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

An Evaluation of the Sensitivity and Applicability of a Droplet Digital Polymerase Chain Reaction Assay to Simultaneously Detect Pseudomonas aeruginosa and Pseudomonas fragi in Foods

Achieving effective control over microbial contamination necessitates the precise and concurrent identification of numerous pathogens. As a common bacterium in the environment, Pseudomonas is rich in variety. It not only has pathogenic strains, but also spoilage bacteria that cause food spoilage. In this research, we devised a remarkably sensitive duplex droplet digital PCR (dddPCR) reaction system to simultaneously detect pathogenic Pseudomonas aeruginosa (P. aeruginosa) and spoilage Pseudomonas fragi (P. fragi). By employing comparative genomics, we identified four genes of P. fragi. Through a specific analysis, the RS22680 gene was selected as the detection target for P. fragi, and the lasR gene was chosen for P. aeruginosa, which were applied to construct a dddPCR reaction. In terms of specificity, sensitivity and anti-interference ability, the constructed dddPCR detection system was verified and analyzed. The assay showed excellent sensitivity and applicability, as evidenced by a limit of detection of 100 cfu/mL. When the concentration of natural background bacteria in milk or fresh meat was 100 times that of the target detection bacteria, the method was still capable of completing the absolute quantification. In the simulation of actual sample contamination, P. aeruginosa could be detected after 3 h of enrichment culture, and P. fragi could be detected after 6 h. The established dddPCR detection system exhibits exceptional performance, serving as a foundation for the simultaneous detection of various pathogenic bacteria in food products.

Monitoring the Photorhabdus spp. bacterial load in Heterorhabditis bacteriophora dauer juveniles over different storage times and temperatures: A molecular approach

Biological control products based on the entomopathogenic nematode Heterorhabditis bacteriophora can vary in virulence (quality). The influence of their symbiotic bacteria Photorhabdus spp. inside the infective dauer juvenile (DJ) on DJ quality has not received much attention in the past. The presence of the bacteria in the DJ is crucial for its biocontrol potential. This investigation provides a method to quantify the bacterial load inside the DJ based on a qPCR technique. Information from the genome of Photorhabdus laumondii strain DE2 was used to identify single copy genes with no homology to any other bacterial accessions. One gene (hereby named CG2) was selected for primers design and for further qPCR experiments. Cross-amplification tests with P. thracensis and P. kayaii, also symbionts of H. bacteriophora, were positive, whereas no amplicons were produced for P. temperata or Xenorhabdus nematophila. We tested our qPCR system in DJ populations carrying defined proportions of bacteria-free (axenic) vs bacteria-carrying nematodes. With an increasing proportion of axenic DJ in a population, virulence declined, and the virulence was proportional to the amount of bacterial DNA detected in the population by qPCR. Along liquid storage over long time, virulence also decreased, and this factor correlated with the reduction of bacterial DNA on the respective DJ population. We observed that stored DJ kept virulent up to 90 days and thereafter the virulence as well as the amount of bacterial DNA drastically decreased. Storage temperature also influenced the bacterial survival. Inside formulated DJ, the loss of bacterial DNA on the DJ population was accelerated under storage temperatures below 7.5 °C, suggesting that reproduction of the bacterial cells takes place when growth temperature is favorable. The role of bacterial survival inside stored DJ can now be adequately addressed using this molecular quality-control technique.

