Coliform detection in cheese is associated with specific cheese characteristics, but no association was found with pathogen detection

Dynamics of microbiota and antimicrobial resistance in on-farm dairy processing plants using metagenomic and culture-dependent approaches

On-farm dairy processing plants, which are situated close to farms and larger dairy processing facilities, face unique challenges in maintaining environmental hygiene. This can impact various stages of dairy processing. These plants operate on smaller scales and use Low-Temperature-Long-Time (LTLT) pasteurization, making them more susceptible to microbial contamination through direct and indirect contact. Antimicrobial-resistant bacteria found on dairy farms pose risks to human health by potentially transferring resistance via dairy products. Our study aimed to investigate microbial distribution and antimicrobial resistance at four key stages: the farm, pre-pasteurization, post-pasteurization, and processing environments. We assessed microbial distribution by quantifying indicator bacteria and conducting metagenomic analysis. Antimicrobial resistance was examined by identifying resistance phenotypes and detecting resistance genes in bacterial isolates and metagenomes. Our results showed that the indicator bacteria were detected at all stages of on-farm dairy processing. We observed a significant reduction in aerobic microbes and coliforms post-pasteurization. However, contamination of the final dairy products increased, suggesting potential cross-contamination during post-pasteurization. Metagenomic analysis revealed that Pseudomonas, a representative psychrotrophic bacterium, was predominant in both the farm (24.1 %) and pre-pasteurization (65.9 %) stages, indicating microbial transfer from the farms to the processing plants. Post-pasteurization, Pseudomonas and other psychrotrophs like Acinetobacter and Enterobacteriaceae remained dominant. Core microbiota analysis identified 74 genera in total, including 13 psychrotrophic bacteria, across all stages. Of the 59 strains isolated from these plants, 49 were psychrotrophic. Antimicrobial resistance analysis showed that 74.6 % (44/59) of isolates were resistant to at least one antibiotic, with cefoxitin-, ampicillin-, amoxicillin-, and ticarcillin-resistant bacteria present at all stages. Identical antimicrobial resistance patterns were observed in isolates from serial stages of the same farm and season, suggesting bacterial transmission across stages. Additionally, 27.1 % (16/59) of isolates carried plasmid-mediated resistance genes, which were also detected in the metagenomes of non-isolated samples, indicating potential antimicrobial resistance gene transmission and their presence in uncultured bacteria. These findings reveal the persistence of antimicrobial-resistant psychrotrophic bacteria in on-farm dairy processing plants, which pose potential health risks via dairy consumption. Our study underscores the importance of both culture-dependent and culture-independent methods to fully understand their distribution and impact.

Occurrence and genomic characterization of antimicrobial-resistant and potential pathogenic Escherichia coli from Italian artisanal food productions of animal origin

Escherichia coli can harbor a broad repertoire of virulence and antimicrobial resistance (AMR) genes, which can be exchanged across the human gastrointestinal microflora, thus posing a public health risk. In this study, 6 batches of artisanal soft cheese and a 6-month ripened fermented dried sausage were investigated to assess the occurrence, phylogeny, and genomic traits (AMR, virulence, and mobilome) of E. coli. 30 and 3 strains isolated from salami and cheese food chains, respectively, were confirmed as E. coli by whole genome sequencing. The accumulation of single nucleotide polymorphism differences within small clusters of strains encompassing batches or processing stages, combined with high serotype and phylogroup diversity, suggested the occurrence of different contamination phenomena among the facilities. A total of 8 isolates harbored plasmid-mediated resistance genes, including one cheese strain that carried an IncQ1 plasmid carrying AMR determinants to macrolides [mph(B)], sulfonamides (sul1, sul2), trimethoprim (dfrA1), and aminoglycosides [aph(3")-Ib and aph(6)-Id]. A pool of virulence-associated genes in the class of adhesion, colonization, iron uptake, and toxins, putative ColV-positive iron uptake systems sit, iro, or iuc (8 salami and 2 cheese), plasmid-encoded hemolysin operon hlyABCD (one salami), and potential atypical enteropathogenic E. coli (3 salami environment) were reported. Overall, our findings underscore the importance of routine surveillance of E. coli in the artisanal food chain to prevent the dissemination of AMR and virulence.

Assessment of the Microbiological Safety and Hygiene of Raw and Thermally Treated Milk Cheeses Marketed in Central Italy between 2013 and 2020

A profile of the microbial safety and hygiene of cheese in central Italy was defined based on an analysis of 1373 cheeses sampled under the Italian National Control Plan for Food Safety spanning the years 2013 to 2020 and tested according to Commission Regulation (EC) No. 2073/2005 (as amended). A total of 97.4% of cheese samples were assessed as being satisfactory for food safety criteria and 80.5% for process hygiene criteria. Staphylococcal enterotoxin was found in 2/414 samples, while Salmonella spp. and Listeria monocytogenes were detected in 15 samples out of 373 and 437, respectively. Escherichia coli and coagulase-positive staphylococci counts were found unsatisfactory in 12/61 and 17/88 cheese samples, respectively. The impact of milking species, milk thermal treatment, and cheese hardness category was considered. A statistically significant association (p < 0.05) was found between milk thermal treatment and the prevalence of coagulase-positive staphylococci and Listeria monocytogenes and between hardness and unsatisfactory levels of Escherichia coli. The data depict a contained public health risk associated with these products and confirm, at the same time, the importance of strict compliance with good hygiene practices during milk and cheese production. These results can assist in bolstering risk analysis and providing insights for food safety decision making.

