Current Trends of Enterococci in Dairy Products: A Comprehensive Review of Their Multiple Roles

Searching for antibiotic-susceptible bioprotective lactic acid bacteria to control dangerous biological agents in artisanal cheese

Minas artisanal cheese (MAC) samples (n = 59) from 16 municipalities across five traditional MAC-producing regions in Brazil were used to prospect antibiotic-susceptible protective lactic acid bacteria (LAB) against three pathogenic bacteria found in the MAC. From 291 LAB isolates, 84 genetically diverse strains were selected via rep-PCR. MALDI-TOF identification revealed multiple species, predominantly Enterococcus faecalis (n = 37), Enterococcus faecium (n = 21), Lactiplantibacillus plantarum (n = 5) and Lacticaseibacillus rhamnosus (n = 3). The antagonistic activity of these strains was evaluated against Enterococcus faecalis ATCC 29212, Listeria monocytogenes ATCC 5779, and Escherichia coli O157:H7 using spot-on-lawn assays. Several strains showed strong inhibitory effects against E. coli and L. monocytogenes, with halo/colony ratios reaching 4.86 and 4.47, respectively. No antimicrobial peptide producing strain was observed. Antibiotic susceptibility was tested against nine antibiotics, and five strains were susceptible to all antibiotics, while 53 strains were susceptible to 5-8 antibiotics. However, five strains were resistant to all antibiotics, showing the highest resistance to gentamicin (66.7%), cotrimoxazole (58.3%), and streptomycin (57.2%). Resistance genes (aacA-aphD, ermA/B, tetM/O/K/L/S, blaZ, and vanA/B) were screened, and 40 strains harbored at least one gene. Taken together, these results revealed three antibiotic-susceptible bioprotective lactobacilli (L. rhamnosus 52, L. plantarum 177, and L. plantarum 272G) as superior strains, whose efficacy in eliminating E. coli O157 and Listeria monocytogenes in the milk matrix between 7- and 21-days post-inoculation was confirmed. These findings confirm the potential of these autochthonous lactobacilli to improve the safety of dairy, paving the way for their applications in product development in future projects.

A novel Enterococcus durans with antimicrobial, anti-diabetes and anti-alzheimer activities isolated from Egypt

Enterococcus sp. is a subset of lactic acid bacteria that have beneficial effects on human health including prevention of gut chronic diseases, controlling Alzheimer and diabetes. The study involves morphological and biochemical identification of Enterococcus sp. and 16S rRNA gene sequencing methods, alongside an exploration of it's antimicrobial, anti-diabetes and anti-Alzheimer efficacy. The cell-free supernatant (CFS) derived from this isolate (Enterococcus durans) exhibited a significant antibacterial activity against both Gram-positive (Bacillus subtilis, Staphylococcus aureus, Enterococcus faecalis) with inhibition zones of 31.1, 33 and 27 mm, respectively and Gram-negative (Escherichia coli, Klebsiella pneumoniae, Salmonella typhi) bacteria, recording inhibition zones of 24, 25 and 30 mm, respectively. The least values of MIC and MBC were 15.62 µg/ml and 31.25 µg/ml, respectively; in case of Bacillus subtilis and Staphylococcus aureus. The highest MIC and MBC were 62.5 µg/ml and 250 µg/ml respectively, when testing CFS against Klebsiella pneumonia. Notably, the stability of CFS was maintained at various temperatures, including autoclaving conditions (121 ℃). The isolate displayed tolerance across a wide pH range (2.5-9.5), with enhanced activity observed at acidic pH levels. Butyrylcholinesterase inhibition was estimated to be 84.6%, while amylase inhibition was 97.6% & 94.2%, respectively. GC-MS revealed metabolites not defined previously in enterococci: 1H-purin-6-amine, [(2-fluorophenyl) methyl]-(29.72%), hexadecanoic acid, 2, 3 dihydroxypro polyester (18.60%), oleic acid (11.60%) and 9-octadecenamide (6.54%). Hence, our strain is a reservoir of strong bioactive compounds, with antimicrobial, anti-diabetes and anti- Alzheimer potentials.

A Meta-Analysis on the In Vitro Antagonistic Effects of Lactic Acid Bacteria from Dairy Products on Foodborne Pathogens

Raw milk and traditional fermented foods such as artisanal cheese represent a natural source of lactic acid bacteria (LAB). They can produce antimicrobial compounds, such as bacteriocins and lactic acid, which may be exploited in dairy biopreservation. This study aimed to conduct a systematic review and meta-analysis to synthesize the inhibition diameter (ID) of LAB against L. monocytogenes, S. aureus, and Salmonella spp. Literature electronic searches were performed on PubMed, Scopus, and Web of Science, to identify articles that reported data on in-vitro antimicrobial activity by LAB isolated from dairy foods. A total of 1665 papers were retrieved, and 20 primary studies were selected according to the selection criteria, of which 397 observations were extracted. Random-effects meta-regression models were employed to describe the effects of LAB genus, pathogen concentration, susceptibility method, incubation time, inoculation volume, agar type and pH on the IDs for L. monocytogens, S. aureus, and Salmonella spp. L. monocytogens was the most susceptible pathogen (p < 0.05) to the LAB effects, followed by S. aureus and Salmonella spp. As a whole, LAB from the Lacticaseibacillus genus were the most effective (p < 0.05) in inhibiting L. monocytogens (21.49 ± 2.654 mm), followed by S. aureus (21.06 ± 2.056 mm). Salmonella spp. presented higher (p < 0.05) susceptibility to Lactobacillus genus (19.93 ± 2.456 mm). From the results, a general trend could be observed for the well-diffusion method to produce higher (p < 0.05) ID estimates than the spot and disk methods (30.73 ± 2.530 mm vs. 21.98 ± 1.309 mm vs. 13.39 ± 1.403 mm for L. monocytogenes; 22.37 ± 1.073 mm vs. 14.91 ± 2.312 mm vs. 20.30 ± 2.319 mm for Salmonella spp.), respectively. Among the tested moderators, the pathogen's inoculum concentration, the in vitro susceptibility assay itself, incubation time and inoculation volume on agar are determinant parameters to be looked at when designing a robust and reproducible experimental plan. The in vitro results reinforced that LAB can be useful in controlling the development of pathogenic bacteria frequently found in the dairy industry.

Detection of glycopeptide resistance and virulence genes in enterococci isolated from cheese and investigation of the clonal relationship of E. faecium species with rectal surveillance isolates

OBJECTIVE

This study aimed to investigate the presence of glycopeptide resistance and virulence genes in Enterococcus spp. isolated from cheese and the clonal relationship of E. faecium species with rectal surveillance isolates.

MATERIALS AND METHOD

The study included 50 E. faecium species identified by the BD Phoenix 100 automatic identification system from surveillance cultures sent to the Kahramanmaraş Sütçü İmam University's microbiology laboratory and Enterococcus species from various packaged and unpackaged cheese samples. Multiplex polymerase chain reaction was used to investigate the presence of glycopeptide resistance and virulence genes in enterococci isolates. The clonal relationship between E. faecium isolates was evaluated using the Enterobacterial Repetitive Intergenic Consensus polymerase chain reaction method.

RESULTS

Bacterial growth was detected in 33 of the cheese samples. The study included E. faecium and E. faecalis species. Glycopeptide resistance genes were detected in 11 E. faecalis isolates, including vanD (61.1 %) and vanB (44.4 %). None of the glycopeptide resistance genes were detected in E. faecium isolates. Additionally, virulence genes were detected in 5 (31.25 %) E. faecium and 12 (66.6 %) E. faecalis isolates. Glycopeptide resistance genes were more common in isolates from packaged cheeses (p = 0.045).

CONCLUSION

Four E. faecium strains isolated from cheeses were closely related to the rectal surveillance isolates. This suggests that the health risks associated with enterococci in cheese must be carefully analyzed.

