Comparison of MALDI-TOF MS Biotyper and 16S rDNA sequencing for the identification of Pseudomonas species isolated from fish

The exploration of dominant spoilage bacteria in blue mussels (Mytilus edulis) stored under different modified atmospheres by MALDI-TOF MS in combination with 16S rRNA sequencing

Few studies have addressed species-level identification of spoilage bacteria in blue mussels packed under modified atmospheres (MAs). We investigated the effect of MAs and seasons on the tentative species-level of dominant spoilage bacteria in blue mussels. Summer (s) and winter (w) blue mussels were stored at 4 °C in the atmospheres (%CO2/O2/N2): A40s (30/40/30), B60s (40/60/0), C60s (0/60/40), A40w (30/40/30), and D75w (25/75/0). In total, 122 culturable isolates were obtained at the final stage of shelf life, when mortality was high (56-100%) and total psychrotrophic bacteria counted >7 log CFU g-1. Biochemical properties were analyzed using gram reactions, catalase and oxidase activities, and salt tolerance tests. Culturable isolates were identified through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16 S rRNA gene sequence analysis. Spoilage potential tests were investigated by evaluating protease, lipase, and fermentation activities as well as gas and H2S production. The culturable isolates showed tolerance to varied salt concentrations. Psychromonas arctica, Pseudoalteromonas elyakovii, and Shewanella frigidimarina were dominating in specific MAs. Winter blue mussels resulted in a higher variation of spoilage bacteria, including S. frigidimarina, S. vesiculosa, S. polaris, Micrococcus luteus, Paeniglutamicibacter terrestris sp. nov., and Alteromonas sp.

Comparison of MALDI-TOF mass spectrometry and 16S rDNA sequencing for identification of environmental bacteria: a case study of cave mussel-associated culturable microorganisms

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used as a rapid and cost-effective method for pathogen identification in clinical settings. In comparison, its performance in other microbiological fields, such as environmental microbiology, is still being tested, although isolates of environmental microbes are essential for in-depth in vivo studies of their biology, including biotechnological applications. We investigated the applicability of MALDI-TOF MS for the identification of bacterial isolates from a highly oligotrophic environment - Dinaric Karst caves, which likely harbor specific microorganisms. We cultured bacteria from the shell surface of the endemic mussel Congeria jalzici, one of the three known cave mussels in the world that lives in the Dinaric karst underground. The bacterial isolates were obtained by swabbing the shell surface of mussels living in microhabitats with different amounts of water: 10 air-exposed mussels, 10 submerged mussels, and 10 mussels in the hygropetric zone. A collection of 87 pure culture isolates was obtained, mostly belonging to the phylum Bacillota (72%), followed by Pseudomonadota (16%), Actinomycetota (11%), and Bacteroidota (1%). We compared the results of MALDI-TOF MS identification (Bruker databases DB-5989 and version 11, v11) with the results of 16S rDNA-based phylogenetic analysis, a standard procedure for bacterial identification. Identification to the genus level based on 16S rDNA was possible for all isolates and clearly outperformed the results from MALDI-TOF MS, although the updated MALDI-TOF MS database v11 gave better results than the DB-5989 version (85% versus 62%). However, identification to the species-level by 16S rDNA sequencing was achieved for only 17% of isolates, compared with 14% and 40% for the MALDI-TOF MS databases DB-5989 and v11 database, respectively. In conclusion, our results suggest that continued enrichment of MALDI-TOF MS libraries will result with this method soon becoming a rapid, accurate, and efficient tool for assessing the diversity of culturable bacteria from different environmental niches.

Lytic activity of phages against bacterial pathogens infecting diabetic foot ulcers