Aloe barbadensis Based Bioactive Edible Film Improved Lipid Stability and Microbial Quality of the Cheese

An attempt was made to develop a bioactive edible film using carrageenan and A. vera gel for enhancing the storage quality of cheese using kalari, a popular Himalayan cheese, as a food-model system. The film was evaluated for various physicomechanical and oxidative properties (ABTS (2,2-azino-bis (3-ethylbenzothiazoline-6-sulfonate)) and DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activities, total flavonoid and phenolic contents). Based on preliminary trials, 1% A. vera gel was found to be optimum. The addition of the gel resulted in a significant decrease in moisture content, transparency, solubility, and water-vapor transmission rate and increased the thickness and density of the film. The film showed antimicrobial properties against E. coli and significantly (p < 0.05) decreased the lipid-oxidation (thiobarbituric acid reactive substances, free-fatty acids, and peroxide values) and increased microbial-quality (total-plate, psychrophilic, and yeast/molds) of the samples during 4-week refrigerated storage (4 ± 1 °C). The film also exhibited a significant positive impact on the sensory quality of the cheese, indicating the potential for commercial applications for quality control of cheese during storage.

Microbiological Quality and Safety of Traditional Raw Milk Cheeses Manufactured on a Small Scale by Polish Dairy Farms

Polish raw milk artisanal cheese may pose a threat to consumer safety due to pathogen presence. The aim of this study was to assess the microbiological safety, quality and physicochemical composition of cow’s and goat’s milk fresh cheeses produced by farmers on a small scale. A total of 62 samples of six cheese types were analyzed for Listeria monocytogenes, Salmonella spp., lactic acid bacteria and coliform presence and concentration levels. The physicochemical analysis estimated energy, water, protein, fat, carbohydrate, ash and salt content. The cheeses were also tested for heavy metal contamination. Listeria monocytogenes and Salmonella spp. were not detected in any of the samples. Coliforms were present in all the goat’s milk cheeses and only in two of the cow’s milk cheeses. Low levels of cadmium, below 0.008 ppm, were detected in three of the cows’ milk samples. The raw milk cheeses studied were free of the pathogens examined and were of high nutritional value.

Metataxonomic Mapping of the Microbial Diversity of Irish and Eastern Mediterranean Cheeses

The distinct sensorial characteristics of local cheeses influence consumer preferences, and make an essential contribution to the local economy. Microbial diversity in cheese is among the fundamental contributors to sensorial and qualitative characteristics. However, knowledge regarding the existence of microbial patterns associated with regional production practices in ripened cheeses remains limited. The present research was conducted to test the hypothesis that the background metagenome of cheeses could be used as a marker of their origin. We compared Irish versus Eastern Mediterranean cheeses-namely Greek and Cypriot-using High Throughput Sequencing (HTS). The study identified a significantly distinct separation among cheeses originating from the three different countries, in terms of the total microbial community composition. The use of machine learning and biomarkers discovery algorithms defined key microbes that differentiate each geographic region. Finally, the development of interaction networks revealed that the key species developed mostly negative interactions with the other members of the communities, highlighting their dominance in the community. The findings of the present research demonstrate that metagenome could indeed be used as a biological marker of the origin of mature cheeses, and could provide further insight into the dynamics of microbial community composition in ripened cheeses.

Loads of Coliforms and Fecal Coliforms and Characterization of Thermotolerant Escherichia coli in Fresh Raw Milk Cheese

The aim of this study was to assess the hygienic status of raw milk cheese and determine the trends of virulence and antimicrobial resistance in thermotolerant Escherichia coli. Two hundred samples of karish, a popular Egyptian fresh raw milk cheese, were analyzed for coliforms and fecal coliforms using a standard most probable number (MPN) technique. Overall, 85% of samples were unsuitable for consumption, as they exceeded Egyptian standards for coliforms (10 MPN/g), and 65% of samples exhibited coliforms at 44.5 °C. Of 150 recovered thermotolerant strains, 140 (93.3%) were identified as E. coli. Importantly, one Shiga toxin-producing E. coli (STEC) strain carrying a striking virulence pattern, stx1−, stx2+, eae−, was detected. Eleven strains (7.8%, 11/140) showed resistance to third-generation cephalosporins. Antibiotic resistance genes included bla_SHV, bla_CTX-M, qnrS, tet(A), and tet(B), which were present in 4.3%, 2.8%, 0.71%, 2.1%, and 0.71% of isolates, respectively. In conclusion, this study indicated that hygienic-sanitary failures occurred throughout the production process of most retail karish cheese. Furthermore, our findings emphasize the need for adopting third-generation cephalosporin-resistant E. coli as an indicator for monitoring antimicrobial resistance in raw milk cheese to identify the potential public health burden associated with its consumption.

