Enumeration of viable Escherichia coli by real-time PCR with propidium monoazide

Viability and removal assessment of Escherichia coli and Salmonella spp. by real-time PCR with propidium monoazide in the hygienization of sewage sludge using three anaerobic processes

Sewage sludge should be stabilized for its beneficial use and pathogens, among other factors, should comply with environmental regulations. Three sludge stabilization process were compared to assess their suitability for producing Class A biosolids: MAD-AT (mesophilic (37 °C) anaerobic digestion (MAD) followed by an alkaline treatment (AT)); TAD (thermophilic (55 °C) anaerobic digester); and TP-TAD (mild thermal (80 °C, 1 h) pretreatment (TP) followed by a TAD). E. coli and Salmonella spp. were determined, differentiating three possible states: total cells (qPCR), viable cells using the propidium monoazide method (PMA-qPCR), and culturable cells (MPN). Culture techniques followed by the confirmative biochemical tests identified the presence of Salmonella spp. in PS and MAD samples, while the molecular methods (qPCR and PMA-qPCR) showed negative results in all samples. The TP + TAD arrangement reduced the concentration of total and viable E. coli cells in a greater extent than the TAD process. However, an increase of culturable E. coli was observed in the corresponding TAD step, indicating that the mild thermal pretreatment induced the viable but non-culturable state in E. coli. In addition, the PMA technique did not discriminate viable from non-viable bacteria in complex matrices. The three processes produced Class A biosolids (fecal coliforms < 1000 MPN/gTS and Salmonella spp, < 3 MPN/gTS) maintaining compliance after a 72 h storage period. It appears that the TP step favors the viable but not culturable state in E. coli cells, a finding that should be considered when adopting mild thermal treatment in sludge stabilization process arrangements.

Improving Mycoplasma hyopneumoniae diagnostic capabilities by harnessing the infection dynamics

Mycoplasma hyopneumoniae remains one of the most problematic bacterial pathogens for pig production. Despite an abundance of observational and laboratory testing capabilities for this organism, diagnostic interpretation of test results can be challenging and ambiguous. This is partly explained by the chronic nature of M. hyopneumoniae infection and its tropism for lower respiratory tract epithelium, which affects diagnostic sensitivities associated with sampling location and stage of infection. A thorough knowledge of the available tools for routine M. hyopneumoniae diagnostic testing, together with a detailed understanding of infection dynamics, are essential for optimizing sampling strategies and providing confidence in the diagnostic process. This study reviewed known information on sampling and diagnostic tools for M. hyopneumoniae and summarized literature reports of the dynamics of key infection outcomes, including clinical signs, lung lesions, pathogen detection, and humoral immune responses. Such knowledge could facilitate better understanding of the performance of different diagnostic approaches at various stages of infection.

Specific detection of Lysobacter antibioticus strains in agricultural soil using PCR and real-time PCR

Lysobacter antibioticus is an important biocontrol bacteria against phytopathogens in soil, and with the ability to produce nonvolatile antimicrobial metabolites has been extensively characterised. It is important to establish applicable techniques to detect and monitor L. antibioticus directly and accurately in soil samples. We developed and tested 13 primer sets according to phenazine gene (phzA, phzB, phzD, phzF, phzS) and the cyclohexanone monooxygenase gene (phzNO1); a pair of primer phzNO1 F1/phzNO1 R1 based on the cyclohexanone monooxygenase (phzNO1) gene of L. antibioticus strain OH13 was selected and optimized polymerase chain reaction (PCR) amplification conditions for rapid and accurate detection. After screening eight strains of L. antibioticus, two strains of Lysobacter enzymogenes, one strain of Lysobacter capsici, Arthrobacterium, Bacillus, Microbacterium, Burkholderia, Pseudomonas and other bacterial strains isolated from different agricultural soils, the phzNO1 F1/phzNO1 R1 primers amplified a single PCR band of about 229 bp from L. antibioticus. The detection sensitivity with primers phzNO1 F1/phzNO1 R1 was 5.14 × 104 fg/25μL of genomic DNA and 2.254 × 1010 to 2.254 × 1011 colony-forming units/mL for the soil samples. Quantitative PCR assays were to develope as a specific method to monitor the L. antibioticus population in soil as well as guide soil micro-ecological management.