Interplays between cyanobacterial blooms and antibiotic resistance genes

Cyanobacterial harmful algal blooms (cyanoHABs), which are a form of microbial dysbiosis in freshwater environments, are an emerging environmental and public health concern. Additionally, the freshwater environment serves as a reservoir of antibiotic resistance genes (ARGs), which pose a risk of transmission during microbial dysbiosis, such as cyanoHABs. However, the interactions between potential synergistic pollutants, cyanoHABs, and ARGs remain poorly understood. During cyanoHABs, Microcystis and high microcystin levels were dominant in all the nine regions of the river sampled. The resistome, mobilome, and microbiome were interrelated and linked to the physicochemical properties of freshwater. Planktothrix and Pseudanabaena competed with Actinobacteriota and Proteobacteria during cyanoHABs. Forty two ARG carriers were identified, most of which belonged to Actinobacteriota and Proteobacteria. ARG carriers showed a strong correlation with ARGs density, which decreased with the severity of cyanoHAB. Although ARGs decreased due to a reduction of ARG carriers during cyanoHABs, mobile gene elements (MGEs) and virulence factors (VFs) genes increased. We explored the relationship between cyanoHABs and ARGs for potential synergistic interaction. Our findings demonstrated that cyanobacteria compete with freshwater commensal bacteria such as Actinobacteriota and Proteobacteria, which carry ARGs in freshwater, resulting in a reduction of ARGs levels. Moreover, cyanoHABs generate biotic and abiotic stress in the freshwater microbiome, which may lead to an increase in MGEs and VFs. Exploration of the intricate interplays between microbiome, resistome, mobilome, and pathobiome during cyanoHABs not only revealed that the mechanisms underlying the dynamics of microbial dysbiosis but also emphasizes the need to prioritize the prevention of microbial dysbiosis in the risk management of ARGs.

Proteolytic activity and heat resistance of the protease AprX from Pseudomonas in relation to genotypic characteristics

AprX is an alkaline metalloprotease produced by Pseudomonas spp. and encoded by its initial gene of the aprX-lipA operon. The intrinsic diversity among Pseudomonas spp. regarding their proteolytic activity is the main challenge for the development of accurate methods for spoilage prediction of ultra-high temperature (UHT) treated milk in the dairy industry. In the present study, 56 Pseudomonas strains were characterized by assessing their proteolytic activity in milk before and after lab-scale UHT treatment. From these, 24 strains were selected based on their proteolytic activity for whole genome sequencing (WGS) to identify common genotypic characteristics that correlated with the observed variations in proteolytic activity. Four groups (A1, A2, B and N) were determined based on operon aprX-lipA sequence similarities. These alignment groups were observed to significantly influence the proteolytic activity of the strains, with an average proteolytic activity of A1 > A2 > B > N. The lab-scale UHT treatment did not significantly influence their proteolytic activity, indicating a high thermal stability of proteases among strains. Amino acid sequence variation of biologically-relevant motifs in the AprX sequence, namely the Zn²⁺-binding motif at the catalytic domain and the C-terminal type I secretion signaling mechanism, were found to be highly conserved within alignment groups. These motifs could serve as future potential genetic biomarkers for determination of alignment groups and thereby strain spoilage potential.

Peptidomic Fingerprints of Stored UHT Milk Inoculated with Protease Extracts from Different Pseudomonas Strains Relative to aprX Expression and Visible Spoilage

Lately, concern about the protease AprX produced by Pseudomonas has increased in the dairy industry due to its ability to survive UHT treatment and spoil UHT milk. Efficient prediction methods for UHT milk spoilage are currently lacking, mainly due to high diversity in proteolytic potential between Pseudomonas strains. The present study aimed to gain more insight into the variability between Pseudomonas strains regarding proteolytic potential by comparing their proteolytic capability with their aprX expression levels and differences in peptide formation. The variability in aprX expression levels in four Pseudomonas strains were related to physical stability, milk proteolysis and peptidomic cleavage patterns of milk proteins in a storage experiment of UHT milk inoculated with protease extracellular extracts and stored for 45 days at 20 °C. A positive relationship was observed between the relative expression of aprX and milk proteolysis during storage, with the strain Pseudomonas panacis DSM 18529 showing the highest level in both parameters. This strain was the only strain to show visual gelation, which occurred after 21 days. The peptide formation analysis showed a similar protein hydrolysis pattern between strains and high hydrolysis of αs1-caseins during long-term spoilage putatively due to the activity of AprX was observed.