Enterobacteriaceae in food safety with an emphasis on raw milk and meat

There has been a growing interest in traditional dairy (such as raw milk cheeses) and meat products, in recent years. However, these products are suitable and nutrient medium and may be easily contaminated by microorganisms such as Enterobacteriaceae. Enterobacteriaceae are considered to be the indicator bacteria for microbiological quality of food and hygiene status of a production process. Additionally, the food contaminated by Enterobacteriaceae poses a microbiological risk for consumers. In fact, the contamination of raw milk and meat by Enterobacteriaceae amid manufacturing may easily occur from various environmental sources, and this group of bacteria is frequently detected in dairy and meat products. Therefore, monitoring the microbiological quality of the used raw material and maintaining high standards of hygiene in the production process are mandatory for a high quality of traditional products and the safety of the potential consumers. The goal of this review is to present the most recent survey on Enterobacteriaceae growth, number, and distribution in raw milk cheeses and meat, as well as to discuss the sources of contamination and methods of control. KEY POINTS: • Enterobacteriaceae: role and importance in milk and meat products, EU legal regulations • Dynamics, distribution, and survival of Enterobacteriaceae in milk and meat • Mechanisms of control of Enterobacteriaceae in dairy 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.

Population dynamics of coliforms in a commercial Cheddar cheese production facility

The detection of coliforms in young cheese is a potential indication of undesirable microbial growth within the processing environment. The aim of this study was to investigate sources and conditions that lead to the intermittent detection of coliforms (1-3 log cfu/g) in young Cheddar cheese at a single commercial facility. Analysis of historical production data, in combination with iterative investigative sampling events, was performed to determine coliform levels in milk, whey, curd, and surfaces at the beginning, middle, and end of the production day. After sanitation, conveyor belt pieces from the draining and matting conveyor (DMC) were collected and evaluated for bacterial survivors using culture-based methods and scanning electron microscopy. Production data analysis indicated that cheese produced later in the production day (≥16 h) was significantly more likely to test positive for coliforms than cheese made earlier in the production day (<12 h). Enumeration of coliforms in raw and heat-treated milk demonstrated that the subpasteurization thermal treatment (67-70°C, 26-28 s) was effective at reducing, but not eliminating, coliforms. Repeated sampling identified the DMC, particularly the drain belt and belt 1, as a critical area that supported coliform growth during the production day. Coliform levels in whey entering the weir maintained a level of <1 cfu/mL throughout production; however, coliform levels in whey below the drain belt increased from <1 cfu/mL at midday (8 h) to 5.04 log cfu/mL by the end of the production day (~18 h). Routine sanitation inside the DMC resulted in undetectable coliform levels on easily accessible surfaces. However, enrichment and scanning electron microscopy of belt sections revealed pockets of viable coliforms and other bacteria in cracks and defects in conveyor belts, indicating that sanitation did not eliminate all viable bacteria. Low levels of coliforms are present in heat-treated milk and survive sanitation in the DMC and could serve as the initial seed for high levels of coliforms at the end of the production day.

Shiga toxin-producing Escherichia coli isolated from pasteurized dairy products from Bahia, Brazil

The presence of pathogenic Shiga toxin-producing Escherichia coli (STEC) in dairy products represents a public health concern because of its ability to produce the toxins Stx1 and Stx2, which cause intestinal diseases. Monitoring the stages of milk production and checking dairy products for contamination are crucial steps to ensure dairy safety. This study aimed to report the occurrence of thermotolerant coliforms, E. coli, and STEC strains in pasteurized dairy products and to evaluate the antibiotic resistance profiles, serotypes, and characterizations of the STEC isolates by pulsed-field gel electrophoresis. We obtained a total of 138 pasteurized dairy products from 15 processing plants in Bahia, Brazil, to examine coliforms, E. coli, and STEC strains. We found that 43% of samples (59/138) contained thermotolerant coliforms, and 30% (42/138) did not comply with Brazilian regulations. Overall, 6% (9/138) were positive for E. coli and 4% (5/138) were positive for STEC. We recovered 9 STEC isolates from pasteurized cream (2/9), Minas Padrão cheese (2/9), Minas Frescal cheese (4/9), and ricotta (1/9). All isolates were stx2-positive, and 2 were eae-positive. All isolates were negative for the "big 6" STEC serogroups, belonging instead to serotypes ONT:HNT, ONT:H12, O148:H-, OR:H40, OR:HNT, and O148:HNT. Pulsed-field gel electrophoresis revealed 100% genetic similarity among 3 isolates from 2 different samples produced in the same production facility, which may suggest cross-contamination. As well, we found isolates that were 98% similar but in samples produced in different production facilities, suggesting a mutual source of contamination or a circulating strain. Two STEC strains exhibited resistance to streptomycin. Although the isolates presented a low resistance profile and no strain belonged to the "big 6" pathogenic group, the circulation of stx2-positive STEC strains in ready-to-eat products highlights the importance of epidemiological surveillance inside the Brazilian dairy chain.