Detection of viable Escherichia coli in environmental water using combined propidium monoazide staining and quantitative PCR

The objectives of this study were to specifically detect viable Escherichia coli in environmental waters by targeting the ycjM gene in a propidium monoazide (PMA)-qPCR assay. PMA is a viability dye that can inhibit the amplification of DNA from dead cells, thus allowing for the detection and quantification of only viable cells. The ycjM primers were used to target E. coli that directly originated from the feces of warm blooded animals, and avoid false positive detection caused by "naturalized" E. coli that can exist in the environment. In this study, tap water and environmental waters were inoculated with E. coli isolated from animal feces. Following cell collection, samples were treated with PMA, followed by DNA isolation and qPCR detection. For pure cultures, 5 μM PMA with a 10-min light exposure was efficient at inhibiting the amplification of DNA from 10⁵ CFU/mL dead E. coli cells, with a detection limit of 10² CFU/100 mL viable cells. For tap and environmental waters collected in the winter, a 10 μM PMA was required and as low as 10³ CFU/100 mL viable cells could be detected in the presence of 10⁵ CFU/100 mL dead cells. For water samples collected during the summer, 10² CFU/10 mL viable cells could be detected in the presence of 10⁴ CFU/10 mL dead cells, after a 20 μM PMA treatment. No significant differences were found among the PMA-qPCR assay and two other standard culture-based methods for detection of viable E. coli in environmental water. In conclusion, with proper pretreatment of environmental water samples, this PMA-qPCR assay that targets the ycjM gene could quantify viable E. coli cells that directly come from the feces of warm-blooded animals, and therefore effectively and accurately indicate the quality of environmental water.

Persistence of bacterial DNA in orthopedic infections

Polymerase chain reaction (PCR) has been proposed as a method to identify bacteria in clinical samples because it is more sensitive than culture techniques and can produce results rapidly. However, PCR can detect DNA from dead cells and thus cannot distinguish between live and dead cells in a tissue sample. Killed Staphylococcus aureus cells were implanted into the femurs and knee joints of rats to determine the length of time that DNA from dead cells is detectable in a living animal under conditions similar to common orthopedic infections. In the joint infection model studied here, the DNA from the dead planktonic bacteria was detected using PCR immediately after injection or 24 h later, but was undetectable 48 and 72 h after injection. In the biofilm implanted-device model studied, the DNA from these dead biofilm cells was detected by PCR immediately after implantation and at 24 h, but not at 48 or 72 h. Thus, our results indicate that DNA from dead cells does not persist in these animal model systems for more than 2 days, which should reduce concerns about possible false positive results using molecular DNA-based techniques for the detection of pathogens.

Use of real-time PCR with propidium monoazide for enumeration of viable Escherichia coli in anaerobic digestion

A combination of propidium monoazide (PMA) with real-time quantitative polymerase chain reaction (PMA-qPCR) was optimized to enumerate only viable Escherichia coli in anaerobic digestion processes. Repeating the PMA treatment twice and a final concentration of 100 μM resulted in an effective exclusion of DNA from heat-treated E. coli cells. In three anaerobic digestion processes, real-time PCR, PMA-qPCR, and the most probable number method (MPN) were used to estimate the numbers of total, viable, and culturable E. coli cells, respectively. Culturable concentrations of fecal coliforms were also measured by the membrane filter method. For thermophilic digestion, the reductions in total and viable E. coli cells from the digester influent to the effluent were significantly lower than those in culturable cells and fecal coliforms by two to four orders of magnitude. For mesophilic digestion, the differences in the reductions in E. coli and fecal coliforms counts were less than two orders of magnitude. Based on the measurements of viable E. coli determined by the PMA-qPCR method, the microbial quality of digester effluents was discussed for agricultural application, and pasteurization after anaerobic digestion was suggested for the destruction of viable pathogens.