Identification and Functional Analysis of Novel SNPs in Enterocin Genes of Enterococcus faecium GHB21

This study investigates the functional and structural impact of single nucleotide polymorphisms (SNPs) in the enterocin and associated immunity genes of Enterococcus faecium GHB21, a strain known for producing potent antimicrobial peptides. Enterocins, most of them classified as class IIa bacteriocins, exhibit strong activity against pathogens such as Listeria monocytogenes, making them promising candidates for food preservation and therapeutic interventions. Using cloning, sequencing, and bioinformatics tools, we analyzed key enterocin genes (entA, entB and entP) and their associated immunity genes (entAi and entPi). Two novel SNPs were identified that result in amino acid substitutions: G15N in pre-enterocin P (EntP), located within the leader sequence, and V36I in the EntPi immunity protein. Additionally, the V9I mutation within the conserved YGNGV motif of the mature EntP peptide and the G48S mutation in the EntAi immunity protein were analyzed. Protein Variation Effect Analyzer classified all mutations as neutral, indicating minimal disruption to protein function. DynaMut analysis revealed that V9I stabilizes EntP but slightly reduces its flexibility, potentially influencing its interaction with target bacteria. Despite these mutations, the enterocins retained critical structural features, including disulfide bonds and β-sheet arrangements, ensuring their antimicrobial efficacy. These findings underscore the structural resilience of enterocins, supporting their application in food safety and in combating multidrug-resistant pathogens.

Antibiotic Resistance in Fermented Foods Chain: Evaluating the Risks of Emergence of Enterococci as an Emerging Pathogen in Raw Milk Cheese

Fermented foods, particularly fermented dairy products, offer significant health benefits but also present serious concerns. Probiotic bacteria, such as lactic acid bacteria (LAB), found in these foods have been strongly linked to the selection and dissemination of antibiotic resistance genes (ARGs). This study aims to examine the potential risks associated with fermented foods, despite their importance in human nutrition, by analyzing the entire production chain from raw material acquisition to storage. Focusing on cheese production as a key fermented food, the study will investigate various aspects, including dairy farm management, milk acquisition, milk handling, and the application of good manufacturing practices (GMP) and good hygiene practices (GHP) in cheese production. The findings of this review highlight that ARGs found in LAB are similar to those observed in hygiene indicator bacteria like E. coli and pathogens like S. aureus. The deliberate use of antibiotics in dairy farms and the incorrect use of disinfectants in cheese factories contribute to the prevalence of antibiotic-resistant bacteria in cheeses. Cheese factories, with their high frequency of horizontal gene transfer, are environments where the microbiological diversity of raw milk can enhance ARG transfer. The interaction between the raw milk microbiota and other environmental microbiotas, facilitated by cross-contamination, increases metabolic communication between bacteria, further promoting ARG transfer. Understanding these bacterial and ARG interactions is crucial to ensure food safety for consumers.

Genomic evaluation of the probiotic and pathogenic features of Enterococcus faecalis from human breast milk and comparison with the isolates from animal milk and clinical specimens

Enterococcus faecalis is considered a probiotic, commensal lactic acid bacterium in human breast milk (HBM), but there are circulating antibiotic resistant and virulence determinants that could pose a risk in some strains. The study aimed to conduct genomic analysis of E. faecalis isolates recovered from HBM and animal milk and to evaluate their probiotic and pathogenic features through comparative genomics with isolates from clinical specimens (e.g., urine, wound, and blood). Genomic analysis of 61 isolates was performed, including E. faecalis isolates recovered from HBM in Saudi Arabia. Genome sequencing was conducted using the MiSeq system. The fewest antibiotic resistance genes (lsaA, tetM, ermB) were identified in isolates from HBM and animal milk compared to clinical isolates. Several known and unknown mutations in the gyrA and parC genes were observed in clinical isolates. However, 11 virulence genes were commonly found in more than 95% of isolates, and 13 virulence genes were consistently present in the HBM isolates. Phylogenetically, the HBM isolates from China clustered with the probiotic reference strain Symbioflor 1, but all isolates from HBM and animal milk clustered separately from the clinical reference strain V583. Subsystem functions 188 of 263 were common in all analyzed genome assemblies. Regardless of the source of isolation, genes associated with carbohydrate metabolism, fatty acid, and vitamin biosynthesis were commonly found in E. faecalis isolates. In conclusion, comparative genomic analysis can help distinguish the probiotic or pathogenic potential of E. faecalis based on genomic features.

Beyond Harmful: Exploring Biofilm Formation by Enterococci Isolated from Portuguese Traditional Cheeses

This study investigated the biofilm-forming capabilities of Enterococcus isolates from Portuguese traditional cheeses with protected designation of origin (PDO) status, specifically Azeitão and Nisa. Given the absence of added starter cultures in the cheesemaking process, the characteristics of these cheeses are intrinsically linked to the autochthonous microbiota present in the raw materials and the production environment. Our findings demonstrate that all isolates possess biofilm production abilities, which are crucial for their colonization and persistence within cheese factories, thereby maintaining factory-specific microbial heritage. Through an integrated analysis utilizing principal component analysis (PCA), a direct correlation between biofilm formation and cell viability was established. Notably, these results underscore the adaptive capacity of enterococci to survive environmental fluctuations and their role in the unique characteristics of Portuguese traditional cheeses. Overall, this research enhances our understanding of the microbial dynamics in cheese production and highlights the importance of enterococci in preserving cheese quality and heritage.

Identification, Safety Assessment, and Antimicrobial Characteristics of Cocci Lactic Acid Bacteria Isolated from Traditional Egyptian Dairy Products

The main objective of this study is to isolate and identify lactic acid bacteria (LAB) from various Egyptian dairy products, examine their antibacterial and hemolysis potential, and ensure their safety when used as starter cultures in different dairy industries. Egyptian dairy products are often made without the use of commercial starter cultures, using raw milk and artisanal methods. The most popular traditional dairy products are Laban Rayeb and Zabady, as well as the cheese varieties of Ras, Domiati, and Karish. The microbial communities used for fermentation and the diversity of lactic acid bacteria are the most important factors that can affect the quality of these products. In order to investigate the diversity of cocci lactic acid bacteria in Egyptian dairy products, 70 samples of raw or fermented milk and cheeses were collected from traditional cheese-making factories, local markets, and farmhouses located in the Delta area of Egypt. Following this, the LAB were isolated from the samples. One hundred fifty-seven isolates of Gram-positive, catalase-negative, and cocci bacterial species were identified via rep-PCR, and some isolates were confirmed using pheS and 16S rRNA gene sequencing, as follows: Streptococcus infantarius subsp. infantarius (three isolates), Enterococcus hirae (three isolates), Enterococcus faecium (ninety-six isolates), Enterococcus faecalis (forty isolates), Enterococcus durans (six isolates), Lactococcus garvieae (one isolate), Pediococcus acidilactici (seven isolates), and Lactococcus lactis subsp. Lactis (one isolate). These findings validate that five strains have strong antibacterial activity against Escherichia coli, Salmonella typhimurium, and Listeria monocytogenes, and one hundred thirty-four strains were safe for hemolysis. The five strains were selected as protective cultures, including Pediococcus acidilactici, Lactococcus lactis subsp. lactis, E. faecalis, and E. faecium.

Microbiological Evaluation of Two Mexican Artisanal Cheeses: Analysis of Foodborne Pathogenic Bacteria in Cotija Cheese and Bola de Ocosingo Cheese by qPCR

Cotija and Bola de Ocosingo are artisanal ripened cheeses produced in Mexico. Both are made with raw bovine milk from free-grazing cows and with no starter cultures. Unlike culture-based techniques, molecular methods for pathogen detection in food allow a shorter turnaround time, higher detection specificity, and represent a lower microbiological risk for the analyst. In the present investigation, we analyzed 111 cheese samples (95 Cotija and 16 Bola de Ocosingo) by qPCR (TaqMan®) after an enrichment-culture step specific to each foodborne bacterium. The results showed that 100% of the samples were free of DNA from Listeria monocytogenes, Brucella spp., Escherichia coli enterotoxigenic (ETEC), and O157:H7; 9% amplified Salmonella spp. DNA; and 11.7%, Staphylococcus aureus DNA. However, the threshold cycle (Ct) values of the amplified targets ranged between 23 and 30, indicating DNA from non-viable microorganisms. Plate counts supported this assumption. In conclusion, 100% of the cheeses analyzed were safe to consume, and the enrichment step before DNA extraction proved essential to discern between viable and non-viable microorganisms. Hygienic milking, milk handling, cheese manufacturing, and ripening are crucial to achieve an adequate microbiological quality of cheeses made with raw milk.