Listeria monocytogenes inhibition by lactic acid bacteria and coliforms in Brazilian fresh white cheese

INTRODUCTION

Minas fresh cheese (MFC), a Brazilian white cheese, is one of the most popular cheeses nationwide. Studies have shown that Listeria monocytogenes occurrence in this product is generally low, while high populations of coliforms can be found. This study aimed to evaluate the influence of coliforms in the behavior of L. monocytogenes in MFC.

METHODS

Pasteurized milk was inoculated with L. monocytogenes and coliforms, and the acidification was made by lactic acid or by the addition of a starter culture. The cheeses of each production were divided into 3 groups and stored at 5 ºC, 12 ºC and cycles of 5 ºC followed by 25 ºC. In predetermined days, samples were taken and L. monocytogenes, coliforms and lactic acid bacteria populations were evaluated, besides the pH, water activity (aw), titratable acidity and NaCl concentration.

RESULTS

The inhibition of L. monocytogenes in the presence of coliforms was observed (p < 0.05), except for those samples prepared with lactic acid and stored at temperature cycles. The values of pH and aw were not sufficiently low to cause inhibition; however, titratable acidity was higher in cheeses containing coliforms. In vitro tests containing lactic acid and L. monocytogenes showed that the bacterium is sensitive to concentration of lactic acid ≥ 0.3%, indicating that lactic acid produced by coliforms strongly influences the population of L. monocytogenes.

CONCLUSIONS

Thus, it can be concluded that coliforms negatively impact populations of L. monocytogenes in MFC. We strongly recommend that producers of MFC adopt good hygiene practices to not only avoid contamination with L. monocytogenes, but also coliforms.

Microbiological quality and safety of Brazilian artisanal cheeses

The establishment of norms that regulates the production and trade of Brazilian Artisanal Cheeses (BAC) has been stimulating many small farmers for this activity. The predominance of lactic acid bacteria (LAB) is a typical characteristic of BAC, which confers desirable attributes to artisanal cheeses. However, these products can be contaminated by other microbial groups, including those that indicate hygienic failures during production and may cause spoilage, or even microorganisms that pose risks to consumers' health. A systematic review of the literature published from January 1996 to November 2020 was carried out to identify scientific data about production characteristics and microbiological aspects of BAC, with a major focus on quality and safety status of these traditional products. Studies that fulfilled the inclusion criteria indicated that artisanal chesses produced in Brazil still do not satisfactorily meet the microbiological criteria established by the national laws, mainly due to the high counts of coagulase-positive Staphylococcus and coliforms. Despite low prevalence, pathogens such as Salmonella and Listeria monocytogenes were isolated in some BAC. This review contributed to better understanding microbiological aspects of BAC, the data compiled by the authors highlight the need to improve hygiene practices along the production chain of these traditional cheeses.

Isolation of enterotoxigenic Staphylococcus aureus harboring seb gene and enteropathogenic Escherichia coli (serogroups O18, O114, and O125) from soft and hard artisanal cheeses in Egypt

Background:

Soft and hard artisanal cheeses are regularly consumed in Egypt. These products are usually processed from raw milk which may harbor many pathogenic and spoilage microorganisms.

Aim:

To evaluate the safety of some artisanal cheeses in Egypt, such as Ras, Domiati, and Mish, through chemical and microbiological examination.

Methods:

One hundred and fifty random samples of traditional Ras, Domiati, and Mish cheeses (50 each) were microbiologically and chemically analyzed. Counts of total bacteria, presumptive coliform, staphylococci, yeast, and mold were estimated. Furthermore, isolation of Escherichia coli and Staphylococcus aureus was performed, followed by PCR confirmation; isolates of E. coli were examined for the presence of virulence genes; on the other hand, the detection of the five classical enterotoxin genes of S. aureus was performed using multiplex PCR. Regarding chemical analysis, moisture, salt, and acidity content were measured. Correlations between chemical and microbial findings were investigated.

Results:

Mean counts of total bacteria, presumptive coliform, staphylococci, yeast, and mold were (2 × 10⁸, 3 × 10⁶ and 1 × 10⁷ ), (3 × 10⁵, 5 × 10 and 5 × 10²), (1 × 10⁶, 4 × 10⁵and 1 × 10⁵), (3 × 10⁵, 1 × 10⁵ and 5 × 10⁵), and (7 × 10³, 4 × 10³ and 3 × 10⁴) for Ras, Domiati and Mish cheeses, respectively. Serological identification of suspected E. coli revealed that E. coli O125 was isolated from Ras and Domiati samples, E. coli O18 was recovered from Ras samples, while E. coli O114 was isolated from Mish samples. PCR results revealed that all detected isolates of E. coli were positive for both iss (increased serum survival) and fimH (type 1 fimbriae) genes. Concerning isolated S. aureus, all examined products were harboring S. aureus enterotoxigenic strains, with seb and sed genes being the most common. The mean values of moisture, salt, and acidity were (30.03, 56.44, and 58.70), (3.30, 6.63, and 7.56) and (0.65, 0.68, and 0.50) for Ras, Domiati, and Mish cheeses, respectively.

