Brazilian Artisanal Cheeses: Diversity, Microbiological Safety, and Challenges for the Sector

Raw milk cheeses from Beira Baixa, Portugal-A contributive study for the microbiological hygiene and safety assessment

Due to specific bacterial microbiota, raw milk cheeses have appreciated sensory properties. However, they may pose a threat to consumer safety due to potential pathogens presence. This study evaluated the microbiological contamination of 98 raw milk cheeses from Beira Baixa, Portugal. Presence and enumeration of Coagulase Positive Staphylococci (CPS), Listeria monocytogenes, Salmonella spp., pathogenic Escherichia coli, and indicator microorganisms (non-pathogenic E. coli and Listeria spp.) was attained. E. coli antimicrobial resistance (AMR) was also evaluated. PCR and/or Whole genome sequencing (WGS) was used to characterize E. coli, Salmonella spp. and L. monocytogenes isolates. Sixteen cheeses (16.3%) were classified as Satisfactory, 59 (60.2%) as Borderline and 23 (23.5%) as Unsatisfactory/Potential Injurious to Health. L. monocytogenes, CPS > 104 cfu g-1, Extraintestinal pathogenic E. coli (ExPEC) and Salmonella spp. were detected in 4.1%, 6.1%, 3.1% and 1.0% of the samples, respectively. Listeria innocua (4.1%) and E. coli > 104 cfu g-1 (16.3%) were also detected. AMR E. coli was detected in 23/98 (23.5%) of the cheese samples, of which two were multidrug resistant. WGS identified genotypes already associated to human disease and Listeria spp. cluster analysis indicated that cheese contamination might be related with noncompliance with Good Hygiene Practices during cheese production.

Evaluation of Extraction Methods to Detect Noroviruses in Ready-to-Eat Raw Milk Minas Artisanal Cheese

This study aimed to assess two homogenization methods to recover norovirus from Minas artisanal cheese (MAC) made with raw bovine milk obtained from four microregions of the Minas Gerais state, Brazil, with different ripening times and geographical and abiotic characteristics. For this purpose, 33 fiscal samples were artificially contaminated with norovirus GI and GII, and Mengovirus (MgV), used as an internal process control (IPC). TRIzol® reagent and Proteinase K homogenization methods were evaluated for all samples were then subjected to RNA extraction using viral magnetic beads and RT-qPCR Taqman® for viral detection/quantification. Proteinase K method showed better efficiency results for both norovirus GI and GII, with means recovery efficiency of 45.7% (95% CI 34.3-57.2%) and 41.4% (95% CI 29.1-53.6%), respectively, when compared to TRIzol method (16.6% GI, 95% CI 8.4-24.9%, and 12.3% GII, 95% CI 7.0-17.6%). The limits of detection for norovirus GI and GII for this method were 101GC/g and 103GC/g, respectively, independent of cheese origin. MgV was detected and revealed in 100% success rate in all types of cheese, with mean recovery efficiency of 25.6% for Proteinase K, and 3.8% for the TRIzol method. According to cheese origin, Triangulo Mineiro MAC had the highest mean recovery rates for the three viral targets surveyed (89% GI, 87% GII, and 51% MgV), while Serro MAC showed the lowest rates (p < 0.001). Those results indicate that the proteinase K adapted method is suitable for norovirus GI and GII detection in MAC and corroborated MgV as an applicable IPC to be used during the process.