Complications of diabetes, such as diabetic foot ulcers (DFUs), are common, multifactorial in origin, and costly to treat. DFUs are the cause of nearly 90% of limb amputations among persons with diabetes. In most chronic infections such as DFU, biofilms are involved. Bacteria in biofilms are 100-1000 times more resistant to antibiotics than their planktonic counterparts. Multidrug-resistant (MDR) Staphylococcus aureus and Pseudomonas aeruginosa infections in DFUs may require alternative therapeutic agents such as bacteriophages ("phages"). This study describes the lytic activity of phage cocktails AB-SA01 (3-phage cocktail) and AB-PA01 (4-phage cocktail), which target S. aureus and P. aeruginosa, respectively. The host range and lytic effect of AB-SA01 and AB-PA01 on a planktonic culture, single-species biofilm, and mixed-species biofilm were evaluated. In vitro testing showed that 88.7% of S. aureus and 92.7% of P. aeruginosa isolates were susceptible to AB-SA01 and AB-PA01, respectively, in the planktonic state. The component phages of AB-SA01 and AB-PA01 infected 66% to 94.3% of the bacterial isolates tested. Furthermore, AB-SA01 and AB-PA01 treatment significantly (p < 0.05) reduced the biofilm biomass of their hosts, regardless of the antibiotic-resistant characteristics of the isolates and the presence of a non-susceptible host. In conclusion, the strong lytic activity, broad host range, and significant biofilm biomass reduction of AB-SA01 and AB-PA01 suggest the considerable potential of phages in treating antibiotic-resistant S. aureus and P. aeruginosa infections alone or as coinfections in DFUs.

Biosurfactant from Pseudomonas fragi enhances the competitive advantage of Pseudomonas but reduces the overall spoilage ability of the microbial community in chilled meat

Biosurfactants from Pseudomonas spp. have been reported to exhibit antibacterial and anti-adhesive properties, but their role during meat spoilage remains unclear. In this study, the biosurfactant was isolated from an isolate of Pseudomonas fragi with strong spoilage potential, and its surface tension and emulsification ability were determined. The chemical and microbial characteristics of the biosurfactant-treated meat samples were periodically analyzed. The results demonstrated that the biosurfactant produced by P. fragi could reduce surface tension and showed good emulsification properties. For the in situ spoilage trials, biosurfactant from P. fragi changed the microbial diversity on meat, helping Pseudomonas establish a dominant position in the population. However, biosurfactant treatment caused chicken meat to exhibit a weaker spoilage state, as indicated by the growth of psychrophilic microorganisms, total volatile basic nitrogen (TVBN) and meat color. These results provide practical information for understanding the role of P. fragi biosurfactant during chilled meat storage.

Influence of Storage Packaging Type on the Microbiological and Sensory Quality of Free-Range Table Eggs

The studies aimed to assess the impact of packaging, storage time, and temperature on the microbiological quality as well as on the sensory quality and functional properties of chicken eggs. The study material consisted of eggs from laying hens kept under free-range conditions. The eggs packed in cardboard and plastic cartons were stored at 5 °C and 22 °C, respectively. The eggs were examined on the day of laying and on days 14 and 28 of storage. The microbiological quality of the shell and contents of the eggs and the foaming properties of the egg white stored in cardboard and plastic packaging as well as the sensory characteristics of the eggs stored in both types of packaging after hard-boiling were examined on all evaluation dates. The type of packaging in which the eggs were stored was shown to influence the microbiological quality of the egg contents. Eggs stored in plastic packaging, on days 14 and 28 of storage, contained more bacteria in egg contents than eggs stored in cardboard packaging (p < 0.05). The type of packaging in which the eggs were stored did not have an effect on the foaming properties of the egg white (p > 0.05) or on the sensory characteristics of the eggs after hard-boiling. Irrespective of the type of packaging, the foaming properties of the egg white and the sensory characteristics of the eggs after hard-boiling deteriorated with storage time. The effect of temperature on egg quality was found. Regardless of the type of packaging, eggs stored at 5 °C after hard-boiling had better yolk colour, smell, and texture than eggs stored at 22 °C (p < 0.05).