Conclusion:

Enterotoxigenic S. aureus harboring seb gene and enteropathogenic E. coli (serogroups O18, O114, and O125) were frequently isolated from soft and hard artisanal cheeses in Egypt. Therefore, strict hygienic measures should be applied during their manufacture, handing, and distribution.

Assessment of overall microbial community shift during Cheddar cheese production from raw milk to aging

Cheese is a fermented dairy product that is made from animal milk and is considered to be a healthy food due to its available nutrients and potential probiotic characteristics. Since the microbes in the cheese matrix directly contribute to the quality and physicochemical properties of cheese, it is important to understand the microbial properties of cheese. In this study, Cheddar cheeses produced on three different dates at the Arbuthnot Dairy Center at Oregon State University were collected to determine the microbial community structure. A total of 773,821 sequencing reads and 271 amplicon sequence variants (ASVs) were acquired from 108 samples. Streptococcus and Lactococcus were observed as the most abundant ASVs in the cheese, which were used as the starter lactic acid bacteria (SLAB). Escherichia coli was detected in the raw milk; however, it was not detected after inoculating with SLAB. According to an alpha diversity analysis, SLAB inoculation decreased the microbial richness by inhibiting the growth of other bacteria present in the milk. A beta diversity analysis showed that microbial communities before the addition of SLAB clustered together, as did the samples from cheese making and aging. Non-starter lactic acid bacteria (NSLAB) were detected 15 weeks into aging for the June 6th and June 26th produced cheeses, and 17 weeks into aging for the cheese produced on April 26th. These NSLAB were identified as an unidentified group of Lactobacillaceae. This study characterizes the changes in the Cheddar cheese microbiome over the course of production from raw milk to a 6-month-aged final product. KEY POINTS: • 271 ASVs were acquired from cheese production from raw milk to 6-month aging. • Addition of SLAB changed the microbial diversity during Cheddar cheese making procedure. • NSLAB were detected more than 15 weeks after aging. Graphical Abstract.

Genotypical characterization of thermotolerant coliforms isolated from food produced by a Solidarity Economic Venture of Bahia (Brazil)

Many Solidarity Economic Venture (SEV) are family farmers who seek to add value to production through artisanal processing, which can lead to food contamination. Thus, this study aimed to genotypically characterize thermotolerant coliforms (TtC) strains from food produced by local agribusinesses of SEV during January to April 2019. Samples from thirteen production units (PU) from the SEV were submitted to a microbiological analysis of thermotolerant coliforms (AFNOR 3M1/2 - 09/89), using a fast count method in Petrifilm™ dishes. The Polymerase Chain Reaction (PCR) technique was used to verify the following virulence genes (VGs) associated with Escherichia coli: stx, typical from enterohemorrhagic E. coli (EHEC); bfpA typical from entheropathogenic E. coli (EPEC) and elt and slt, typical from entherotoxigenic E. coli (ETEC). The results showed that two samples of queijadinha (typical Brazilian candy made with eggs and coconut) and one sample of cassava cake presented characteristic colonies TtC. This way, three strains were isolated in order to perform the PCR technique. However, the genes used in the reaction were not detected in the isolated strains. Therefore, it is suggested that the isolated strains are from E. coli pathotypes with different virulence genes than the ones analyzed belong other types of TtC, such as Enterobacter and Klebsiella. Although the virulence of genes has not been confirmed, the presence of TtC on food indicates hygiene flaws during production and, therefore, measurements to control and prevent contamination should be taken.

Traditional Colonial-type cheese from the south of Brazil: A case to support the new Brazilian laws for artisanal cheese production from raw milk

Artisanal Colonial-type cheese is made from raw milk and is the main cheese produced by rural families of the southern region of Brazil. The aim of this study was to investigate, identify problems, and propose solutions for the current situation of small family farms producing and informally selling artisanal Colonial-type cheese located in the western part of Santa Catarina State in Southern Brazil. A semistructured questionnaire was employed in 12 rural properties to analyze the mode of production. Physical-chemical and microbiological analyses of water, raw milk, and cheese were performed, and it was found that 92, 50, and 100% of the samples, respectively, were outside of the current Brazilian regulatory parameters. None of the cheesemakers involved in this study met the requirements, as established by law, for artisanal cheese production from raw milk. This study concluded that technical support and changes in public policy are needed to ensure the preservation of this artisanal cheese, considering the historical importance and cultural traditions of these local communities and the socioeconomic importance of cheesemaking to family farming. Furthermore, more research on the safety of the cheese produced from raw milk is needed as well as the development of specific microbiological standards for artisanal Brazilian cheeses. Public policies aimed at guaranteeing food safety that formalize the commercialization of these cheeses will increase food security in those communities that currently produce artisanal cheese informally.