Unveiling Safety Concerns in Brazilian Artisanal Cheeses: A Call for Enhanced Ripening Protocols and Microbiological Assessments

Brazilian artisanal cheeses have recently gained significant commercial prominence and consumer favor, primarily due to their distinctive sensory attributes and cultural and historical appeal. Many of these cheeses are made with raw milk and undergo a relatively short ripening period, sometimes ranging from 4 to 8 days, though it is usually shorter than the period stated by law. Moreover, there is insufficient evidence regarding the efficacy of a short ripening period in reducing certain zoonotic foodborne pathogens, such as Brucella spp., Coxiella burnetiid, and Mycobacterium bovis (as part of the Mycobacterium tuberculosis complex). Additionally, a literature analysis revealed that the usual ripening conditions of Brazilian artisanal cheeses made with raw milk may be inefficient in reducing the levels of some hazardous bacterial, including Brucella spp., Listeria monocytogenes, coagulase-positive Staphylococcus, Salmonella, and Coxiella burnetti, to the acceptable limits established by law, thus failing to ensure product safety for all cheese types. Moreover, the assessment of the microbiological safety for this type of cheese should be broader and should also consider zoonotic pathogens commonly found in bovine herds. Finally, a standardized protocol for evaluating the effectiveness of cheese ripening must be established by considering its peculiarities.

Unveiling ochratoxin A and ochratoxigenic fungi in Brazilian artisanal Cheeses: Insights from production to consumption

Ochratoxin A (OTA) is a toxin produced by several Aspergillus species, mainly those belonging to section Circumdati and section Nigri. The presence of OTA in cheese has been reported recently in cave cheese in Italy. As artisanal cheese production in Brazil has increased, the aim of this study was to investigate the presence of ochratoxin A and related fungi in artisanal cheese consumed in Brazil. A total of 130 samples of artisanal cheeses with natural moldy rind at different periods of maturation were collected. Of this total, 79 samples were collected from 6 producers from Canastra region in the state of Minas Gerais, since this is the largest artisanal cheese producer region; 13 samples from one producer in the Amparo region in the state of São Paulo and 36 samples from markets located in these 2 states. Aspergillus section Circumdati occurred in samples of three producers and some samples from the markets. A. section Circumdati colony counts varied from 102 to 106 CFU/g. Molecular analysis revealed Aspergillus westerdijkiae (67 %) as the most frequent species, followed by Aspergillus ostianus (22 %), and Aspergillus steynii (11 %). All of these isolates of A. section Circumdati were able to produce OTA in Yeast Extract Sucrose Agar (YESA) at 25 °C/7 days. OTA was found in 22 % of the artisanal cheese samples, ranging from 1.0 to above 1000 µg/kg, but only five samples had OTA higher than 1000 µg/kg. These findings emphasize the significance of ongoing monitoring and quality control in the artisanal cheese production process to minimize potential health risks linked to OTA contamination.

High throughput qPCR analyses suggest that Enterobacterales of French sheep and cow cheese rarely carry genes conferring resistances to critically important antibiotics for human medicine

Bacteria present in raw milk can carry acquired or intrinsic antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). However, only a few studies have evaluated raw milk cheese as a potential reservoir of ARGs. This study thus aimed at providing new data regarding resistance markers present in raw milk cheese. Sheep (n = 360) and cow (n = 360) cheese samples produced in France were incubated in buffered peptone water supplemented with acriflavin or novobiocin; as corroborated by 16S metabarcoding, samples were enriched in Gram-negative bacteria since Escherichia coli and Hafnia alvei respectively accounted for 40 % and 20 % of the samples' microbiota. Screening of the samples for the presence of 30 ARGs and 16 MGEs by high throughput qPCR array showed that nine ARGs conferring resistances to 1st-generation beta-lactams, aminoglycosides, trimethoprim/sulfonamides and tetracyclines occurred in >75 % of both sheep and cow samples. This is neither surprising nor alarming since these resistance genes are widely spread across the One Health human, animal and environmental sectors. Conversely, genes conferring resistances to last-generations cephalosporins were rarely identified, while those conferring resistances to carbapenems or amikacin, which are restricted to human use, were never detected. Multiple MGEs were detected, the most frequent ones being IncF plasmids, confirming the potential transmission of ARGs. Our results are in line with the few studies of the resistome of milk or milk cheese showing that genes conferring resistances to 1st-generation beta-lactams, aminoglycosides and tetracyclines families are widespread, while those conferring resistances to critically important antibiotics are rare or absent.