Prevalence and Antibiotic Resistance Phenotypes of Pseudomonas spp. in Fresh Fish Fillets

In fresh fish products, excessive loads of Pseudomonas can lead to their rapid spoilage. It is wise for Food Business Operators (FBOs) to consider its presence both in whole and prepared fish products. With the current study, we aimed to quantify Pseudomonas spp. in fresh fillets of Salmo salar, Gadus morhua and Pleuronectes platessa. For all three fish species, we detected loads of presumptive Pseudomonas no lower than 10⁴-10⁵ cfu/g in more than 50% of the samples. We isolated 55 strains of presumptive Pseudomonas and carried out their biochemical identification; 67.27% of the isolates were actually Pseudomonas. These data confirm that fresh fish fillets are normally contaminated with Pseudomonas spp. and the FBOs should add it as a "process hygiene criterion" according to EC Regulation n.2073/2005. Furthermore, in food hygiene, it is worth evaluating the prevalence of antimicrobial resistance. A total of 37 Pseudomonas strains were tested against 15 antimicrobials, and they all were identified as being resistant to at least one antimicrobial, mainly penicillin G, ampicillin, amoxicillin, tetracycline, erythromycin, vancomycin, clindamycin and trimethoprim. As many as 76.47% of Pseudomonas fluorescens isolates were multi-drug resistant. Our results confirm that Pseudomonas is becoming increasingly resistant to antimicrobials and thus should be continuously monitored in foods.

Genotypic and Phenotypic Detection of Polyhydroxyalkanoate Production in Bacterial Isolates from Food

Polyhydroxyalkanoates (PHAs) are widely used in medical and potentially in other applications due to their biocompatibility and biodegradability. Understanding PHA biosynthetic pathways may lead to the detection of appropriate conditions (substrates) for producing a particular PHA type by a specific microbial strain. The aim of this study was to establish a method enabling potentially interesting PHA bacterial producers to be found. In the study, all four classes of PHA synthases and other genes involved in PHA formation (fabG, phaA, phaB, phaG, and phaJ) were detected by PCR in 64 bacterial collection strains and food isolates. Acinetobacter, Bacillus, Cupriavidus, Escherichia, Klebsiella, Lelliottia, Lysinibacillus, Mammaliicoccus, Oceanobacillus, Pantoea, Peribacillus, Priestia, Pseudomonas, Rahnella, Staphylococcus, and Stenotrophomonas genera were found among these strains. Fructose, glucose, sunflower oil, and propionic acid were utilized as carbon sources and PHA production was detected by Sudan black staining, Nile blue staining, and FTIR methods. The class I synthase and phaA genes were the most frequently found, indicating the strains' ability to synthesize PHA from carbohydrates. Among the tested bacterial strains, the Pseudomonas genus was identified as able to utilize all tested carbon sources. The Pseudomonas extremorientalis strain was determined as a prospect for biotechnology applications.

Application of MALDI-TOF MS for identification of environmental bacteria: A review

Bacteria play a variety of roles in the environment. They maintain the balance in the ecosystem and provide different ecosystem services such as in biogeochemical cycling of nutrients, biodegradation of toxic pollutants, and others. Therefore, isolation and identification of different environmental bacteria are important to most environmental research. Due to the high cost and time associated with the conventional molecular techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained considerable attention for routine identification of bacteria. This review aims to provide an overview of the application of MALDI-TOF MS in various environmental studies through bibliometric analysis and literature review. The bibliometric analysis helped to understand the time-variable application of MALDI-TOF MS in various environmental studies. The categorical literature review covers various environmental studies comprising areas like ecology, food microbiology, environmental biotechnology, agriculture, and plant sciences, which show the application of the technique for identification and characterization of pollutant-degrading, plant-associated, disease-causing, soil-beneficial, and other environmental bacteria. Further research should focus on bridging the gap between the phylogenetic identity of bacteria and their specific environmental functions or metabolic traits that can help in rapid advancements in environmental research, thereby, improving time and cost savings.

A review on the application of bioinformatics tools in food microbiome studies

There is currently a transformed interest toward understanding the impact of fermentation on functional food development due to growing consumer interest on modified health benefits of sustainable foods. In this review, we attempt to summarize recent findings regarding the impact of Next-generation sequencing and other bioinformatics methods in the food microbiome and use prediction software to understand the critical role of microbes in producing fermented foods. Traditionally, fermentation methods and starter culture development were considered conventional methods needing optimization to eliminate errors in technique and were influenced by technical knowledge of fermentation. Recent advances in high-output omics innovations permit the implementation of additional logical tactics for developing fermentation methods. Further, the review describes the multiple functions of the predictions based on docking studies and the correlation of genomic and metabolomic analysis to develop trends to understand the potential food microbiome interactions and associated products to become a part of a healthy diet.