Finding a common core microbiota in two Brazilian dairies through culture and DNA metabarcoding studies

Dairy foods are complex ecosystems composed of microorganisms from different origins that can affect flavor and safety of final products. The objective of this paper is to assess the in-house microbiota of two Brazilian dairies and to discuss the possible implications of the taxa determined for food protection. In total, 27 samples from dairies were cultured in selective (Baird Parker, de Man, Rogosa and Sharpe) and non-selective (Brain Heart Infusion) media, and the isolates were identified by Sanger sequencing. Moreover, metagenomic DNA was directly extracted from samples and the structure of the bacterial community was determined by massive DNA sequencing followed by bioinformatics analyses. The results showed the majority of isolates belonged to the group of lactic acid bacteria, but Enterobacteriaceae, Staphylococcacceae, Bacillaceae, Pseudomonadaceae and Moraxellaceae were also detected. From the reads obtained in metataxonomics analyses, a heatmap was constructed and the top 20 OTUs (operational taxonomic units) were determined. Besides, 12 most prevalent bacterial taxa were assigned to the core microbiota of the dairies evaluated, which included Thiomonas thermosulfata, Alkalibacillus salilacus, Pseudomonas clemancea, Erythrobacter aquimans, Tetragenococcus doogicus, Macrococcus brunensis, Pseudomonas ludensis, Streptococcus dentinousetti, Serratia entomophila, Vagococcus teuberi, Lactococcus fujiensis and Tolumonas auensis. In conclusion, the results reveal the presence of bacteria that may be related to spoilage and also foodborne diseases, in microbial niches that also present rare taxa, highlighting the importance to consider culture-independent results to evaluate and improve food safety.

Microbiological Characteristics of Gouda Cheese Manufactured with Pasteurized and Raw Milk during Ripening Using Next Generation Sequencing

Gouda cheese, one of most popular cheeses in the Korea, has been produced from only pasteurized milk in Korean dairy farms. Recently, it has become legally possible to produce ripened cheese manufactured with raw milk in Korea. In the present study, we investigated the physico-chemical and microbiological characteristics of Gouda cheese manufactured with raw (R-GC) or pasteurized milk (P-GC) during manufacturing and ripening. Particularly, this study characterized the bacterial community structure of two cheese types, which are produced without pasteurization during ripening based on next generation sequencing of 16S rRNA gene amplicons. During ripening, protein and fat content increased slightly, whereas moisture content decreased in both P-GC and R-GC. At the 6 wk of ripening, R-GC became softer and smoother and hence, the values of hardness and gumminess, chewiness in R-GC was lower than that of P-GC. Metagenomic analysis revealed that the bacterial genera used a starter cultures, namely Lactococcus and Leuconostoc were predominant in both P-GC and R-GC. Moreover, in R-GC, the proportion of coliform bacteria such as Escherichia, Leclercia, Raoultella, and Pseudomonas were detected initially but not during ripening. Taken together, our finding indicates the potential of manufacturing with Gouda cheese from raw milk and the benefits of next generation sequencing for microbial community composition during cheese ripening.

The protective potential of selected lactic acid bacteria against the most common contaminants in various types of cheese in Egypt

Dairy products, especially cheeses have a great nutritional value and a high consumption level around the world. Considering a widespread consumption of cheeses, there is a growing concern regarding safety and microbiological quality. The current study was designed to conduct a recent evaluation of cheeses microbiological quality. Sixty cheese samples from retailing Egyptian markets were analyzed on different selective microbiological media and 64 bacteria, 35 yeasts and 8 molds were isolated. Out of 60 samples; 26.6% were contaminated with Escherichia coli, 73.3% with Staphylococcus scuiri, 3.33% with Bacillus cereus, 1.66% with Salmonella enterica, and 1.66% with Pseudomonas aeruginosa. The presence of such microorganisms in cheeses referred to the wrong management in cheese manufacturing. These organisms are significant from public health view as they have been associated with the base of human food poisoning. Promising antagonistic behavior was observed using the tested lactic acid bacteria (LAB) either single or in combinations toward the undesired isolates. Lactobacillus helveticus CNRZ 32 (Lb. helveticus) was the most potent culture; recording ≥95% reduction in undesired microbial counts.

