The available literary data suggest the general applicability and benefits of the Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) in the field of microbiological identification. Due to its high reliability, MALDI-TOF might generally be the alternative to the the16s-rRNA sequence-based and serological-based methods. The essence of the technique is to map the unique protein pattern of microbes that contributes to characterizing a wide variety of microorganisms, including bacteria, fungi, and viruses. With its application, the well-known bacterial and fungal species can be quickly identified, thus saving time in clinical diagnostics. In recent years, new protocols have appeared for directly identifying pathogenic strains from patient samples (blood, urine, feces), a major milestone in healthcare applications. On the other hand, these applications only have reliable results under certain conditions (homogeneous infection, adequate cell count, appropriate separation technique). This review aims to introduce and summarize those developments that have been enabled for routine application in the field of clinical diagnosis.

In order to intensify and guarantee the agricultural productivity and thereby to be able to feed the world’s rapidly growing population, irrigation has become very important. In parallel, the limited water resources lead to an increase in usage of poorly characterized sources of water, which is directly linked to a higher prevalence of foodborne diseases. Therefore, analyzing the microorganisms or even the complete microbiome of irrigation water used for food production can prevent the growing numbers of such cases. In this study, we compared the efficacy of MALDI-TOF Mass spectrometry (MALDI TOF MS) identification to 16S rRNA gene Sanger sequencing of waterborne microorganisms. Furthermore, we analyzed the whole microbial community of irrigation water using high-throughput 16S rRNA gene amplicon sequencing. The identification results of MALDI-TOF MS and 16S rRNA gene Sanger sequencing were almost identical at species level (66.7%; 64.3%). Based on the applied cultivation techniques, Acinetobacter spp., Enterobacter spp., Pseudomonas spp., and Brevundimonas spp. were the most abundant cultivable genera. In addition, the uncultivable part of the microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidota, Patescibacteria, and Verrucomicrobiota. Our findings indicate that MALDI-TOF MS offers a fast, reliable identification method and can act as an alternative to 16S rRNA gene Sanger sequencing of isolates. Moreover, the results suggest that MALDI-TOF MS paired with 16S rRNA gene amplicon sequencing have the potential to support the routine monitoring of the microbiological quality of irrigation water.

The continued and improper use of antibiotics has resulted in the emergence of antibiotic resistance (AR). The dissemination of antibiotic-resistant microorganisms occurs via a multitude of pathways, including the food supply. The failure to comply with the regulatory withdrawal period associated with the treatment of domestic animals or the illicit use of antibiotics as growth promoters has contributed to the proliferation of antibiotic-resistant bacteria in meat and dairy products. It was demonstrated that not only do animal and human pathogens act as donors of antibiotic resistance genes, but also that lactic acid bacteria can serve as reservoirs of genes encoding for antibiotic resistance. Consequently, the consumption of fermented foods also presents a potential conduit for the dissemination of AR. This review provides an overview of the potential for the transmission of antibiotic resistance in a range of traditional and novel foods. The literature data reveal that foodborne microbes can be a significant factor in the dissemination of antibiotic resistance.

Serratia marcescens strains from a dairy-producing environment were tested for their inhibitory effect on Listeria monocytogenes, Salmonella Hartford, Yersinia enterocolitica and Escherichia coli. Inhibition of foodborne pathogens was observed in the case of a non-pigmented Serratia strain, while the pigment-producing isolate was able to inhibit only Y. enterocolitica. The co-culturing study in tryptone soya broth (TSB) and milk showed that the growth of Salmonella was inhibited in the first 24 h, but later the pathogen could grow in the presence of the Serratia strain even if its cell concentration was 1000 times higher than that of Salmonella. However, we found that (1) concentrated cell-free supernatants had stronger inhibitory activity, which confirms the extracellular nature of the antagonistic compound(s). We proved that (2) protease and chitinase enzymes can take part in this mechanism, but they are not the main inhibitory compounds. The presence of prodigiosin was observed only in the case of the pigmented strain; thus, (3) we hypothesized that prodigiosin does not take part in the inhibition of the pathogens. However, (4) the combined effect of different extracellular metabolites might be attributed to the inhibitory property. Application of concentrated S. marcescens cell-free supernatant can be an effective antibacterial strategy in the food industry, mainly in the form of a bio-disinfectant on surfaces of food-processing areas.