No evidence for a relationship between farm or transformation process locations and antibiotic resistance patterns of Pseudomonas population associated with rainbow trout (Oncorhynchus mykiss)

AIMS

Study the relationship between antibiotic resistance patterns of Pseudomonas isolated from farmed rainbow trout fillets and farm or transformation process locations.

METHODS AND RESULTS

Pseudomonas strains were isolated from rainbow trout sampled in two differently located farms and filleted in laboratory or in a processing factory. One hundred and twenty-five isolates were confirmed as belonging to Pseudomonas using CFC selective media, Gram staining, oxidase test and quantitative polymerase chain reaction methods. Fifty-one isolates from separate fish fillets were further identified using MALDI-TOF mass spectrometry, and the minimal inhibitory concentrations (MIC) of 11 antibiotics were also determined by microdilution method. Most of the isolates belonged to the Pseudomonas fluorescens group (94.1%), and no relationship was established between antibiotic resistance patterns and sampling locations (farms or filleting areas). Multiple resistance isolates with high MIC values (from 64 µg ml^-1 to more than 1024 µg ml^-1 ) were identified.

CONCLUSIONS

Antibiotic resistance patterns found in Pseudomonas isolates were not influenced by farms or transformation process locations. Seven isolates were found highly resistant to four different antibiotic classes.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study does not provide evidence of a relationship between farm or transformation process locations on antibiotic resistance patterns of Pseudomonas population.

Aroma profile and lactic acid bacteria characteristic of traditional Slovak cheese "May bryndza"

This paper describes the results of the characterization of a traditional Slovak cheese called "May bryndza" with regard to the profiles of volatile organic compounds and lactic acid bacteria. Samples of "May bryndza" cheese produced solely from unpasteurized ewe's milk were collected from 4 different Slovak farms, and samples of the cheese produced from a mixture of 2 types of milk (raw ewe's and pasteurized cow's milk) were collected from 3 different Slovak industrial dairies. There were 15 compounds detected and identified by the electronic nose. The impact of the kind of milk and the kind of dairy on the aroma profile of the product was not confirmed by PCA. The compounds with the highest relative contents in samples were acetoin (2.59%-24.55%), acetic acid (6.69%-13.39%), methoxy-phenyl-oxime (4.49%-8.52%), butanoic acid (1.89%-5.67%), and 2,3-butanediol (0.98%-4.08%), which were determined with gas chromatography. A total of 1533 isolates of LAB were obtained from the "May bryndza" cheese samples. Four families, five genera, and 19 species were identified with mass spectrometry, and isolated bacteria, both from the farm and industry dairies were the most frequently found to belong to Lactococcus lactis subsp. lactis.

Bacterial communities in bovine ejaculates and their impact on the semen quality

Although bacterial contamination of ejaculates may cause difficulties in cattle reproduction, standard protocols for a routine microbiological analysis of bovine semen are still missing. Understanding of the mechanisms of bacterial damage to spermatozoa may contribute to the prevention and management of bacteriospermia in the future. Therefore, this study was designed to investigate bacterial profiles of fresh bovine ejaculates (n = 30), while at the same time we focused on assessing the relationships between bacteriospermia and selected sperm quality parameters as well as an array of oxidative stress and inflammatory markers. The samples were divided into three quality groups according to the sperm motility: Excellent (EX) - over 90% > Good (GO) - between 89% and 80% > Moderate (MO) - under 80%. The results showed a significant increase in reactive oxygen species (ROS) generation in the GO group when compared to the EX group. In the MO group, a deterioration of almost all quality parameters was observed when compared to the EX group. In particular, sperm motility, mitochondrial membrane potential, ROS production and IL-6 concentration exhibited a significant decline. Pearson correlation analysis revealed positive associations among bacterial load and the presence of leukocytes in semen (r = 0.965), malondialdehyde concentration (r = 0.816) and DNA fragmentation (r = 0.784). MALDI-TOF MS Biotyper analysis showed a prevalence of the Staphylococcus genus. The quantification of bacterial colonies revealed a significantly increased (P < 0.01) bacterial load in the MO group when compared with the EX as well as the GO group. Overall, our results suggest that sperm quality may be affected by both, bacterial composition, and bacterial load. It appears that an increased presence of bacterial species triggers the immune response, causes oxidative stress, and thereby contributes to sperm structural alterations while diminishing their fertilization ability.Abbreviations: EX: Excellent; GO: Good; MO: Moderate; MOT: Motility; ROS: Reactive Oxygen Species; MMP: Mitochondrial Membrane Potential; IL-1: Interleukin 1; IL-6: Interleukin 6; IL-8: Interleukin 8; IL-12: Interleukin 12; CRP: C-reactive protein; DNA: Deoxyribonucleic acid; MALDI-TOF MS: Matrix-assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry; LPO: Lipid peroxidation; CFU: Colony-forming units MDA: Malondialdehyde; CASA: Computer-assisted Sperm Analysis; WS: Working solution; RIPA: Radio-immunoprecipitation assay; TBARS: Thiobarbituric Acid Reactive Substances; BHB: D-β-hydroxybutyrate.

