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Characterization of Serratia species and qualitative detection of Serratia marcescens in raw and pasteurized milk by an analytical method based on polymerase chain reaction

DOI: https://doi.org/10.52091/EVIK-2021/2-4-ENG

Submitted: July 2020 – Accepted: December 2020

Authors

1 Hungarian Dairy Research Institute Ltd, Mosonmagyaróvár
2 Széchenyi István University, Wittmann Antal Multidisciplinary Doctoral School in Plant, Animal, and Food Sciences, Mosonmagyaróvár
3 Széchenyi István University, Faculty of Agricultural and Food Sciences, Department of Food Science, Mosonmagyaróvár

Keywords

nosocomial infection, Serratia species, Serratia marcescens, pathogen, prodigiosin, pigment, polymerase chain reaction (PCR), food diagnostics

1. Summary

Serratia species are opportunistic pathogenic microorganisms primarily known as nosocomial infectious agents, which can also cause food quality problems. The appearance of the extracellular pigment-producing Serratia marcescens in cow’s milk causes its red discoloration, posing a challenge to the dairy industry and food certification laboratories. The detection of the bacterium by conventional procedures based on microbiological methods is time-consuming and labor-intensive, and in many cases does not lead to satisfactory results due to the competitive inhibitory effect of the accompanying microflora. Following the analysis of the relevant literature, the published endpoint PCR methods and the primers used for the detection of S. marcescens were evaluated in in silico and in vitro assays, and then the procedure was tested on farm milk samples. Using the method, a total of 60 raw and pasteurized milk samples were analyzed, more than half of which (i.e., 32) were identified as S. marcescens positive. The significance of our work is mainly represented by the application of the published test methods in food industry practice. Our results highlight to the importance of detecting this bacterial species.

2. Introduction and literature review

Nowadays, the impeccable quality and long shelf life of foods is a basic requirement of consumers. Accordingly, there is a growing demand for ever faster, more accurate and more reliable food diagnostic procedures. In this context, molecular diagnostic methods are gaining ground, for example in the rapid detection of pathogenic microorganisms. Polymerase chain reaction (PCR)-based diagnostic kits suitable for the identification of pathogenic microbes are produced by many manufacturers, and these are also used successfully in Hungarian food testing laboratories. These molecular biological tests are mainly suitable for the detection of microbes hose presence poses a high risk to public health (e.g., Escherichia coli, Salmonella Typhimurium, Listeria spp.). Less attention is paid to pathogens that are not required to be tested by law, such as Serratia species present in raw and pasteurized milk.

Serratia species are found in many places in our environment [1]. They are saprophytes or opportunistic pathogens [2], facultative anaerobic, biofilm-forming organisms [1, 3]. S. marcescens grows particularly well in phosphorus-containing environments (e.g., soaps, shampoos) and is also resistant to certain disinfectants [4, 5], so it can cause various nosocomial diseases [6, 7, 8]. Increasing antibiotic resistance of S. marcescens has also been reported in the literature [8, 9, 10]. The bacterium therefore survives and grows easily, so it may find its way into foods under inadequate hygienic conditions. Presumably, it can enter drinking milk as a result of violating hygiene rules, it can grow there and degrade the quality of food [1, 11, 12]. For some species, spoilage is indicated by a characteristic red hue.

In the case of the Hungarian dairy sector, accurate data are not available on the extent of the prevalence of Serratia species and S. marcescens, and on which species cause the infections and degrade milk quality. Nor is there a Hungarian survey on the extent of Serratia contamination of dairy farms. With the exception of a few publications, the available information on the exposure of the dairy industry to Serratia is also lacking at the international level. Such exceptions are a scientific article on the epidemic of mastitis caused by S. marcescens at Finnish diary farms [1], and an older report discussing the role played by pigment-forming Serratia species in mastitis [13].

The following Serratia species may be responsible for the red discoloration of milk: S. marcescens, S. rubidaea, S. plymuthica and S. nematodiphila (Table 1). According to their incidence, S. marcescens is of greater importance. Their characteristic pigment is the red prodigiosin, a water-insoluble secondary metabolite that is produced under specific environmental conditions [14, 15, 16, 17] (Figure 1). The typical red colonies appearing on the culture medium alone do not provide sufficient information to identify Serratia, as certain species of many other genera, not belonging to Enterobacteria, may also produce prodigiosin [14, 18].