Gouda cheese spoilage prevention: Biodegradable coating induced by Bunium persicum essential oil and lactoperoxidase system

This study aimed to prepare an inhibitory edible coating for Gouda cheese based on whey protein containing lactoperoxidase system (LPOS) and Bunium persicum essential oil (EO) in order to control postpasteurization contamination. Using a full factorial design, the effects of LPOS and EO on microbiological characteristics and chemical indices of manufactured Gouda cheeses were evaluated during 90 days of storage time. Listeria, lactic acid bacteria, Enterobacter, Escherichia, and Pseudomonas species were considered as potential pathogenic and spoilage indicators of produced Gouda cheese samples. Chemical properties of cheeses were assessed using the free fatty acid, peroxide value, and thiobarbituric acid experiments. The results showed that bacteria counts remained constant in cheese samples coated with EO and also EO-LPOS. However, the survival of gram-positive lactic acid bacteria and Enterobacter spp. was more pronounced in LPOS-based coating. The most effective treatments on oxidation stability parameters in cheese samples were EO- and EO-LPOS coatings. By the addition of B. persicum EO and LPOS, further inhibition of the lipid oxidation of the cheese samples was achieved. Lipolysis, as a result of lipid degradation, was more pronounced in the control, whey-coated, and whey-LPOS-coated samples in comparison with whey-EO- and whey-EO-LPOS-coated samples during the final days of storage time. These results indicate that antibacterial, lipid oxidation, and oxygen barrier properties of the coatings were developed by the addition of B. persicum EO and LPOS.

Presence of Multidrug-Resistant Shiga Toxin-Producing Escherichia coli, Enteropathogenic Escherichia coli, and Enterotoxigenic Escherichia coli on Fresh Cheeses from Local Retail Markets in Mexico

Cheesemaking is one of the most important industries in Mexico. Among all the Mexican cheeses, fresh cheeses are the most popular and most consumed cheese in Mexico and Latin America. However, in Mexico fresh cheese is frequently made with unpasteurized milk and sold in public markets. This may increase the risk for contamination of dairy products with pathogenic bacteria. The presence of multidrug-resistant pathogenic bacteria in food is an important public health concern. Diarrheagenic Escherichia coli pathotypes (DEPs) are foodborne bacteria. This study investigated the presence of indicator bacteria and multidrug-resistant DEPs in fresh cheeses. A total of 120 fresh cheese samples were collected from public markets in the city of Pachuca, Mexico. The samples were analyzed for presence of fecal coliforms (FC), E. coli, and antibiotic resistant DEPs. FC and E. coli were analyzed using the most-probable-number technique. DEPs were identified using two multiplex PCR methods. Susceptibility to 16 antibiotics was tested for the isolated DEPs strains by the standard assay. The frequency of FC, E. coli, and DEPs in the cheese samples was 50, 40, and 19%, respectively. The identified DEPs included Shiga toxin-producing E. coli (STEC; 8%), enteropathogenic E. coli (EPEC; 6%), and enterotoxigenic E. coli (ETEC; 5%). All isolated strains exhibited resistance to at least five antibiotics. One, one, two, and three STEC strains were resistant to 14, 12, 11, and 10 antibiotics, respectively. One strain of EPEC was resistant to 11 antibiotics, three EPEC strains to 9, and one strain to 7. One, one, and two strains of ETEC were resistant to 10, 8, and 7 antibiotics, respectively. The results of the present study indicate that fresh cheeses made with unpasteurized milk could be a risk for consumers, both for native people and visitors to Mexico.

Changes in the genetic requirements for microbial interactions with increasing community complexity

Microbial community structure and function rely on complex interactions whose underlying molecular mechanisms are poorly understood. To investigate these interactions in a simple microbiome, we introduced E. coli into an experimental community based on a cheese rind and identified the differences in E. coli's genetic requirements for growth in interactive and non-interactive contexts using Random Barcode Transposon Sequencing (RB-TnSeq) and RNASeq. Genetic requirements varied among pairwise growth conditions and between pairwise and community conditions. Our analysis points to mechanisms by which growth conditions change as a result of increasing community complexity and suggests that growth within a community relies on a combination of pairwise and higher-order interactions. Our work provides a framework for using the model organism E. coli as a readout to investigate microbial interactions regardless of the genetic tractability of members of the studied ecosystem.

A 100-Year Review: Advances in goat milk research

In the century of research chronicled between 1917 and 2017, dairy goats have gone from simply serving as surrogates to cows to serving as transgenic carriers of human enzymes. Goat milk has been an important part of human nutrition for millennia, in part because of the greater similarity of goat milk to human milk, softer curd formation, higher proportion of small milk fat globules, and different allergenic properties compared with cow milk; however, key nutritional deficiencies limit its suitability for infants. Great attention has been given not only to protein differences between goat and cow milk, but also to fat and enzyme differences, and their effect on the physical and sensory properties of goat milk and milk products. Physiological differences between the species necessitate different techniques for analysis of somatic cell counts, which are naturally higher in goat milk. The high value of goat milk throughout the world has generated a need for a variety of techniques to detect adulteration of goat milk products with cow milk. Advances in all of these areas have been largely documented in the Journal of Dairy Science (JDS), and this review summarizes such advances.