Tracking microbial quality, safety and environmental contamination sources in artisanal goat cheesemaking factories

A harmonised microbiological survey was performed in two artisanal factories of raw goat milk cheeses (A and B) located in the Andalusian region (Spain). A total of 165 different control points or samples (raw materials, final products, food-contact surfaces [FCS], and air) were examined as microbial and pathogen sources of contamination of artisanal goat raw milk cheeses. For raw milk samples analysed from both producers, the concentrations of aerobic-mesophilic bacteria (AMB), total coliforms, coagulase-positive Staphylococcus spp. (CPS), lactic-acid bacteria (LAB) and moulds and yeasts ranged between 3.48 and 8.59, 2.45-5.48, 3.42-4.81, 4.99-8.59 and 3.35-6.85 log cfu/mL respectively. For the same microbial groups, the analysis of raw milk cheeses revealed concentrations ranging from 7.82 to 8.88, 2.00-6.82, 2.00-5.28, 8.11-9.57 and 2.00-5.76 log cfu/g, respectively. Although the raw material analysed from producer A presented higher microbial loads and between-batch variability, it was B the producer with the most loaded final products. Regarding the microbial air quality, the fermentation area, storage room, milk reception and packaging room were the most AMB loaded places, while the ripening chamber was the area with higher fungal loads in bioareosol from both producers. Conveyor belts, cutting machine, storage boxes and brine tank were highlighted as the most contaminated FCS evaluated. Staphylococcus aureus was the only pathogen detected within the set of 51 isolates from samples as revealed by MALDI-TOF and molecular PCR, with a prevalence of 12.5% for samples from the producer B. The public health risk attributed to the consumption of artisanal goat cheese should not be neglected, and may consider the whole cheesemaking processing chain, from microbiological quality of raw milk to the ready-to-eat final product, especially concerning the presence of S. aureus.

High Level of Interaction between Phages and Bacteria in an Artisanal Raw Milk Cheese Microbial Community

Microbial starter cultures are used in the production of many cheeses around the world, such as Parmigiano-Reggiano, in Italy, Époisses, in France, and Canastra, in Brazil, providing many of the unique features of these cheeses. Bacteriophages (phages) are ubiquitous and well known to modulate the structure of bacterial communities, and recent data indicate that cheeses contain a high abundance of naturally occurring phages. Here, we analyze the viral and bacterial metagenomes of Canastra cheese: a traditional artisanal Brazilian cheese produced using an endogenous starter culture and raw milk. Over 1,200 viral operational taxonomic units were recovered using both isolated viral-like particles and complete metagenomic DNA. Common viral families identified included Siphoviridae and Myoviridae, with 40% of putative phage genomes unidentified at the family level of classification. We observed very high phage diversity, which varied greatly across different cheese producers, with 28% of phage genomes detected in only one producer. Several metagenome-assembled genomes were recovered for lactic acid-producing bacteria, as well as nonstarter bacterial species, and we identified several phage-bacterium interactions, at the strain level of resolution, varying across distinct cheese producers. We postulate that at least one bacterial strain detected could be endogenous and unique to the Canastra cheese-producing region in Brazil and that its growth seems to be modulated by autochthonous phages present in this artisanal production system. This phage-host relationship is likely to influence the fermentation dynamics and ultimately the sensorial profile of these cheeses, with implications for other similar cheese production systems around the world. IMPORTANCE Our work demonstrated a dynamic yet stable microbial ecosystem during cheese production using an endogenous starter culture. This was observed across several distinct producers and was marked by genomic evidence of continued phage-bacterium interactions, such as the presence of bacterial defense mechanisms. Furthermore, we provide evidence of unique microbial signatures for each individual cheese producer studied in the region, a fact that may have profound consequences on product traceability. This was the first effort to describe and understand the bacteriophage composition and ecological dynamics within the Brazilian Canastra cheese production system. The study of this prototypical backslopping production system provides a solid background for further mechanistic studies of the production of many cheeses around the world.