Table 1. Characterization of Serratia species and their pigment production [19–22]
Figure 1. Pure culture of Serratia marcescens on tryptone-soy agar (TSA) (30 °C, 48 h)

There is currently no ISO standard for the detection of Serratia species in foods. In their 2006 book chapter [9], Grimont and Grimont discuss the characteristics of the genus Serratia, as well as aspects of their isolation and identification. However, identification by classical microbiological methods is rather cumbersome and often ineffective due to the inhibitory effect of the accompanying flora, despite the fact that the pink discoloration of the milk sample is clearly visible to the naked eye. Although culture media are available for the selective growth of the bacterium [47], in practice their use does not provide a satisfactory solution. In addition, conventional methods are time and labor intensive.

There are commercially available rapid methods for the determination of S. marcescens, for example the miniaturized test kit from bioMérieux called Rapid ID 32 E, which satisfies the requirements of standard ISO 7218 [48]. However, a colony growing on a culture medium is required to perform the test. Diagnostic tests based on the PCR method, as mentioned before, could provide a solution to overcome the difficulties of detection. At present, however, only the Genesig product of Primerdesign can be mentioned as a molecular diagnostic kit for the detection of S. marcescens [49].

The literature relevant for the food industry and, in particular, the dairy industry, is rather poor on the detection of Serratia species, including S. marcescens, by either endpoint PCR or real-time PCR methods. Hejazi et al. [50] carried out the serotyping of S. marcescens by the RAPD-PCR technique. Serological samples from patients in need of hospital care were used in their study. Iwaya et al. [6] also tested blood samples for S. marcescens strains using a real-time PCR method. Zhu et al. [51] performed molecular characterization of S. marcescens strains by RFLP and PCR methods, while Joyner et al. [2] detected S. marcescens strains in marine and other aquatic environmental samples (e.g., coral mucus, sponge pore water, sediment, sewage, wastewater and diluted wastewater) by real-time PCR. A study of Bussalleu and Althouse, published in 2018, reports a conventional endpoint PCR technique suitable for the identification of S. marcescens that effectively detects the presence of the microorganism in wild boar semen [52].

Our goal was the set up a classical PCR method suitable for the detection of S. marcescens in milk. The significance of our work lies in the fact that PCR-based methods described in the literature and the primers used were analyzed, then the procedure deemed appropriate was adopted to food hygiene analytical practice. In our experiments, qualitative determination of the possible S. marcescens contamination underlying the discoloration of factory, raw and pasteurized milk samples was performed.

3. Materials and methods

3.1. In silico studies

Based on the literature, three primer pairs (Table 2) were selected, which were evaluated by computer modeling, by so-called in silico analysis, as well as in vitro experiments in order to find the most suitable one for subsequent PCR assays.

Table 2. Serratia marcescens-specific primer pairs used in this study

In our in silico studies, the specificity of the a primer sequences was verified by comparison with a DNA database (NCBI BLAST) [54]. Comparison with the database allows for homology search (“blasting”). Following this, the suitability of the primers, i.e., whether a possible PCR reaction takes place with the selected genomes, was tested with a molecular biology software (SnapGene 5.1.5.) [55]. In the latter case, positive and negative control genomes were downloaded from the NCBI database, and then the SnapGene software was used, in an in silico way, to investigate whether the PCR reaction would take place with the primer pairs. The positive and negative controls used for reference purposes were whole chromosome genomes (Table 3).

Table 3. Genomes of bacterial strains used as positive and negative controls in in silico analyses and their reactions to primer pairs

* Primerek: A. Fpfs1 és Rpfs2; B. FluxS1 és RluxS2; C. Serratia2-for és Serratia2-rev.

Jelmagyarázat:

3.2. In vitro experimental studies

To confirm the results of the in silico studies, in vitro were performed in which the selected primer pairs were tested in laboratory PCR analyses on genomic DNA samples of selected strains of bacteria (several S. marcescens strains were used as positive control and Lactobacillus delbrueckii subsp. delbrueckii, Streptococcus thermophilus, Enterococcus faecalis and Micrococcus luteus were used as negative controls). The microorganisms were bacterial strains belonging to the collection of MTKI Kft. and coming from factory environment, determined by genetic identification.

When putting together the components required for the PCR reaction, 5.2 µL of PCR grade sterile water, 10 µL of DreamTaq Green 2× PCR Master Mix (Thermo Fisher Scientific, Waltham, Massachusetts, USA), 0.4 µL (10 pmol/µl) primer and 4 µL of isolated bacterial genomic DNA were used for each reaction. The negative control of the reactions was PCR grade sterile water. The program parameters of the PCR instrument (Mastercycler Nexus Gradient; Eppendorf International, Hamburg, Germany) were as follows: 95 °C for 1 minute, then for 40 cycles 95 °C for 15 seconds, 59.5 °C for 15 seconds, 72 °C for 10 seconds and, finally, 72 °C for 7 minutes [52].