Assessment of the potential use of MALDI-TOF MS for the identification of bacteria associated with chilled vacuum-packaged lamb meat

The focus of this study was to compare the effectiveness of MALDI-TOF MS and partial 16S rRNA gene sequencing for the identification of bacteria isolated from VP lamb meat stored chilled at 5 °C for 21 days, at the same time gaining insights into bacterial changes over time. The identity of bacterial isolates on non-selective and selective agars was determined by both methods and results compared. Results showed that total bacterial numbers increased over the 21 days (as expected) with Staphylococcus and Pseudomonas (day 0) being replaced by Carnobacterium, Brochothrix and members of the Enterobacteriaceae family by day 21. A high level of agreement (86-100%) for bacterial isolates' identity at genus level was observed between MALDI-TOF MS and partial 16S rRNA gene-based sequencing for isolates where identification was possible. With its cheaper cost and faster turnaround time, once optimized, MALDI-TOF MS could become a useful alternative to 16S rRNA gene-sequencing for the rapid identification of red meat bacterial isolates.

Main bacterial species causing clinical disease in ornamental freshwater fish in Brazil

Bacterial diseases are common in ornamental fish, more frequently associated with ubiquitous bacteria from the aquarium environment. The disease can lead to fish mortality and cause high economic losses if not rapidly controlled. The aim of this study was to identify the main causative bacterial agents of infection in ornamental fish with different clinical signs. A total of 126 freshwater fish, from 12 families and 38 species, with clinical signs were collected in a wholesaler in São Paulo, SP, Brazil. Samples were taken from the eye, skin ulcers, kidneys, and gills, plated on MacConkey, CHROMagar Orientation, and blood agar and incubated under aerobic and anaerobic conditions. Bacterial identification was performed by MALDI-TOF mass spectrometry. From the 126 studied animals, 112 were positive for bacterial isolation. Among the positive animals, 32.1% presented infection caused by a single bacterial species, while in the remaining 67.9%, two to six different bacterial species were identified. A total of 259 bacterial strains were obtained and classified among 46 bacterial species. The species of higher frequency were Aeromonas veronii (26.3%), Aeromonas hydrophilla (16.2%), Shewanella putrefaciens (7.3%), Citrobacter freundii (8.1%), Vibrio albensis (5.8%), and Klebsiella pneumoniae (4.2%). MALDI-TOF MS showed to be a rapid method for diagnosis of bacterial disease outbreaks in ornamental fish establishments.

New Arctic Bacterial Isolates with Relevant Enzymatic Potential

Fragments of wood drifting in the vicinity of Spitzbergen were used for the isolation of microorganisms, carried out using atypical carbon sources: colloidal chitin, cellulose and carboxymethylcellulose, xylan, casein, tributrin and olive oil. Purified cultures were subjected to a three-step identification: with classical methods, using MALDI-TOF MS Biotyper whole-cell protein fingerprinting, and molecular analysis of 16S rDNA. Subsequently, a preliminary assessment of the enzymatic potential of isolates was carried out. As a result, cellulolytic activity was observed in more than 50% of the bacterial strains, exhibiting activity of 0.30–0.40 U/mL. Over 53% of the isolates demonstrated xylanolytic activity, of which the highest reached from 0.40 to 0.90 U. Polygalacturonase activity of 0.003–1.6 was also demonstrated in half of the bacterial strains studied. Proteolytic activity of isolates did not exceed 0.3 U. An important highlight was the ability of fluorescent dye production by certain strains, grown on skim milk-agar, but also on pure meat extract.