DNA extraction leads to bias in bacterial quantification by qPCR

Quantitative PCR (qPCR) has become a widely used technique for bacterial quantification. The affordability, ease of experimental design, reproducibility, and robustness of qPCR experiments contribute to its success. The establishment of guidelines for minimum information for publication of qPCR experiments, now more than 10 years ago, aimed to mitigate the publication of contradictory data. Unfortunately, there are still a significant number of recent research articles that do not consider the main pitfalls of qPCR for quantification of biological samples, which undoubtedly leads to biased experimental conclusions. qPCR experiments have two main issues that need to be properly tackled: those related to the extraction and purification of genomic DNA and those related to the thermal amplification process. This mini-review provides an updated literature survey that critically analyzes the following key aspects of bacterial quantification by qPCR: (i) the normalization of qPCR results by using exogenous controls, (ii) the construction of adequate calibration curves, and (iii) the determination of qPCR reaction efficiency. It is primarily focused on original papers published last year, where qPCR was applied to quantify bacterial species in different types of biological samples, including multi-species biofilms, human fluids, and water and soil samples. KEY POINTS: • qPCR is a widely used technique used for absolute bacterial quantification. • Recently published papers lack proper qPCR methodologies. • Not including proper qPCR controls significantly affect experimental conclusions.

Naked-Eye Detection of Food-Borne Pathogens Using Multiplex Hyperbranched Rolling Circle Amplification and Magnetic Particles

Food safety is a significant public health issue in both developed and developing countries. Previous detection methods struggle to meet the current demands. We have proposed a new way to detect pathogens, allowing detection to be visualized by the naked eye. Using our newly developed assay, when target genes are present in the reaction, corresponding padlock probes form closed-loop molecules. Each reaction tube contains a pair of universal primers for identifying target genes. The ring padlock probes and corresponding universal primers start hyperbranched rolling circle amplification (HRCA) under the action of the polymerase, so as to gain branched chain amplification products, which are irreversibly entangled with magnetic particles to form aggregated magnetic particle clusters, and the detection results are visible to naked eyes. On the contrary, by using linear probes, the clustering of magnetic particles will not be produced. This method was applied to the detection of five food-borne pathogens enterohemorrhagic Escherichia coli (EHEC), enterotoxigenic Escherichia coli (ETEC), enteropathogenic Escherichia coli (EPEC), enteroinvasive Escherichia coli (EIEC) and Escherichia coli (E. coli), with detection limits of 1 × 10³, 1 × 10⁴, 1 × 10³, 1 × 10⁴ and 1 × 10² CFU/mL, respectively. This method can realize multiplex automatic detection of nucleic acid and shows great development potential in the field of molecular diagnosis.

Biochemical, microbiological, and structural evaluations to early detect age gelation of milk caused by proteolytic activity of Pseudomonas fluorescens

Heat–stable peptidase AprX, released by Pseudomonas species in raw milk during cold storage, can cause gelation of UHT milk since it is able to split caseinomacropeptides (CMPtot) from κ-casein, so inducing aggregation of casein micelles. Identifying raw milk susceptibility to gelation would allow UHT milk manufacturers to select appropriate processing conditions or give the milk a different destination. Two approaches, i.e., detection of free CMPtot and evidence of casein aggregates, were evaluated as possible indicators for early detecting milk destabilization. With this aim, microfiltered milk was inoculated with a P. fluorescence strain and incubated at either 4 or 25 °C. The presence of CMPtot was detected using capillary electrophoresis after 96 and 24 h at the two temperatures, respectively, when milk also became heat unstable and small flocks of protein appeared. Confocal laser scanning microscopy evidenced initial aggregates of casein micelles after 48 and 24 h at 4 and 25 °C, respectively. Keeping the milk at 25 °C/24 h could be a useful condition to accelerate milk destabilization. Despite the similar timing of instability detection, presence of CMPtot was the only trait specific for AprX activity.