For size separation of the DNA segments formed during the PCR reaction, a 10 µL sample was analyzed on a 2% agarose gel [TBE buffer (Tris-borate-EDTA) (10×), Thermo Fisher Scientific; Agarose DNA Pure Grade, VWR International, Debrecen, Hungary; ECO Safe Nucleic Acid Staining Solution 20.000×, Pacific Image Electronics, Torrance, California, USA]. The DNA size marker was the GeneRuler Low Range DNA Ladder (Thermo Fisher Scientific). Gel documentation was performed using the Gel Doc Universal Hood II gel documentation equipment and software (Bio-Rad, Hercules, California, USA).

3.3. analysis of raw and pasteurized milk samples

On the one hand, we used in our study factory raw and pasteurized milk samples in the case of which S. marcescens contamination was suspected due to their pink discoloration. On the other hand, factory raw and pasteurized milk samples that arrived at the laboratory together with the above samples but not exhibiting discoloration were also tested.

For the DNA digestion and purification process, the NucleoSpin Microbial DNA kit (Macherey-Nagel, Düren, Germany) was used according to the manufacturer’s instructions. The reaction tubes containing the eluted DNA were stored in a freezer at -20 °C.

Next, the suitability of DNA isolation and the amplifiability of the samples were checked by 16S rDNS polymerase chain reaction, using primers 27f (5’-AGAGTTGATCMTGGCTCAG-3’) and 1492r (5’-TACGGYTACCTTGTTACGACTT-3’). The total volume of the PCR reaction for 1 sample was 5.6 µL of PCR grade sterile water, 10 µL DreamTaq Green 2× PCR Master Mix, 0.2 µL (10 pmol/µl) of the primers and 4 µL of isolated bacterial genomic DNA. The negative control of the reactions was PCR grade sterile water. The program parameters of the PCR instrument were as follows: 95 °C for 4 minutes, then for 40 cycles 95 °C for 20 seconds, 54 °C for 30 seconds, 72 °C for 1 minute and, finally, 72 °C for 5 minutes.

For the separation of the DNA segments formed during the PCR reaction, a 5 µL sample was analyzed on a 1% agarose gel. The DNA size marker was the GeneRuler 1 kb Plus DNA Ladder (Thermo Fisher Scientific). The DNA sample tested was judged to be suitable for further PCR analysis if the length of the copies of the amplified DNA fragment was as expected (~1500 bp).

In the next step, samples were subjected to S. marcescens-specific PCR analysis and gel electrophoresis as described in subsection IN VITRO EXPERIMENTAL STUDIES. The results were evaluated on the basis of the presence/absence principle.

In order to check the suitability of the method, PCR results of the milk samples were compared with the few available API (bioMérieux, Budapest, Hungary) test results in a control test. The method was then used to detect the presence of S. marcescens in raw and pasteurized milks.

4. Results

In our in silico studies, when examining the homology of the primers, they showed similarity primarily to S. marcescens chromosome genomes. However, matches were also found in the case of S. rubidaea and S. nematodiphila strains and some non-Serratia species. These results were taken into account during the selection of reference genomes designed for our SnapGene software studies. The need for further investigation was justified by the fact that appropriate homology or the matching of the basis do not automatically mean that the PCR reaction will take place, because the direction of the primers, their melting temperature and the size of the PCR product formed are also critical, among other things.

In the SnapGene test, PCR reactions were predicted with the following parameters: our analyses were performed with at least 15 bases matching and the exclusion of single isolated mismatches. The minimum melting temperature was 50 °C and the maximum length of the fragment obtained as the result of the amplification was 3 kbp.

As shown in Table 3, when matched with the S. marcescens genomes, the primer pair Serratia2-for and Serratia2-rev showed amplification in all cases. The PCR reaction generally resulted in six or seven amplicons on the 16S rDNA sections. The adhesion site of the Fpfs1–Rpfs2 and FluxS1–RluxS2 primer pairs is located outside the 16S rDNA in most S. marcescens strains, but in some cases they did not show in silico amplification, so their sensitivity did not prove to be adequate. In the negative control genomes, the completion of a PCR reaction was predicted by the primer pair Serratia2-for and Serratia2-rev in some cases for certain S. rubidaea and S. nematodiphila strains. Using primers Fpfs1–Rpfs2, the PCR reaction would take place in the case of a S. nematodiphila strain. Primers FluxS1–RluxS2 did not predict the occurrence of a reaction on any of the selected negative control genomes (Table 3).