Occurrence of Enterococci in the Process of Artisanal Cheesemaking and Their Antimicrobial Resistance

Enterococci are a group of microorganisms that have a controversial position from some scientific points of view. The species of the greatest clinical importance are E. faecalis and E. faecium, which are common agents of nosocomial infections. However, enterococci also have important applications in the dairy industry, as they are used as non-starter lactic acid bacteria (NSLAB) in a variety of cheeses, especially artisanal cheeses. The aim of this study was to determine the presence of representatives from the Enterococcus genus using PCR and MALDI-TOF MS methods on samples of raw milk, processing environment swabs, and cheese from four different artisanal dairy plants in Slovakia. Among the 136 isolates of enterococci, 9 species of genus Enterococci (E. faecalis, E. faecium, E. durans, E. devriesi, E. hirae, E. italicus, E. casseliflavus, E. malodoratus, and E. gallinarum) were identified and were tested for their antimicrobial resistance (AMR) to 8 antibiotics (amoxicillin, penicillin, ampicillin, erythromycin, levofloxacin, vancomycin, rifampicin, and tetracycline); most of them were resistant to rifampicin (35.3%), ampicillin (22.8%), and tetracycline (19.9%). A PCR analysis of vanA (4.41%) and tetM (14.71%) revealed that antimicrobial resistance genes were present in not only phenotypic resistant isolates of enterococci but also susceptible isolates. The investigation of antimicrobial resistance in enterococci during the cheesemaking process can be a source of valuable information for public health in the concept of "One Health".

Phenotypic and genotypic characterization of antimicrobial resistances reveals the effect of the production chain in reducing resistant lactic acid bacteria in an artisanal raw ewe milk PDO cheese

Antimicrobial resistance (AMR) is a significant public health threat, with the food production chain, and, specifically, fermented products, as a potential vehicle for dissemination. However, information about dairy products, especially raw ewe milk cheeses, is limited. The present study analysed, for the first time, the occurrence of AMRs related to lactic acid bacteria (LAB) along a raw ewe milk cheese production chain for the most common antimicrobial agents used on farms (dihydrostreptomycin, benzylpenicillin, amoxicillin and polymyxin B). More than 200 LAB isolates were obtained and identified by Sanger sequencing (V1-V3 16S rRNA regions); these isolates included 8 LAB genera and 21 species. Significant differences in LAB composition were observed throughout the production chain (P ≤ 0.001), with Enterococcus (e.g., E. hirae and E. faecalis) and Bacillus (e.g., B. thuringiensis and B. cereus) predominating in ovine faeces and raw ewe milk, respectively, along with Lactococcus (L. lactis) in whey and fresh cheeses, while Lactobacillus and Lacticaseibacillus species (e.g., Lactobacillus sp. and L. paracasei) prevailed in ripened cheeses. Phenotypically, by broth microdilution, Lactococcus, Enterococcus and Bacillus species presented the greatest resistance rates (on average, 78.2 %, 56.8 % and 53.4 %, respectively), specifically against polymyxin B, and were more susceptible to dihydrostreptomycin. Conversely, Lacticaseibacillus and Lactobacillus were more susceptible to all antimicrobials tested (31.4 % and 39.1 %, respectively). Thus, resistance patterns and multidrug resistance were reduced along the production chain (P ≤ 0.05). Genotypically, through HT-qPCR, 31 antimicrobial resistance genes (ARGs) and 6 mobile genetic elements (MGEs) were detected, predominating Str, StrB and aadA-01, related to aminoglycoside resistance, and the transposons tnpA-02 and tnpA-01. In general, a significant reduction in ARGs and MGEs abundances was also observed throughout the production chain (P ≤ 0.001). The current findings indicate that LAB dynamics throughout the raw ewe milk cheese production chain facilitated a reduction in AMRs, which has not been reported to date.

Biodiversity and antibiotic resistance profile provide new evidence for a different origin of enterococci in bovine raw milk and feces

Enterococci are widely distributed in dairy sector. They are commensals of the gastrointestinal tract of animals, thus, via fecal contamination, could reach raw milk and dairy products. The aims of this study were: 1) to investigate the enterococcal diversity in cow feces and milk samples and 2) to evaluate the antibiotic resistance (AR) of dairy-related enterococci and their ability to transfer resistance genes. E. faecalis (59.9%), E. faecium (18.6%) and E. lactis (12.4%) were prevalent in milk, while E. faecium (84.2%) and E. hirae (15.0%) were dominant in bovine feces. RAPD-PCR highlighted a high number of Enterococcus biotypes (45 from milk and 37 from feces) and none of the milk strains exhibited genetic profiles similar to those of feces biotypes. A high percentage of enterococci isolated from milk (71%) were identified as multidrug resistant and resistance against streptomycin and tetracycline were widespread among milk strains while enterococci from feces were commonly resistant to linezolid and quinupristin/dalfopristin. Only E. faecalis strains were able to transfer horizontally the tetM gene to Lb. delbrueckii subsp. lactis. Our results indicated that Enterococcus biotypes from milk and bovine feces belong to different community and the ability of these microorganisms to transfer AR genes is strain-dependent.

Isolation, identification, and characterization of thermophilic lactic acid bacteria isolated from whey of Kars Kashar cheeses

Kars Kashar cheese is an artisanal pasta-filata type cheese and geographically marked in Eastern Anatolia of Turkey. The aims of this research were to determine for the first time thermophilic lactic acid bacteria (LAB) of Kars Kashar cheese and characterize the technological properties of obtained isolates. In our research, a number of 15 samples of whey were collected from the different villages in Kars. These samples were incubated at 45 °C and used as the source material for isolating thermophilic LAB. A total of 250 colonies were isolated from thermophilic whey, and 217 of them were determined to be presumptive LAB based on their Gram staining and catalase test. A total of 170 isolates were characterized by their phenotypic properties and identified using the MALDI-TOF mass spectrometry method. Phenotypic identification of isolates displayed that Enterococcus and Lactobacillus were the predominant microbiota. According to MALDI-TOF MS identification, 89 isolates were identified as Enterococcus (52.35%), 57 isolates as Lactobacillus (33.53%), 23 isolates as Streptococcus (13.53%), and one isolate as Lactococcus (0.59%). All thermophilic LAB isolates were successfully identified to the species level and it has been observed that MALDI-TOF MS can be successfully used for the identification of selected LAB. The acidification and proteolytic activities of the isolated thermophilic LAB were examined, and the isolates designated for use as starter cultures were also genotypically defined.

In Vitro and In Silico Characterization of N-Formylated Two-Peptide Bacteriocin from Enterococcus faecalis CAUM157 with Anti-Listeria Activity

Enterococcus faecalis CAUM157 (KACC 81148BP), a Gram-positive bacteria isolated from raw cow's milk, was studied for its bacteriocin production. The antimicrobial activity of CAUM157 was attributed to a two-peptide class IIb bacteriocin with potent activity against food-borne pathogen Listeria monocytogenes and periodontal disease-causing pathogens (Prevotella intermedia KCTC 15693 T and Fusobacterium nucleatum KCTC 2488 T). M157 bacteriocins exhibit high temperature and pH stability and resist hydrolytic enzyme degradation and detergent denaturation, potentially due to their structural conformation. Based on amino acid sequence, M157A and M157B were predicted to be 5.176 kDa and 5.182 kDa in size, respectively. However, purified bacteriocins and chemically synthesized N-formylated M157 peptides both showed 5.204 kDa (M157A) and 5.209 kDa (M157B) molecular mass, confirming the formylation of the N-terminal methionine of both peptides produced by strain CAUM157. Furthermore, the strain demonstrated favorable growth and fermentation with minimal bacteriocin production when cultured in whey-based media, whereas a 1.0% tryptone or soytone supplementation resulted in higher bacteriocin production. Although Ent. faecalis CAUM157 innately harbors genes for virulence factors and antimicrobial resistance (e.g., tetracycline and erythromycin), its bacteriocin production is valuable in circumventing the need for live microorganisms, particularly in food applications for pathogen control.