Evaluation of quantitative PCR combined with PMA treatment for molecular assessment of microbial water quality

Microbial water quality assessment currently relies on cultivation-based methods. Nucleic acid-based techniques such as quantitative PCR (qPCR) enable more rapid and specific detection of target organisms and propidium monoazide (PMA) treatment facilitates the exclusion of false positive results caused by DNA from dead cells. Established molecular assays (qPCR and PMA-qPCR) for legally defined microbial quality parameters (Escherichia coli, Enterococcus spp. and Pseudomonas aeruginosa) and indicator organism group of coliforms (implemented on the molecular detection of Enterobacteriaceae) were comparatively evaluated to conventional microbiological methods. The evaluation of an extended set of drinking and process water samples showed that PMA-qPCR for E. coli, Enterococcus spp. and P. aeruginosa resulted in higher specificity because substantial or complete reduction of false positive signals in comparison to qPCR were obtained. Complete compliance to reference method was achieved for E. coli PMA-qPCR and 100% specificity for Enterococcus spp. and P. aeruginosa in the evaluation of process water samples. A major challenge remained in sensitivity of the assays, exhibited through false negative results (7-23%), which is presumably due to insufficient sample preparation (i.e. concentration of bacteria and DNA extraction), rather than the qPCR limit of detection. For the detection of the indicator group of coliforms, the evaluation study revealed that the utilization of alternative molecular assays based on the taxonomic group of Enterobacteriaceae was not adequate. Given the careful optimization of the sensitivity, the highly specific PMA-qPCR could be a valuable tool for rapid detection of hygienic parameters such as E. coli, Enterococcus spp. and P. aeruginosa.

Use of propidium monoazide for the enumeration of viable Brettanomyces bruxellensis in wine and beer by quantitative PCR

Brettanomyces bruxellensis is a current problem in winemaking all over the world, and the question if B. bruxellensis has a positive or negative impact on wine is one of the most controversial discussions in the world. The presence of live B. bruxellensis cells represents the risk of growth and an increase in cell numbers, which is related to the potential production of volatile phenols. In this work, the optimisation of a PMA-quantitative PCR (qPCR) method to enumerate only viable cells was carried out using the standard strain B. bruxellensis DSMZ 70726. The obtained detection limits were 0.83 log CFU/mL in red wine, 0.63 log CFU/mL in white wine and 0.23 log CFU/mL in beer. Moreover, the quantification was also performed by Reverse Transcription quantitative PCR (RT-qPCR), and the results showed a higher detection limit for all of the trials.

Propidium monoazide-quantitative polymerase chain reaction for viable Escherichia coli and Pseudomonas aeruginosa detection from abundant background microflora

Nucleic acid-based techniques represent a promising alternative to cultivation-based microbial water quality assessment methods. However, their application is hampered by their innate inability to differentiate between living and dead organisms. Propidium monoazide (PMA) treatment was proposed as an efficient approach for alleviating this limitation. In this study, we demonstrate the performance of PMA-quantitative polymerase chain reaction (qPCR) for the detection of indicator organisms (Escherichia coli and Pseudomonas aeruginosa) in a background of a highly abundant and complex microflora. Treatment with 10 μM PMA resulted in the complete or significant reduction of the false positive signal arising from the amplification of DNA from dead cells.

Use of propidium monoazide for the enumeration of viable Oenococcus oeni in must and wine by quantitative PCR

Malolactic fermentation is an important step in winemaking, but it has to be avoided in some cases. It's carried out by lactic acid bacteria belonging mainly to the genus Oenococcus, which is known to be a slow growing bacterium. Classical microbiological methods to enumerate viable cells of Oenococcus oeni in must and wine take 7-9 days to give results. Moreover, RT-qPCR technique gives accurate quantitative results, but it requires time consuming steps of RNA extraction and reverse transcription. In the present work we developed a fast and reliable quantitative PCR (qPCR) method to enumerate cells of Oenococcus oeni, directly, in must and wine. For the first time we used a propidium monoazide treatment of samples to enumerate only Oenococcus oeni viable cells. The detection limit of the developed method is 0.33 log CFU/mL (2.14 CFU/mL) in must, and 0.69 log CFU/mL (4.90 CFU/mL) in wine, lower than that of the previously developed qPCR protocols.