In S. marcescens genomes selected as positive controls in in vitro experiments, all three primer pairs gave signals according to the expected fragment size, and none gave a signal on the negative controls. The analysis carried out with the primer pair Serratia2-for and Serratia2-rev is shown in Figure 2. In the case of negative samples, the weak signals at around 50 bp are caused by the accumulation of the byproduct aspecific DNA fragments, primer dimers.

Based on the results of in silico analyses and in vitro studies, primers Serratia2-for and Serratia2-rev were considered to be suitable for further work, despite the fact that their specificity was not perfect. The decision was based on the probable frequency of occurrence of S. marcescens on the one hand and the importance of avoiding samples with false negative results on the other.

In order to check the suitability of the method that had been set up, factory milk samples were tested in a control study. Some of the milk samples (n=10) exhibited pink discoloration. Using our test method, nine samples were found to be positive for the microbe sought. We also had API test results for four of the samples. The four API-positive samples were also found to be positive in the PCR assay. The method was then used to detect S. marcescens in raw and pasteurized milks.

Some of the milk samples showed peach-pink discoloration (Figure 3), but it was not clear in many cases due to the pale or yellowish tint. A total of 60 samples were analyzed. Of these, 32 (53.3%) gave positive results and 28 (46.7%) gave negative results for the presence of S. marcescens.

Figure 4 shows the result of one of our assays, the separation by gel electrophoresis. It can be clearly seen that the positive control strain gave a positive signal, while the negative control sample gave a negative signal, and positive signals were obtained for three test samples. The weak signals appearing in the case of negative samples are again caused by the accumulation of primer dimers.

Figure 2. Results of PCR analysis with Serratia2-for and Serratia2-rev primers on the genome of selected bacterial strains. Lanes: 1. Serratia marcescens 551R; 2. Serratia marcescens 1911; 3. Lactobacillus delbrueckii subsp. delbrueckii 0801; 4. Streptococcus thermophilus 1102; 5. Enterococcus faecalis 1101; 6. Micrococcus luteus CLTB1; 7. Negative control (sterile water); M: Molecular weight marker
Figure 3. Milk samples. Left sample is netive and right sample is positive for Serratia marcescens, based on the result of PCR test
Figure 4. Gel electrophoresis image of Serratia marcescens-specific PCR assay. Lanes 1 to 7: Milk samples; K+: Positive control (genomic DNA from Serratia marcescens); K-: Negative control (sterile water); M: Molecular weight marker

5. Discussion

When evaluating our results, it is important to take into account that the PCR analysis is a method suitable for the amplification and detection of the target DNA in the sample, based on which it is not possible to determine whether the amplified S. marcescens-specific DNA comes from viable, dead or so-called VBNC cells. In the VBNC (“viable but not culturable”) state, the cells are viable, metabolically active, but cannot be propagated by classical culture methods. This condition is reversible.

The objective of our work was to establish a classical PCR method for the detection of S. marcescens. Using the test procedure applied, qualitative determination of the S. marcescens contamination responsible for the discoloration of milk samples can be carried out.

Although the experiments presented here focused on the detection of pigment-producing S. marcescens, a future genus-level study could identify all 20 Serratia species (Table 1). The significance of the detection of other Serratia species is evidenced by the fact that, although the genus Pseudomonas is the main cause of the spoilage of chilled raw milk, the dangers of Serratia species in this respect are also known [56]. In addition to Pseudomonas strains, Serratia strains have also been identified in many cases as causes of milk spoilage. Members of the genus Serratia have been detected in dairy plants [3, 12], in raw milk samples stored at 4° C [56, 57, 58] and in milk containers [59]. It was noted by Grimont and Grimont [9] already a decade and a half ago that raw milk lots can occasionally be contaminated with Serratia species, and the species most often occurring in diary products are S. liquefaciens and S. grimesii.

The presence of psychotrophic Serratia species (e.g., S. liquefaciens) in raw milk can cause spoilage even after heat treatment. Baglinière et al. found that the thermally stable Ser2 protease produced by S. liquefaciens may be a significant factor in the destabilization of UHT milk [11, 60].

In conclusion, it can be stated that a genus-level study would be an interesting research project that would fill a gap, and which would allow the monitoring of raw milk in this respect, the wide detection of Serratia species. Presumably, the results would provide useful information not only to the stakeholders of the dairy economy and the dairy industry, but could also have an impact on Hungarian regulatory and monitoring practice.

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