Bacterial Composition and Interactions in Raw Milk and Teat Skin of Dairy Cows

The microbiota in raw milk plays an important role in the health of dairy cows and the safety of dairy products, which might be influenced by that in teat skin. However, the microbiota composition in raw milk and teat skin, as well as the bacterial interaction between the two adjacent spatial locations, remains elusive. Here, we investigated the composition, diversity, and co-occurrence network of the bacterial communities in raw milk and on teat skin, as well as the shift of bacterial communities during the teat bath using 469 samples from 156 individual cows. We observed that raw milk and teat skin harbored significantly different bacterial communities according to an assessment of the genera numbers (p < 0.05) and PCoA analysis (ANOSIM p < 0.05). The microbiota in raw milk was dominated by Proteobacteria (58.5% in relative abundance) at the phylum level and by Pseudomonas (51.2%) at the genus level, while that in teat skin was dominated by Firmicutes (46.9%) at the phylum level and by Pseudomonas (11.0%) at the genus level. We observed a massive difference between the bacterial subnetworks in raw milk and teat, and the bacterial abundance in these two adjacent spatial locations was positively correlated (p < 0.05). Using Bayesian algorithms, we identified that 92.1% of bacteria in raw milk were transferred from teat skin, while 63.6% of bacteria on teat skin were transferred from raw milk. Moreover, microbiota composition in teat skin could be affected by the teat bath with iodine disinfectant, which tended to be more similar to that in raw milk after the teat bath (p < 0.05), while the abundance of the dominant genus Pseudomonas significantly increased (p < 0.05). These findings expand our knowledge on the microbiota composition in teat skin and raw milk, as well as the interaction between these two adjacent spatial locations.

Rapid Identification of Pseudomonas fluorescens Harboring Thermostable Alkaline Protease by Real-Time Loop-Mediated Isothermal Amplification

ABSTRACT

Thermostable alkaline protease (TAP) harbored by Pseudomonas fluorescens decomposes protein in milk and dairy products, leading to milk and dairy product spoilage during storage. Thus, a specific, sensitive, rapid, and simple method is required to detect TAP-harboring P. fluorescens. Two sets of primers targeting the aprX and gyrB genes of P. fluorescens were designed. The detection system and conditions were optimized, and a real-time loop-mediated isothermal amplification (real-time LAMP) method was developed for the simultaneous detection of TAP-harboring P. fluorescens in two separate reaction tubes. The phylogenetic tree targeting aprX showed that P. fluorescens and Pseudomonas lurida clustered on the same branch. The phylogenetic tree targeting gyrB showed that P. fluorescens clustered on the same branch with 95% confidence value, whereas P. lurida clustered on different branches. DNA of 16 strains of P. fluorescens and 34 strains of non-P. fluorescens was detected by real-time LAMP. TAP-harboring P. fluorescens can only be identified when the real-time LAMP detection results of both aprX and gyrB are positive. The dissociation temperatures of aprX and gyrB in the real-time LAMP-amplified products were approximately 90.0 and 88.0°C, respectively. The detection limits of the real-time LAMP targeting aprX and gyrB were 4.9 CFU per reaction in pure culture and 2.2 CFU per reaction in skimmed milk. The coefficient of variation of the repeatability test was less than 2%, indicating that the established real-time LAMP of P. fluorescens targeting gyrB and aprX has good stability and repeatability. Real-time LAMP was used to test 200 raw milk samples for the presence of TAP-harboring P. fluorescens in 3 h, and the coincidence rate of the results with those obtained using the traditional method, which takes at least 5 to 7 days, was 100%. Real-time LAMP will be a practical and effective method for accurate and rapid identification of TAP-harboring P. fluorescens in raw milk.