Technological and Enzymatic Characterization of Autochthonous Lactic Acid Bacteria Isolated from Viili Natural Starters

Viili, a Finnish ropy fermented milk, is traditionally manufactured through spontaneous fermentation, by mesophilic lactic acid bacteria and yeast-like fungi, or back-slopping. This study evaluated four natural viili starters as sources of lactic acid bacteria for dairy production. Back-slopping activation of the studied viili samples was monitored through pH and titratable acidity measurements and enumeration of mesophilic lactic acid bacteria. Sixty lactic acid bacteria isolates were collected, molecularly identified, and assayed for acidification performance, enzymatic activities, production of exopolysaccharides (EPSs), presence of the histidine decarboxylase (hdcA) gene of Gram-positive bacteria, and production of bacteriocins. A neat predominance of Lactococcus lactis emerged among the isolates, followed by Enterococcus faecalis, Enterococcus faecium, Enterococcus durans, Enterococcus lactis, and Lactococcus cremoris. Most isolates exhibited proteolytic activity, whereas only a few enterococci showed lipase activity. Five isolates identified as L. cremoris, L. lactis, and E. faecalis showed a good acidification performance. Most of the isolates tested positive for leucine arylamidase, whereas only one E. durans and two L. lactis isolates were positive for valine arylamidase. A few isolates also showed a positive reaction for beta-galactosidase and alpha- and beta-glucosidase. None of the isolates produced EPSs or bacteriocins. The hdcA gene was detected in five isolates identified as L. lactis and E. faecium. A few L. cremoris and L. lactis isolates for potential use as starter or adjunct cultures for dairy processing were finally identified.

Study on application of biocellulose-based material for cheese packaging

Bacterial cellulose (BC, biocellulose) is a natural polymer of microbiological origin that meets the criteria of a biomaterial for food packaging. The aim of the research was to obtain biocellulose and test its chemical as well as physical characterization as a potential packaging for Dutch-type cheeses. Four variants of biocellulose-based material were obtained: not grinded and grinded variants obtained from YPM medium (YPM-BCNG and YPM-BCG, respectively) and not grinded and grinded variants from acid whey (AW) (AW-BCNG and AW-BCG, respectively). It was demonstrated that AW-BCNG exhibited the highest thermostability and the highest degradation temperature (348 °C). YPM-BCG and YPM-BCNG demonstrated higher sorption properties (approx. 40 %) compared to AW-BCG and AW-BCNG (approx. 15 %). Cheese packaged in biocellulose (except for YPM-BCNG) did not differ in water, fat, or protein content compared to the control cheese. All of the biocellulose packaging variants provided the cheeses with protection against unfavourable microflora. It was demonstrated that cheeses packaged in biocellulose were characterized by lower hardness, fracturability, gumminess, and chewiness than the control cheese sample. The results obtained indicate that BC may be a suitable packaging material for ripening cheeses, which shows a positive impact on selected product features.

Study of an Enterococcus faecium strain isolated from an artisanal Mexican cheese, whole-genome sequencing, comparative genomics, and bacteriocin expression

Enterococci are ubiquitous microorganisms in almost all environments, from the soil we step on to the food we eat. They are frequently found in naturally fermented foods, contributing to ripening through protein, lipid, and sugar metabolism. On the other hand, these organisms are also leading the current antibiotic resistance crisis. In this study, we performed whole-genome sequencing and comparative genomics of an Enterococcus faecium strain isolated from an artisanal Mexican Cotija cheese, namely QD-2. We found clear genomic differences between commensal and pathogenic strains, particularly in their carbohydrate metabolic pathways, resistance to vancomycin and other antibiotics, bacteriocin production, and bacteriophage and CRISPR content. Furthermore, a bacteriocin transcription analysis performed by RT-qPCR revealed that, at the end of the log phase, besides enterocins A and X, two putative bacteriocins not reported previously are also transcribed as a bicistronic operon in E. faecium QD-2, and are expressed 1.5 times higher than enterocin A when cultured in MRS broth.

An Integrated Comprehensive Peptidomics and In Silico Analysis of Bioactive Peptide-Rich Milk Fermented by Three Autochthonous Cocci Strains

Bioactive peptides (BPs) are molecules of paramount importance with great potential for the development of functional foods, nutraceuticals or therapeutics for the prevention or treatment of various diseases. A functional BP-rich dairy product was produced by lyophilisation of bovine milk fermented by the autochthonous strains Lactococcus lactis subsp. lactis ZGBP5-51, Enterococcus faecium ZGBP5-52 and Enterococcus faecalis ZGBP5-53 isolated from the same artisanal fresh cheese. The efficiency of the proteolytic system of the implemented strains in the production of BPs was confirmed by a combined high-throughput mass spectrometry (MS)-based peptidome profiling and an in silico approach. First, peptides released by microbial fermentation were identified via a non-targeted peptide analysis (NTA) comprising reversed-phase nano-liquid chromatography (RP nano-LC) coupled with matrix-assisted laser desorption/ionisation-time-of-flight/time-of-flight (MALDI-TOF/TOF) MS, and then quantified by targeted peptide analysis (TA) involving RP ultrahigh-performance LC (RP-UHPLC) coupled with triple-quadrupole MS (QQQ-MS). A combined database and literature search revealed that 10 of the 25 peptides identified in this work have bioactive properties described in the literature. Finally, by combining the output of MS-based peptidome profiling with in silico bioactivity prediction tools, three peptides (75QFLPYPYYAKPA86, 40VAPFPEVFGK49, 117ARHPHPHLSF126), whose bioactive properties have not been previously reported in the literature, were identified as potential BP candidates.

Enterocins Produced by Enterococci Isolated from Breast-Fed Infants: Antilisterial Potential

Enterocins are bacteriocins synthesized by Enterococcus strains that show an interesting antimicrobial effectiveness against foodborne pathogens such as Listeria monocytogenes. The objectives of this study were to identify and analyze the expression of enterocin genes of Enterococcus isolated from breast-fed infants and evaluate their ability to inhibit three human isolates of virulent L. monocytogenes, as well as some probiotic bacteria. The susceptibility of the strains of L. monocytogenes to fifteen antibiotics was tested, detecting their resistance to cefoxitin (constitutively resistant), oxacillin, and clindamycin. The production of enterocins A, B, and P was observed in Enterococcus faecium isolates, while enterocin AS-48 was detected in an Enterococcus faecalis isolate. AS-48 showed antilisterial activity by itself, while the joint action of enterocins A and B or B and P was necessary for inhibiting L. monocytogenes, demonstrating the synergistic effect of those combinations. The presence of multiple enterocin genes does not assure the inhibition of L. monocytogenes strains. However, the expression of multiple enterocin genes showed a good correlation with the inhibition capacity of these strains. Furthermore, the potential beneficial strains of lactobacilli and bifidobacteria examined were not inhibited by any of the enterocins produced individually or in combination, with the exception of Bifidobacterium longum BB536, which was inhibited by enterocin AS-48 and the joint production of enterocins A and B or B and P. The enterocins studied here could be candidates for developing alternative treatments against antibiotic-resistant bacterial infections. Moreover, these selected enterocin-producing E. faecium strains isolated from breast-fed infants could be used as probiotic strains due to their antilisterial effect, as well as the absence of virulence factors.

In Vitro Interaction between Mycoplasma agalactiae and Small Ruminants' Endogenous Bacterial Strains of Enterococcus spp. and Coagulase-Negative Staphylococcus

Recently, an antimicrobial effect on Mycoplasma agalactiae (Ma), the main etiological agent of contagious agalactia (CA), was reported in vitro with strains of Enterococcus spp. from ovine and caprine milk. The aim of this work was to evaluate the interaction of Ma with the same Enterococcus spp. isolated from other anatomical locations (vagina) and other bacterial populations present in milk, such as coagulase-negative staphylococci (CNS). The vaginal Enterococcus strains and the raw milk CNS were isolated from sheep and goats. Experimental in vitro conditions were prepared to assess the growth of Ma with and without the presence of these strains. The selected vaginal strains were identified as Enterococcus (E.) hirae and E. mundtii, and the strains of CNS were identified as Staphylococcus petrasii. Different interactions of Ma with ovine and caprine wild vaginal strains of Enterococcus and dairy strains of CNS are described for the first time: Ma can grow exponentially during 15 h with the selected strains, although with certain strains, its optimal growth can be negatively affected (p < 0.05). The colonization and/or excretion of Ma could, therefore, be influenced by certain endogenous bacterial strains. Our results increase the knowledge about possible bacterial ecology dynamics surrounding CA.

