Simultaneous quantification of the most common and proteolytic Pseudomonas species in raw milk by multiplex qPCR

The heat-stable peptidase AprX, secreted by psychrotolerant Pseudomonas species in raw milk, is a major cause of destabilization and premature spoilage of ultra-high temperature (UHT) milk and milk products. To enable rapid detection and quantification of seven frequent and proteolytic Pseudomonas species (P. proteolytica, P. gessardii, P. lactis, P. fluorescens, P. protegens, P. lundensis, and P. fragi) in raw milk, we developed two triplex qPCR assays taking into account species-dependent differences in AprX activity. Besides five species-specific hydrolysis probes, targeting the aprX gene, a universal rpoB probe was included in the assay to determine the total Pseudomonas counts. For all six probes, linear regression lines between C-q value and target DNA concentration were obtained in singleplex as well as in multiplex approaches, yielding R-2 values of > 0.975 and amplification efficiencies of 85-97%. Moreover, high specificity was determined using genomic DNA of 75 Pseudomonas strains, assigned to 57 species, and 40 other bacterial species as templates in the qPCR. Quantification of the target species and total Pseudomonas counts resulted in linear detection ranges of approx. 10(3)-10(7) cfu/ml, which correspond well to common Pseudomonas counts in raw milk. Application of the assay using 60 raw milk samples from different dairies showed good agreement of total Pseudomonas counts calculated by qPCR with cell counts derived from cultivation. Furthermore, a remarkably high variability regarding the species composition was observed for each milk sample, whereby P. lundensis and P. proteolytica/P. gessardii were the predominant species detected.

Automated summary

Two triplex qPCR assays were developed for rapid detection and quantification of seven frequent and proteolytic Pseudomonas species in raw milk, along with a universal probe for total Pseudomonas counts. The assays showed high specificity and accurate quantification within linear detection ranges suitable for raw milk samples. Variability in species composition was observed in raw milk samples, with P. lundensis and P. proteolytica/P. gessardii being the predominant species detected.