HIGHLIGHTS

Establishment and Evaluation of a Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Pseudomonas fluorescens in Raw Milk

Raw milk is susceptible to microbial contamination during transportation and storage. Pseudomonas fluorescens producing heat-resistant enzymes have become the most common and harmful psychrophilic microorganisms in the cold chain logistics of raw milk. To rapidly detect P. fluorescens in raw milk, the protease gene aprX was selected as a detection target to construct a set of primers with strong specificity, and a loop-mediated isothermal amplification (LAMP) assay was established. The detection thresholds of the LAMP assay for pure cultured P. fluorescens and pasteurized milk were 2.57 × 10² and 3 × 10² CFU/mL, respectively. It had the advantages over conventional method of low detection threshold, strong specificity, rapid detection, and simple operation. This LAMP assay can be used for online monitoring and on-site detection of P. fluorescens in raw milk to guarantee the quality and safety of dairy products.

Maternal IgA2 Recognizes Similar Fractions of Colostrum and Fecal Neonatal Microbiota

Microbiota acquired during labor and through the first days of life contributes to the newborn’s immune maturation and development. Mother provides probiotics and prebiotics factors through colostrum and maternal milk to shape the first neonatal microbiota. Previous works have reported that immunoglobulin A (IgA) secreted in colostrum is coating a fraction of maternal microbiota. Thus, to better characterize this IgA-microbiota association, we used flow cytometry coupled with 16S rRNA gene sequencing (IgA-Seq) in human colostrum and neonatal feces. We identified IgA bound bacteria (IgA+) and characterized their diversity and composition shared in colostrum fractions and neonatal fecal bacteria. We found that IgA2 is mainly associated with Bifidobacterium, Pseudomonas, Lactobacillus, and Paracoccus, among other genera shared in colostrum and neonatal fecal samples. We found that metabolic pathways related to epithelial adhesion and carbohydrate consumption are enriched within the IgA2+ fecal microbiota. The association of IgA2 with specific bacteria could be explained because these antibodies recognize common antigens expressed on the surface of these bacterial genera. Our data suggest a preferential targeting of commensal bacteria by IgA2, revealing a possible function of maternal IgA2 in the shaping of the fecal microbial composition in the neonate during the first days of life.

Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk

Full-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the species-level classification was improved in comparison to short amplicon sequencing. Therefore, we anticipate that this approach might be useful for the detection of possible mastitis-causing species, as well as for the control of spoilage-associated microorganisms. In a proof of concept, we showed that we were able to identify several putative mastitis-causing or mastitis-associated species such as Streptococcusuberis, Streptococcusagalactiae, Streptococcusdysgalactiae, Escherichiacoli and Staphylococcusaureus, as well as several Candida species. Overall, the presented full-length approach for the sequencing of SSU rRNA is easy to conduct, able to be standardized, and allows the screening of microorganisms in labs with Illumina sequencing machines.

A Milk Foodomics Investigation into the Effect of Pseudomonas fluorescens Growth under Cold Chain Conditions

Pseudomonas fluorescens is a psychrotrophic species associated with milk spoilage because of its lipolytic and proteolytic activities. Consequently, monitoring P. fluorescens or its antecedent activity in milk is critical to preventing quality defects of the product and minimizing food waste. Therefore, in this study, untargeted metabolomics and peptidomics were used to identify the changes in milk related to P. fluorescens activity by simulating the low-temperature conditions usually found in milk during the cold chain. Both unsupervised and supervised multivariate statistical approaches showed a clear effect caused by the P. fluorescens inoculation on milk samples. Our results showed that the levels of phosphatidylglycerophosphates and glycerophospholipids were directly related to the level of contamination. In addition, our metabolomic approach allowed us to detect lipid and protein degradation products that were directly correlated with the degradative metabolism of P. fluorescens. Peptidomics corroborated the proteolytic propensity of P. fluorescens-contaminated milk, but with lower sensitivity. The results obtained from this study provide insights into the alterations related to P. fluorescens 39 contamination, both pre and post heat treatment. This approach could represent a potential tool to retrospectively understand the actual quality of milk under cold chain storage conditions, either before or after heat treatments.