Strategies to Overcome Antimicrobial Resistance in Nosocomial Infections, A Review and Update

Nosocomial infections, also known as healthcare-associated infections, are a significant global concern due to their strong association with high mortality and morbidity in both developed and developing countries. These infections are caused by a variety of pathogens, particularly the ESKAPE group of bacteria, which includes the six pathogens Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. These bacteria have demonstrated noteworthy resistance to different antibiotics. Antimicrobial resistance mechanisms can manifest in various forms, including restricting drug uptake, modifying drug targets, inactivating drugs, active drug efflux, and biofilm formation. Accordingly, various strategies have been developed to combat antibiotic-resistant bacteria. These strategies encompass the development of new antibiotics, the utilization of bacteriophages that specifically target these bacteria, antimicrobial combination therapy and the use of peptides or enzymes that target the genomes or essential proteins of resistant bacteria. Among promising approaches to overcome antibiotic resistance, the CRISPR/Cas system stands out and offers many advantages. This system enables precise and efficient editing of genetic material at specific locations in the genome. Functioning as a bacterial "adaptive immune system," the CRISPR/Cas system recognizes, degrades, and remembers foreign DNA sequences through the use of spacer DNA segments that are transcribed into CRISPR RNAs (crRNA). This paper has focused on nosocomial infections, specifically the pathogens involved in hospital infections, the mechanisms underlying bacterial resistance, and the strategies currently employed to address this issue. Special emphasis has been placed on the application of CRISPR/Cas technology for overcoming antimicrobial resistance.

Profile of lactic acid bacteria (MALDI-TOF-MS) and physico-chemical and microbiological characteristics of the raw milk and fresh artisanal cheese from Serra Geral, Minas Gerais, Brazil

Artisanal cheese from Serra Geral, Minas Gerais, Brazil, stands out for its cultural asset and socio-economic relevance. However, standards of identity and quality and the peculiar terroir associated with the edaphoclimatic conditions have not been established. Therefore, the production flow diagram and the physico-chemical and microbiological quality of the raw milk, pingo (natural starter culture), production benches, water and fresh cheese were investigated for the first time. In addition, lactic acid bacteria (LAB) from cheese and its production environment were identified by MALDI-TOF. For that, 12 cheese making facilities were selected. The raw milk and pingo showed adequate physico-chemical characteristics for cheesemaking; however, high microbial counts were found. In the water, total and thermotolerant coliforms were also identified. The fresh cheeses were classified as 'high moisture and fat' and 'soft mass'. Most physico-chemical parameters were satisfactory; however, there were high counts of total coliforms, Staphylococcus spp. and coagulase-positive staphylococci. There were high counts of LAB in the raw milk, pingo, bench surface and fresh cheese. A total of 84 microbial biotypes from MRS agar were isolated. Lactococcus lactis was the predominant LAB, followed by Lactococcus garvieae. Leuconostoc mesenteroides (benches), Leuconostoc pseudomesenteroides (fresh cheese), and Enterococcus faecium (pingo) were identified sporadically. These results indicate the risks to public health associated with the consumption of the fresh cheese, and measures to improve its safety are needed.

Antilisterial activity of raw sheep milk from two native Epirus breeds: Culture-dependent identification, bacteriocin gene detection and primary safety evaluation of the antagonistic LAB biota

Raw milk from native small ruminant breeds in Epirus, Greece, is a valuable natural source of autochthonous lactic acid bacteria (LAB) strains with superior biotechnological properties. In this study, two bulk milks (RM1, RM2) from two local sheep yards, intended for traditional Kefalotyri cheese production, were preselected for bacteriocin-like antilisterial activity by in vitro tests. Their antagonistic LAB biota was quantified followed by polyphasic (16S rRNA gene sequencing; IGS for Enterococcus; a multiplex-PCR for Leuconostoc) identification of 42 LAB (RM1/18; RM2/24) isolates further evaluated for bacteriocin encoding genes and primary safety traits. Representative isolates of the numerically dominant mesophilic LAB were Leuconostoc mesenteroides (10) in both RMs, Streptococcus parauberis (7) in RM2, and Lactococcus lactis (1) in RM1; the subdominant thermophilic LAB isolates were Enterococcus durans (8), E. faecium (6), E. faecalis (3), E. hirae (1), E. hermanniensis (1), Streptococcus lutetiensis (2), S. equinus (1) and S. gallolyticus (1). Based on their rpoB, araA, dsr and sorA profiles, six Ln. mesenteroides strains (8 isolates) were atypical lying between the subspecies mesenteroides and dextranicum, whereas two strains profiled with Ln. mesenteroides subsp. jonggajibkimchi that is first-time reported in Greek dairy food. Two RM1 E. faecium strain biotypes (3 isolates) showed strong, enterocin-mediated antilisterial activity due to entA/entB/entP possession. One E. durans from RM1 possessed entA and entP, while additional nine RM2 isolates of the E. faecium/durans group processed entA or entP singly. All showed direct (cell-associated) antilisterial activity only, as also both S. lutetiensis strains from RM2 did strongly. Desirably, no LAB isolate was β-hemolyrtic, or cytolysin-positive, or possessed vanA, vanB for vancomycin resistance, or agg, espA, hyl, and IS16 virulence genes. However, all three E. faecalis from RM2 possessed gelE and/or ace virulence genes. In conclusion, all Ln. mesenteroides strains, the two safe, enterocin A-B-P-producing E. faecium strains, and the two antilisterial S. lutetiensis strains should be validated further as potential costarter or adjunct cultures in Kefalotyri cheese. The prevalence of α-hemolytic pyogenic streptococci in raw milk, mainly S. parauberis in RM2, requires consideration in respect to subclinical mastitis in sheep and the farm hygiene overall.

The Controversial Nature of Some Non-Starter Lactic Acid Bacteria Actively Participating in Cheese Ripening

This mini review deals with some controversial non-starter lactic acid bacteria (NSLAB) species known to be both human and animal pathogens but also health-promoting and probiotic. The focus is on Lactococcus garvieae, two Streptococcus species (S. uberis and S. parauberis), four Weissella species (W. hellenica, W. confusa, W. paramesenteroides, and W. cibaria), and Mammalicoccus sciuri, which worldwide, are often found within the microbiotas of different kinds of cheese, mainly traditional artisanal cheeses made from raw milk and/or relying on environmental bacteria for their ripening. Based on literature data, the virulence and health-promoting effects of these bacteria are examined, and some of the mechanisms of these actions are reviewed. Additionally, their possible roles in cheese ripening are also discussed. The analysis of the literature data available so far showed that, in general, the pathogenic and the beneficial strains, despite belonging to the same species, show somewhat different genetic constitutions. Yet, when the safety of a given strain is assessed, genomic analysis on its own is not enough, and a polyphasic approach including additional physiological and functional tests is needed.

Enterococcus faecium C171: Modulating the Immune Response to Acute Lethal Viral Challenge

Commensal bacteria modulate acute immune responses to infection in hosts. In this study, Enterococcus faecium C171 was screened and isolated. This strain has similar basic characteristics to the reference probiotic, including strong anti-inflammatory and anti-infective effects. E. faecium C171 inhibits the production of pro-Caspase-1 and significantly reduces the production of interleukin-1β (IL-1β) in vitro. These reactions were confirmed using the Transwell system. Live E. faecium C171 mainly exerted an inhibitory effect on acute inflammation, whereas the anti-infective and immune-activating effects were primarily mediated by the E. faecium C171-produced bacterial extracellular vesicles (Efm-C171-BEVs). Furthermore, in the specific pathogen-free (SPF) chicken model, oral administration of E. faecium C171 increased the relative abundance of beneficial microbiota (Enterococcus and Lactobacillus), particularly Enterococcus, the most important functional bacteria of the gut microbiota. E. faecium C171 significantly inhibited the acute inflammatory response induced by a highly virulent infectious disease, and reduced mortality in SPF chickens by 75%. In addition, E. faecium C171 induced high levels of CD3+, CD4-, and CD8- immunoregulatory cells and CD8+ killer T cells, and significantly improved the proliferative activity of T cells in peripheral blood mononuclear cells, and the secretion of interferon-γ. These findings indicate that E. faecium C171 and Efm-C171-BEVs are promising candidates for adjuvant treatment of acute inflammatory diseases and acute viral infections.