The characteristic of sheep cheese “Bryndza” from different regions of Slovakia based on microbiological quality

The aim of our study was to describe microorganisms which occur in the traditional Slovak cheese „Bryndza“. There were a total of 60 cheese samples collected from ten different farms during May 2019. The microbiota studies included the total bacterial count, coliforms, enterococci, lactic acid bacteria, yeasts and microscopic fungi. The total bacterial counts were cultivated on plate count agar at 30 °C in aerobic conditions, lactic acid bacteria on MRS at 37 °C in anaerobic conditions, coliform on VRBL and VRBG at 37 °C in aerobic condition, yeasts and microscopic fungi on MEA at 25 °C under aerobic condition. Gram-positive, Gram-negative and yeasts isolates were identified with MALDI-TOF MS Biotyper. Totally, a number of 1175 isolates of G-, G+ and yeast were identified with score higher than 2 and moulds. Escherichia coli and Stenotrophomonas maltophilia were the most frequently identified species of Gram-negative and Leuconostoc mesenteroides ssp. mesenteroides and Lactococcus lactis ssp. lactis from Gram-positive bacteria. Yarrowia lipolitica and Kluyveromyces lactis were the most distributed yeasts. Lactic acid bacteria group was represented by Lactobacillus, Lactococcus, Leuconostoc and Pediococcus. The most abundant genera of lactic acid bacteria were Lactobacillus with 11 species. This study describes the indigenous microbiota of the traditional ewe's milk cheeses from Slovakia.

Antibiotics Versus Natural Biomolecules: The Case of In Vitro Induced Bacteriospermia by Enterococcus Faecalis in Rabbit Semen

Male subfertility is a global issue in human reproduction as well as in animal reproduction. Bacterial infection and semen contamination are still widely overlooked. As the collection of ejaculates is not a sterile process, it is necessary to add antimicrobial agents to avoid a possible depreciation of semen samples. As traditionally used antibiotics have been questioned because of an ever-increasing bacterial resistance, natural bioactive molecules could offer an alternative because of their antibacterial and antioxidant properties. As such, we decided to compare the effects of selected natural biomolecules (resveratrol-RES, quercetin-QUE and curcumin-CUR) with routinely used antibiotics in animal biotechnologies (penicillin-PEN, gentamicin-GEN and kanamycin-KAN) on the rabbit sperm vitality in the presence of Enterococcus faecalis. Changes in the sperm structural integrity and functional activity were monitored at 0, 2, 4 and 6 h. Computer-assisted sperm analysis (CASA) was used for the assessment of spermatozoa motility. Production of reactive oxygen species (ROS) was evaluated using chemiluminiscence, while the mitochondrial membrane potential (ΔΨm) was examined using the JC-1 dye. Finally, the sperm chromatin dispersion (SCD) test was used to assess DNA fragmentation, and changes to the membrane integrity were evaluated with the help of annexin V/propidium iodide. The motility assessment revealed a significant sperm motility preservation following treatment with GEN (p < 0.001), followed by PEN and CUR (p < 0.01). QUE was the most capable substance to scavenge excessive ROS (p < 0.001) and to maintain ΔΨm (p < 0.01). The SCD assay revealed that the presence of bacteria and antibiotics significantly (p < 0.05) increased the DNA fragmentation. On the other hand, all bioactive compounds readily preserved the DNA integrity (p < 0.05). In contrast to the antibiotics, the natural biomolecules significantly maintained the sperm membrane integrity (p < 0.05). The microbiological analysis showed that GEN (p < 0.001), KAN (p < 0.001), PEN (p < 0.01) and CUR (p < 0.01) exhibited the strongest antibacterial activity against E. faecalis. In conclusion, all selected biomolecules provided protection to rabbit spermatozoa against deleterious changes to their structure and function as a result of Enterococcus faecalis contamination. Therefore, administration of RES, QUE and/or CUR to rabbit semen extenders in combination with a carefully selected antibacterial substance may be desirable.