sensitive and specific multiplex PCR assay has been developed to detect the presence of Escherichia coli O157:H7 from naturally contaminated raw milk samples within 10 h. The primers explored in the assay were targeted against the uidR gene specific for all types of E. coli and the fliCH7 gene specific for the h7 flagellar antigen of E. coli O157:H7. The multiplex PCR assay developed was found to be highly specific as it produced PCR products of 152 bp (E. coli specific) and 625 bp (E. coli O157:H7 specific). The assay was tested for its specificity against different serotypes of E. coli as well as other pathogenic strains like Salmonella, Shigella, Klebsiella, Enterobacter, Staphylococcus aureus, Lactobacillus and Lactococcus etc. When this multiplex PCR assay was directly applied to 24 raw milk samples collected from different sources, E. coli O157:H7 could be detected in one of the milk samples without 4 h enrichment in CT-SMAC broth and three samples after 4 h enrichment in CT-SMAC broth. However, all the pasteurized milk samples gave a negative signal for this organism.

Detection of Escherichia coli O157 by peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) and comparison to a standard culture method

Despite the emergence of non-O157 Shiga toxin-producing Escherichia coli (STEC) infections, E. coli serotype O157 is still the most commonly identified STEC in the world. It causes high morbidity and mortality and has been responsible for a number of outbreaks in many parts of the world. Various methods have been developed to detect this particular serotype, but standard bacteriological methods remain the gold standard. Here, we propose a new peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) method for the rapid detection of E. coli O157. Testing on 54 representative strains showed that the PNA probe is highly sensitive and specific to E. coli O157. The method then was optimized for detection in food samples. Ground beef and unpasteurized milk samples were artificially contaminated with E. coli O157 concentrations ranging from 1 × 10(-2) to 1 × 10(2) CFU per 25 g or ml of food. Samples were then preenriched and analyzed by both the traditional bacteriological method (ISO 16654:2001) and PNA-FISH. The PNA-FISH method performed well in both types of food matrices with a detection limit of 1 CFU/25 g or ml of food samples. Tests on 60 food samples have shown a specificity value of 100% (95% confidence interval [CI], 82.83 to 100), a sensitivity of 97.22% (95% CI, 83.79 to 99.85%), and an accuracy of 98.33% (CI 95%, 83.41 to 99.91%). Results indicate that PNA-FISH performed as well as the traditional culture methods and can reduce the diagnosis time to 1 day.

Detection of Escherichia coli O157:H7 using immunomagnetic separation and mPCR in Turkish foods of animal origin

The present study was conducted to investigate the presence of Escherichia coli O157:H7 in food samples of animal origin and to detect its virulence genes by immunomagnetic separation technique and multiplex PCR (mPCR). A total of 500 samples (consisting of diced meat, minced meat, burger, raw cow's milk and raw cow's milk cheese) were analysed. Escherichia coli O157:H7 was detected in 5 (1%) of 500 analysed samples including two diced meat, one minced meat and two raw-milk cheese. None of the burger samples tested contained E. coli O157:H7. Three isolates obtained from minced and diced meat were found to carry stx1 , stx2 , hlyA and eaeA genes whereas two isolates from raw-milk cheese were found to harbour the stx1 , eaeA and hlyA genes. The results of this study suggest that raw meat and raw-milk cheese tested could pose public health problems in consumers with regard to their virulence factors.

SIGNIFICANCE AND IMPACT OF THE STUDY

Escherichia coli (E. coli) O157:H7 is an important human pathogen. Escherichia coli 0157:H7 infections have been associated with consumption of uncooked meat and meat products, as well as unpasteurized dairy products. This study demonstrated that without specific tests for E. coli virulence factors raw meat and raw-milk cheese could pose public health problems to Turkish consumers.

In-house validation of a multiplex real-time PCR method for simultaneous detection of Salmonella spp., Escherichia coli O157 and Listeria monocytogenes

A wide variety of qPCR methods currently exist for Salmonella spp., Escherichia coli O157 and Listeria monocytogenes detection. These methods target several genes and use different detection chemistries, either in simplex or in multiplex formats. However, the majority of these methods have not been carefully validated, and the number of validated methods that use multiplex qPCR is even lower. The aim of the present study was to develop and validate a multiplex qPCR method from previously validated simplex qPCR primers and probes. A modified broth medium was selected and primary and secondary enrichment times were further optimized. Efficiency of the newly combined qPCR system was comprised between 91% and 108%, for simplex and multiplex analyses. A total of 152 food and environmental, natural and spiked samples, were analyzed for the evaluation of the method obtaining values above 91% that were reached for all the quality parameters analyzed. A very low limit of detection (5 cfu/25 g after enrichment) for simultaneous identification of these 3 pathogens was obtained.

Development of a multiplex PCR assay for detection of Shiga toxin-producing Escherichia coli, enterohemorrhagic E. coli, and enteropathogenic E. coli strains

Escherichia coli O157:H7 and other pathogenic E. coli strains are enteric pathogens associated with food safety threats and which remain a significant cause of morbidity and mortality worldwide. In the current study, we investigated whether enterohemorrhagic E. coli (EHEC), Shiga toxin-producing E. coli (STEC), and enteropathogenic E. coli (EPEC) strains can be rapidly and specifically differentiated with multiplex PCR (mPCR) utilizing selected biomarkers associated with each strain’s respective virulence genotype. Primers were designed to amplify multiple intimin (eae) and long polar fimbriae (lpfA) variants, the bundle-forming pilus gene bfpA, and the Shiga toxin-encoding genes stx1 and stx2. We demonstrated consistent amplification of genes specific to the prototype EHEC O157:H7 EDL933 (lpfA1-3, lpfA2-2, stx1, stx2, and eae-γ) and EPEC O127:H6 E2348/69 (eae-α, lpfA1-1, and bfpA) strains using the optimized mPCR protocol with purified genomic DNA (gDNA). A screen of gDNA from isolates in a diarrheagenic E. coli collection revealed that the mPCR assay was successful in predicting the correct pathotype of EPEC and EHEC clones grouped in the distinctive phylogenetic disease clusters EPEC1 and EHEC1, and was able to differentiate EHEC1 from EHEC2 clusters. The assay detection threshold was 2 × 10⁴ CFU per PCR reaction for EHEC and EPEC. mPCR was also used to screen Argentinean clinical samples from hemolytic uremic syndrome and diarrheal patients, resulting in 91% sensitivity and 84% specificity when compared to established molecular diagnostic procedures. In conclusion, our mPCR methodology permitted differentiation of EPEC, STEC and EHEC strains from other pathogenic E. coli; therefore, the assay becomes an additional tool for rapid diagnosis of these organisms.