Safety evaluation of enterococci isolated from raw milk and artisanal cheeses made in Slovenia and Serbia

Enterococci represent a significant part of the non-starter LAB microbiota of artisanal cheeses produced mainly from raw milk. Common approaches to safety evaluation of enterococci isolates include assessment of antimicrobial resistance and virulence potential. Hence, a collection of 47 (n = 22, Serbia; n = 25, Slovenia) dairy enterococcal isolates, of which E. faecalis (n = 28), E. faecium (n = 11), E. durans (n = 5), E. casseliflavus (n = 2), and E. gallinarum (n = 1), was analyzed. The susceptibility to 12 antimicrobials was tested using a broth microdilution method, and the presence of the selected antimicrobial resistance and virulence genes was investigated using PCR. Isolates were resistant to tetracycline (TET) (25.5%), erythromycin (ERY) (17.0%), gentamycin and chloramphenicol (CHL) (∼6%). No resistance to ampicillin (AMP), ciprofloxacin (CIP), daptomycin (DAP), linezolid (LZD), teicoplanin (TEI), tigecycline (TGC) and vancomycin (VAN) was detected. Among all the resistance determinants analyzed, ermB gene was detected most frequently. All 10 virulence genes analyzed were detected with a distribution of cpd (72.3%), cob and ccf (70.2%), gelE (68.1%), hyl (59.6%), agg (53.2%) and esp (46.8%). The genes encoding cytolysin (cylA, cylM and cylB) were amplified to a lesser extent (21.3%, 21.3% and 12.8%, respectively). However, due to the limited number of enterococci isolates analyzed in the present study, further studies are still required in order to better document the safety status of dairy enterococci.

Effect of honey bee forage plants in Tunisia on diversity and antibacterial potential of lactic acid bacteria and bifidobacteria from Apis mellifera intermissa and its products

Lactic acid bacteria and bifidobacteria (LAB and Bifido), isolated from the gastrointestinal tract of Apis mellifera intermissa (BGIT), honey (H), propolis (P) and bee bread (BB) of hives set in different vegetations (wildflowers, caraway, orange blossom, Marrubium vulgare, Eucalyptus and Erica cinerea), were subjected to analysis of their antibacterial potential. Isolates able to inhibit Staphylococcus aureus were selected and identified with MALDI-TOF MS leading to 154 strains representing 12 LAB and Bifido species. Lactiplantibacillus plantarum, Pediococcus pentosaceus and Enterococcus faecalis were predominantly found in all matrices. BGIT showed the highest LAB and Bifido diversity with exclusive occurrences of five species (including Bifidobacterium asteroides and Limosilactobacillus fermentum). Honey was the second origin harboring an important variety of LAB species of which Apilactobacillus kunkeei and Enterococcus mundtii were characteristic of both H and BGIT. Principal components analysis revealed associations between antibacterial activities of LAB and Bifido, matrices and honey bee forage plants. Inhibition trends of S. aureus and Citrobacter freundii were highlighted with: L. plantarum from BGIT, P, H of bees feeding on E. cinerea; Pediococcus pentosaceus from BGIT, P, BB associated with E. cinerea; and Bifidobacterium asteroides from BGIT/orange blossom system. However, Enterococcus faecium associated with BGIT/Eucalyptus system antagonized Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii. Our findings highlighted noteworthy effects of bee forage plants on the antibacterial activity of LAB and Bifido. Our approach could be useful to identify multiple conditions promoting antibacterial potency of LAB and Bifido under the combined effects of feeding plants and living matrices.

Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation

Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.

Biofilm Formation Capacity and Presence of Virulence Determinants among Enterococcus Species from Milk and Raw Milk Cheeses

Bacterial biofilm is one of the major hazards facing the food industry. Biofilm-forming ability is one of the most important virulence properties of enterococci. The genus Enterococcus includes pathogenic, spoilage, and pro-technological bacteria. The presence of enterococci in milk and dairy products is usually associated with inadequate hygiene practices. The study examined the isolates' capacity for biofilm formation and identification of the genetic determinants of its formation among 85 Enterococcus strains isolated from raw milk (n = 49) and soft-ripened cheeses made from unpasteurized milk (n = 36). E. faecalis and E. faecium were the dominant species. The obtained results showed that 41.4% isolates from milk and 50.0% isolates from cheeses were able to form biofilm. All of the isolates analyzed had at least one of the studied genes. As regards the isolates from raw milk, the most prevalent gene was the gelE (85.6%), followed by the asa1 (66.7%). None of the isolates from cheeses showed the presence of cylA and sprE. The most prevalent gene among the strains from this source was the epbC (94.4%), followed by the gelE (88.9%). In isolates from both sources, the presence of proteins from the Fsr group was noted the least frequently. Nevertheless, results showed that were no significant differences between the biofilm-producing Enterococcus spp. and non-biofilm-producing isolates in term of occurrences of tested virulence genes. The ability to produce a biofilm by enterococci isolated from raw milk or ready-to-eat products emphasizes the need for continuous monitoring of the mechanisms of microbial adhesion.

Tetracycline Resistance Genes in the Traditional Swedish Sour Herring surströmming as Revealed Using qPCR

Antibiotic resistance (AR) represents a global concern for human health. To the best of the authors' knowledge, no study addressing AR in surströmming, a traditional Swedish fermented herring, has been performed to date. The aim of the present research was to study the prevalence of tet(O), tet(S), tet(W), tet(K), and tet(M) genes encoding for resistance to tetracycline using quantitative PCR (qPCR) applied to ready-to-eat surströmming samples collected from three producers located in Sweden. The tet(M) gene was found in all the analyzed samples, and it was also the most abundant among the tested tet genes; moreover, tet(O) was the least frequently detected gene. As a general trend, all the analyzed samples showed a high occurrence of the target genes, with slight variations among the producers. A principal component analysis did not reveal any separation among the samples or producers. All the collected data allowed for a drawing of a first picture of the occurrence of tetracycline resistance genes in ready-to-eat surströmming samples. Since no differences among the samples manufactured by the different producers were observed, it is likely that the detected genes were homogeneously spread among the microbial species shared by the herrings used as raw materials. Moreover, it can be hypothesized that the presence of the detected genes was also the result of a selective pressure of the natural marine environment on the herrings' gut microbiota and, hence, on the pro-technological microorganisms responsible for the fermentation of surströmming. However, the contribution of the manufacturers to the contamination of the processed herrings cannot be excluded.

Acrylamide adsorption by Enterococcus durans and Enterococcus faecalis: In vitro optimization, simulated digestive system and binding mechanism

Acrylamide is an unsaturated amide that forms in heated, starchy food products. This study was conducted to (1) examine the ability of 38 LAB to remove acrylamide; (2) optimize acrylamide removal of selected LAB under various conditions (pH, temperature, time and salt) using the Box-Behnken design (BBD); (3) the behavior of the selected LAB under the simulated gastrointestinal conditions; and (4) investigate the mechanism of adsorption. Out of the 38 LAB, Enterococcus durans and Enterococcus faecalis had the highest results in removing acrylamide, with 33 and 30% removal, respectively. Those two LAB were further examined for their binding abilities under optimized conditions of pH (4.5-6.5), temperature (32°C - 42°C), time (14-22 h), and NaCl (0-3% w/v) using BBD. pH was the main factor influenced the acrylamide removal compared to other factors. E. durans and E. faecalis exhibited acrylamide removal of 44 and 53%, respectively, after the in vitro digestion. Zeta potential results indicated that the changes in the charges were not the main cause of acrylamide removal. Transmission electron microscopes (TEM) results indicated that the cell walls of the bacteria increased when cultured in media supplemented with acrylamide.