Global Regulatory Frameworks for Fermented Foods: A Review

In recent years, there has been a global resurgence of public interest in fermented foods. In parallel, there have been several new studies that associate the consumption of fermented foods with a variety of beneficial impacts. These combined developments have led to a renewed focus in research and innovation vis-à-vis fermented foods, particularly traditional fermented foods, with an aim to harness this information to develop novel fermented foodstuffs and ingredients and make them available in the market. Consequently, an ever greater and more diverse array of fermented foods, including functional fermented foods with health benefits, are becoming available for public consumption in global markets, with the number expected to grow substantially in the coming decade. This rapidly expanding portfolio of commercially available fermented foods has in turn required an evolution in the corresponding global regulatory frameworks. Due to the innovative and emerging nature of these foods, combined with historical differences in regulator approaches, significant disharmony exists across these frameworks, with individual nations and organizations often adopting unique approaches relating to the establishment of standards and specifications. In this review, we provide an overview of the current regulatory frameworks for a diversity of fermented foods across multiple jurisdictions, with special emphasis on differences in legislative structures and approaches, regulatory harmonization, and current legislative limitations. Overall, the review provides important perspective and context in relation to current global fermented food regulatory practices with possible directions and recommendations for future legislative efforts.

Staphylococcus aureus from Minas Artisanal Cheeses: Biocide Tolerance, Antibiotic Resistance and Enterotoxin Genes

Staphylococcus aureus is a common contaminant in artisanal raw-milk cheeses. Tolerance of S. aureus to biocides is a threat to disinfection in the cheese production environment, while antibiotic resistance and enterotoxin production are additional health concerns. This study aimed to evaluate the tolerance of S. aureus isolated from Minas artisanal cheeses to the biocides benzalkonium chloride, hexadecylpyridinium chloride, cetrimide, triclosan, hexachlorophene, and chlorhexidine, and the simultaneous occurrence of genes coding for antibiotic resistance (mecA, aacA-aphD, and tetK), efflux pumps [qacA/B and smr (qacC/D)], and enterotoxins (sea, seb, sec, sed, see, seg, seh, sei, and sej). Among the tested isolates, 38.2% were resistant to at least one biocide, and 73.1% were positive for one or more antibiotic resistance gene. Most of the biocide-tolerant and antibiotic-resistant isolates harbored efflux pump genes, and were positive for at least one staphylococcal enterotoxin gene. The study highlights the need for correct hygiene monitoring programs to ensure the safety of these products.

Assessing the Microbiological Safety Parameters of Minas Artisanal Cheese Samples in Retail Environments in São Paulo, Brazil

Minas artisanal cheese is the best known and most consumed type of cheese in Brazil. Prepared with raw bovine milk and starter cultures, these cheeses face many opportunities for post-processing contamination during their transport to commercial establishments as well as in how they are stored, displayed, and maintained for cutting/slicing at retail establishments. It is a common practice for retailers to purchase entire cheeses from the producers, cut them into smaller pieces for retail sale, and store them at room temperature instead of properly refrigerating them. This study evaluated the microbiological safety parameters of samples of Minas artisanal cheeses collected at retail establishments in the city of São Paulo, Brazil, to more realistically assess consumer exposure to the most common pathogens. Samples were submitted for investigation of Salmonella spp., Listeria monocytogenes, and the counts of total coliforms, Escherichia coli, and coagulase-positive enterotoxigenic staphylococci using culture and real-time PCR methods. A worrisome number of samples failed to comply with the current Brazilian legislation for foods in retail environments and presented more than one non-compliance issue. Results highlighted that quality and safety management tools, such as good hygiene practices and HACCP, in retail environments deserve more attention to reduce the possible risks to consumer health.