Meta-analysis of the global prevalence of Enterococcus spp. in foods: Antibiotic resistance profile of Enterococcus faecalis and Enterococcus faecium

Aim: The objective of this study was to evaluate the prevalence and diversity of Enterococcus spp. and antibiotic-resistant Enterococcus faecalis and Enterococcus faecium isolates in different foods worldwide.

Method and Result: This study used meta-analytical methods. Besides, Web of Science (n= 705), Medline (n= 6), and Scopus (n= 1.338) were searched for studies in the years 1995-2021 using related keywords. Results showed that the pooled prevalence for Enterococcus spp. and antibiotic-resistant of E. faecalis and E. faecium isolates were found 0.41 (95% C.I. 0.34-0.47), 0.25 (95% C.I. 0.13-0.38), respectively. According to the results of the subgroup analysis, the lowest and highest prevalence of Enterococcus spp. in food types were calculated for red meat (0.56), and fermented foods (0.29). Also, as a result of subgroup analyses by country the highest prevalence of Enterococcus spp. was calculated in studies conducted in Slovakia (0.74). In contrast, the lowest prevalence was calculated in studies conducted in Georgia (0.07).

Conclusion: The meta-analyses improved our understanding of the prevalence of Enterococcus spp. and the antibiotic resistance of E. faecalis and E. faecium isolates in different foods and provided results that can be useful as input for quantitative microbiological risk evaluation modeling.

Significance and Impact of Study: We demonstrated the antibiotic resistance of E. faecalis and E. faecium in foods and gaps that could be addressed in the future. Therefore, it is believed that the results compiled herein will contribute to the epidemiological surveillance of the presence and antibiotic resistance of E. faecalis and E. faecium in foods.

Evolution and antimicrobial resistance of enterococci isolated from Pecorino and goat cheese manufactured on-farm in an area facing constraints as per EU Regulation 1305/2013 in Umbria, Italy

The latest EU regulation on geographical indications (EU Regulation No. 1151/2012) has introduced a set of new tools for the protection and enhancement of food products in rural areas, under the group name of optional quality term (OQT). The Commission Delegated EU Regulation, No. 665/2014, regulated the conditions for the use of the optional quality term mountain product (MP), to support the implementation of a mountain value chain. This new tool is aimed at promoting local development, maintaining the economic activities in mountain areas, and redistributing wealth, whilst, at the same time, promoting the territory. Pecorino and goat cheeses are typical Italian cheeses made usually with whole raw ewe’s or raw goat’s milk, without starter culture addition. In an attempt to characterize these productions, the aim of this study was to investigate the evolution of enterococci during the production and ripening of Pecorino cheese made in three different farms, located in Umbria, Italy in areas facing natural or other specific constraints as stipulated by Regulation 1305/2013 on support for rural development by the European Agricultural Fund for Rural Development (EAFRD). Enterococci are enteric organisms which are commonly isolated from ewe and goat’s milk production in Umbria, Italy. Counts of enterococci in raw milk ranged from 1.75 for ovine milk to 3.62 for ewe milk and a marked reduction was observed after thermization especially in ovine milk. Out of 100 isolates, 69 were E. faecium, 23 E. durans, 8 E. faecalis and 2 E. casseliflavus and the distribution of species between farms and between samples showed a prevalence of E. faecium in ovine farms and E. durans in ewes farms, with an equal dis-tribution between samples. High percentages of susceptible isolates were found for amoxicil-lin/clavulanic acid, ampicillin, chloramphenicol, sulphamethoxazole, sulphamethoxazole/ trimethoprim, ticarcillin, vancomycin. A high prevalence of resistant strains (>30%) was ob-served for amikacin, ciprofloxacin, ceftriaxone, kanamycin, tetracycline. A comparison of this re-sults with those of previous works on similar dairy products revealed high levels of resistance to antimicrobials which needs to be addressed.

Two Screening Assays to Detect Vancomycin-Resistant Enterococcus spp

Enterococci have become major nosocomial pathogens. An increasing number of these infections are as a result of vancomycin-resistant enterococci. Accurate detection of vancomycin-resistant enterococci (VRE) is important, so that appropriate therapy and infection control measures may be instituted, including veterinary surveillance. Two screening assays to detect vancomycin resistance in enterococci are proposed. Barnes Basal Medium agar (Ba) and Brain Heart Infusion (BHI) broth (plus 1% TTC-2,3,5-triphenyltetrazolium chloride) with several concentrations of vancomycin were used in this work. Five Enterococcus casseliflavus strains with low-level resistance to vancomycin (4 µg/mL) were used. Both media were able to quickly detect the breakpoint of the vancomycin-resistant strains used in this work, and also provided insight into the dynamics of the antibiotic effect at a low concentration on the tested bacterial suspensions.

Metataxonomic sequencing to assess microbial safety of Turkish white cheeses

High-throughput sequencing has provided a way to monitor the large diversity of microorganisms in fermented foods that have complex microbiota. Up to date, many kinds of cheese have been characterized with the metataxonomic approach, but the safety of unpacked Turkish white cheeses, which are widely consumed in Turkey, has not been assessed. In this study, fifteen unpacked white cheeses sold in public bazaars in Ankara province have been collected and subjected to microbial enumeration as well as physicochemical analysis. Five white cheeses, which have relatively the highest foodborne pathogens, out of fifteen white cheeses, have been analyzed by next-generation sequencing and metataxonomic analysis. According to the results, abundant families were Lactobacillaceae, Oceanospirillaceae, Enterococcaceae, Pseudomonadaceae, and Vibrionaceae. Staphylococcus aureus, E. coli, and Salmonella, which are indicators of bad hygiene and sanitation conditions, were found in cheeses. In conclusion, culture-independent methods such as metataxonomic can be important to evaluate the safety of foods.

Purification, Characterization, Mode of Action, and Application of Jileicin, a Novel Antimicrobial from Paenibacillus jilinensis YPG26

Antimicrobial compounds from the commensal gut microbiota have gained much attention due to their multifunctionality in maintaining good health in the host and killing multidrug-resistant bacteria. Our previous study showed that Paenibacillus jilinensis YPG26 isolated from chicken intestine can antagonize multiple pathogens. Herein, we characterized a bacteriocin-like inhibitory substance, jileicin, purified from P. jilinensis YPG26. Mass spectrometry analysis revealed that jileicin was a protein consisting of 211 amino acids, which showed 88.98% identity to the SIMPL domain-containing protein. The jileicin showed a relatively broad-spectrum antibacterial ability, especially against enterococci. Additionally, the jileicin exhibited good stability after various treatments, no detectable resistance, no significant cytotoxicity, and very low levels of hemolytic activity. The mode of action against Enterococcus faecium demonstrated that jileicin could destroy cell membrane integrity, increase cell membrane permeability, and eventually lead to cell death. Furthermore, jileicin was efficient in controlling the growth of E. faecium in milk. In conclusion, jileicin, as a newly identified antibacterial agent, is expected to be a promising candidate for application in the food, pharmaceutical, and biomedical industries.

Growth and Biocontrol of Listeria monocytogenes in Greek Anthotyros Whey Cheese without or with a Crude Enterocin A-B-P Extract: Interactive Effects of the Native Spoilage Microbiota during Vacuum-Packed Storage at 4 °C

Effective biopreservation measures are needed to control the growth of postprocess Listeria monocytogenes contamination in fresh whey cheeses stored under refrigeration. This study assessed growth and biocontrol of inoculated (3 log₁₀ CFU/g) L. monocytogenes in vacuum-packed, fresh (1-day-old) or ‘aged’ (15-day-old) Anthotyros whey cheeses, without or with 5% of a crude enterocin A-B-P extract (CEntE), during storage at 4 °C. Regardless of CEntE addition, the pathogen increased by an average of 2.0 log₁₀ CFU/g in fresh cheeses on day 15. Gram-negative spoilage bacteria also increased by an average of 2.5 log₁₀ CFU/g. However, from day 15 to the sell-by date (days 35–40), L. monocytogenes growth ceased, and progressively, the populations of the pathogen declined in most cheeses. This was due to an unmonitored, batch-dependent natural acidification by spoilage lactic acid bacteria, predominantly Leuconostoc mesenteroides, which reduced the cheese pH to 5.5, and finally to ≤5.0. The pH reductions and associated declines in pathogen viability were greater in the CEntE-treated samples within each batch. L. monocytogenes failed to grow in cheeses previously ‘aged’ in retail for 15 days. Overall, high population levels (>7.5 log₁₀ CFU/g) of psychrotrophic Enterobacteriaceae, particularly Hafnia alvei, were associated with an extended growth and increased survival of L. monocytogenes during storage.

Omics Approaches to Assess Flavor Development in Cheese

Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.

Assessment of the Microbiological Quality and Biochemical Parameters of Traditional Hard Xinotyri Cheese Made from Raw or Pasteurized Goat Milk

Traditional hard Xinotyri cheese was manufactured using raw or pasteurized goat milk, without starter cultures, and the changes in microbiological and biochemical characteristics were studied during ripening and storage. Mesophilic lactic acid bacteria (LAB) predominated (>8.5 log CFU/g) in freshly fermented Xinotyri cheeses (pH 4.5–4.6), regardless of milk pasteurization. Enterobacteria, pseudomonads and staphylococci were suppressed below 6 and 4–5 log CFU/g in fresh cheeses from raw and pasteurized milk, respectively. Salmonella and Listeria spp. were absent in 25 g cheese samples. Coagulase-positive staphylococci exceeded the 5-log safety threshold in fresh raw milk cheeses, which also had 10-fold higher levels of enterococci than pasteurized milk cheeses. Non-LAB groups declined <100 CFU/g, whereas yeasts increased to 5–6 log CFU/g in both cheeses during ripening. Milk pasteurization affected the protein, fat, ash, moisture, nitrogen fractions, total free fatty acids and total free amino acids content of cheeses. Primary proteolysis, detectable by urea-PAGE, was more intense in raw milk cheeses than in pasteurized milk cheeses. However, the hydrophilic and hydrophobic peptides and their ratio in the water-soluble fraction were similar in both cheeses. Cheeses discriminated clearly according to the milk kind (raw, pasteurized) and the stage of ripening, based on the examined biochemical characteristics.

Assessment of the Spoilage Microbiota during Refrigerated (4 °C) Vacuum-Packed Storage of Fresh Greek Anthotyros Whey Cheese without or with a Crude Enterocin A-B-P-Containing Extract

Although fresh whey cheeses are prone to rapid deterioration, mainly by psychrotrophic Gram-negative bacteria and lactic acid bacteria (LAB), data on the specific spoilage species in traditional Greek whey cheeses are scarce. Therefore, this study quantified growth and characterized the primary spoilage bacteria in fresh Anthotyros whey cheeses stored at 4 °C in a vacuum for 40 days, without or with an added 5% (v/w) of an enterocin A-B-P crude extract (CEntE). Psychrotrophic Pseudomonas spp., Aeromonas spp., Hafnia spp. and Serratia spp. grew faster than LAB during early storage. However, LAB outgrew the Gram-negative bacteria and prevailed by mid to late storage in all cheese batches, causing a strong or milder batch-dependent natural acidification. Two major non-slime-producing and two minor biotypes of Leuconostoc-like bacteria, all identified as Leuconostoc mesenteroides by 16S rRNA sequencing, dominated the LAB association (76.7%), which also included four subdominant Carnobacterium maltaromaticum biotypes (10.9%), one Leuconostoc lactis biotype (3.3%) and few Lactococcus (1.6%), mesophilic Lactobacillus (0.8%) and Enterococcus (0.8%). Growth and distribution of LAB and Gram-negative species were strongly batch-dependent and plant-dependent. The CEntE neither retarded growth nor altered the whey cheese spoilage association but enhanced LAB growth and the declines of Gram-negative bacteria by late storage.

Characterization of Bacterial Microbiota of P.D.O. Feta Cheese by 16S Metagenomic Analysis

Background: The identification of bacterial species in fermented PDO (protected designation of origin) cheese is important since they contribute significantly to the final organoleptic properties, the ripening process, the shelf life, the safety and the overall quality of cheese. Methods: Ten commercial PDO feta cheeses from two geographic regions of Greece, Epirus and Thessaly, were analyzed by 16S metagenomic analysis. Results: The biodiversity of all the tested feta cheese samples consisted of five phyla, 17 families, 38 genera and 59 bacterial species. The dominant phylum identified was Firmicutes (49% of the species), followed by Proteobacteria (39% of the species), Bacteroidetes (7% of the species), Actinobacteria (4% of the species) and Tenericutes (1% of the species). Streptococcaceae and Lactobacillaceae were the most abundant families, in which starter cultures of lactic acid bacteria (LAB) belonged, but also 21 nonstarter lactic acid bacteria (NSLAB) were identified. Both geographical areas showed a distinctive microbiota fingerprint, which was ultimately overlapped by the application of starter cultures. In the rare biosphere of the feta cheese, Zobellella taiwanensis and Vibrio diazotrophicus, two Gram-negative bacteria which were not previously reported in dairy samples, were identified. Conclusions: The application of high-throughput DNA sequencing may provide a detailed microbial profile of commercial feta cheese produced with pasteurized milk.

In-Depth Investigation of the Safety of Wooden Shelves Used for Traditional Cheese Ripening

The main goal of this research was to characterize the bacterial diversity of the wooden boards used for aging traditional Sicilian cheeses and to evaluate whether pathogenic bacteria are associated with these surfaces. Eighteen cheese dairy factories producing three traditional cheese typologies (PDO Pecorino Siciliano, PDO Piacentinu Ennese, and Caciocavallo Palermitano) were selected within the region of Sicily. The wooden shelf surfaces were sampled by a destructive method to detach wood splinters as well as by a nondestructive brushing to collect microbial cells. Scanning electron microscopy showed the presence of almost continuous bacterial formations on the majority of the shelves analyzed. Yeasts and fungal hyphae were also visualized, indicating the complexity of the plank communities. The amplicon library of the 16S rRNA gene V3-V4 region was paired-end sequenced using the Illumina MiSeq system, allowing the identification of 14 phyla, 32 classes, 52 orders, 93 families, and 137 genera. Staphylococcus equorum was identified from all wooden surfaces, with a maximum abundance of 64.75%. Among cheese-surface-ripening bacteria, Brevibacterium and Corynebacterium were detected in almost all samples. Several halophilic (Halomonas, Tetragenococcus halophilus, Chromohalobacter, Salimicrobium, Marinococcus, Salegentibacter, Haererehalobacter, Marinobacter, and Idiomarinaceae) and moderately halophilic (Salinicoccus, Psychrobacter, and Salinisphaera) bacteria were frequently identified. Lactic acid bacteria (LAB) were present at low percentages in the genera Leuconostoc, Lactococcus, Lactobacillus, Pediococcus, and Streptococcus. The levels of viable microorganisms on the wooden shelves ranged between 2.4 and 7.8 log CFU/cm2. In some cases, LAB were counted at very high levels (8.2 log CFU/cm2). Members of the Enterobacteriaceae family were detected in a viable state for only six samples. Coagulase-positive staphylococci, Salmonella spp., and Listeria monocytogenes were not detected. Seventy-five strains belonged to the genera Leuconostoc, Lactococcus, Pediococcus, Enterococcus, Lactobacillus, and Weissella. IMPORTANCE This study provides evidence for the lack of pathogenic bacteria on the wooden shelves used to ripen internal bacterially ripened semihard and hard cheeses produced in Sicily. These three cheeses are not inoculated on their surfaces, and surface ripening is not considered to occur or, at least, does not occur at the same extent as surface-inoculated smear cheeses. Several bacterial groups identified from the wooden shelves are typically associated with smear cheeses, strongly suggesting that PDO Pecorino Siciliano, PDO Piacentinu Ennese, and Caciocavallo Palermitano cheese rind contributes to their final organoleptic profiles.