Microbiological criteria and ecology of commercially available processed cheeses according to the product specification and physicochemical characteristics

Although global cheese manufacturers release a variety of products onto the market, research on the microbiological quality and safety of cheese has focused mainly on conventional cheeses made from milk. Here, this study aimed to investigate commercially processed cheese products produced by mixing conventional cheeses after melting. Two approaches were used: a summary and comparison of legal definitions and standards/regulations regarding the microbiological criteria used by major cheese traders in the global market (Australia/New Zealand, China, European Union, Japan, Mexico, Republic of Korea, and the United States) and a comprehensive microbiological analysis of commercial products (n = 800), along with an assessment of salinity, pH, water activity, and heating conditions. The results of the literature search showed that major importing countries (China, Japan, Mexico, and the Republic of Korea) have stricter microbiological criteria for commercially available cheese products than major exporters (Australia/New Zealand, EU, and the USA). The former set limits with respect to the number of total coliforms in the product. Microbiological analyses were designed according to global standards and recommendations. No test sample contained detectable levels of Clostridium perfringens, enterohemorrhagic Escherichia coli, Listeria monocytogenes, Salmonella, or Staphylococcus aureus. In addition, no coliform bacteria (including E. coli) were detected. Overall, 79.9% of the samples contained detectable aerobic plate counts (1.0-7.8 log CFU/g); these levels varied significantly according to product type (grated cheese > chunks; cream cheese > portions or sliced) (p < .05). There was no significant association between microbe levels and salinity, water activity, pH, and heating conditions. The results can be used to develop a comprehensive database about commercially processed cheese products available in the global market and, as such, may be helpful for both national authorities and cheese manufacturers when considering novel strategic management plans for microbiological quality and safety.

Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area - A pilot study

With the advent of high-throughput sequencing technologies, it is possible to comprehensively analyze the microbial community of foods without culturing them in the laboratory. The estimation of all microbes inhabiting a food commodity (food microbiota) therefore may shed light on the microbial quality and safety of foods. In this study, we utilized high-throughput pyrosequencing of 16S rRNA genes as well as traditional microbiological methods to evaluate the bacterial diversity and the predicted metabolic pathways associated with the bacterial communities of selected foods (romaine lettuce, cabbage, deli meat, and chicken legs, total 200 samples) procured from small and large retail outlets located in Memphis-Shelby County, Tennessee, USA. For high-throughput sequencing, microbial genomic DNA was directly extracted from the food products and subjected to genetic sequencing. Aerobic plate count of all food samples was also performed. Foods from small stores (such as corner stores) were found to contain higher bacterial counts as compared to large stores (such as supermarkets). High-throughput pyrosequencing in tandem with bioinformatics analyses revealed a comprehensive picture of the bacterial ecology of foods at different taxonomic levels. Firmicutes and Proteobacteria were the most abundant phyla across all products. At the genus level, Enterobacter and Pantoea in vegetables, and Bacillus and Aeromonas in animal products were found to be the most abundant. The bacterial predicted metabolic pathways such as inosine-5'-phosphate biosynthesis I, methylglyoxal (MG) degradation pathways, urea cycle, dTDP-l-rhamnose biosynthesis I, and mevalonate pathway I differed in foods procured from small stores as compared to large groceries or supermarkets. The results from this study revealed that the bacterial ecology (both in terms of numbers and types of bacteria) of food commodities might differ based on the vending outlet type (large vs. small) of retail stores. The overall estimation bacterial communities in foods by high-throughput sequencing method may be useful to identify potential taxa responsible for food spoilage. Moreover, the data from pyrosequencing of 16S rRNA genes can also be applied to infer major metabolic pathways in bacteria inhabiting different foods. This may reflect the role of these pathways in food-bacteria interaction and adaptation.

The Evolving Role of Coliforms As Indicators of Unhygienic Processing Conditions in Dairy Foods

Testing for coliforms has a long history in the dairy industry and has helped to identify raw milk and dairy products that may have been exposed to unsanitary conditions. Coliform standards are included in a number of regulatory documents (e.g., the U.S. Food and Drug Administration's Grade "A" Pasteurized Milk Ordinance). As a consequence, detection above a threshold of members of this method-defined, but diverse, group of bacteria can result in a wide range of regulatory outcomes. Coliforms are defined as aerobic or facultatively anaerobic, Gram negative, non-sporeforming rods capable of fermenting lactose to produce gas and acid within 48 h at 32-35°C; 19 genera currently include at least some strains that represent coliforms. Most bacterial genera that comprise the coliform group (e.g., Escherichia, Klebsiella, and Serratia) are within the family Enterobacteriaceae, while at least one genus with strains recognized as coliforms, Aeromonas, is in the family Aeromonadaceae. The presence of coliforms has long been thought to indicate fecal contamination, however, recent discoveries regarding this diverse group of bacteria indicates that only a fraction are fecal in origin, while the majority are environmental contaminants. In the US dairy industry in particular, testing for coliforms as indicators of unsanitary conditions and post-processing contamination is widespread. While coliforms are easily and rapidly detected, and are not found in pasteurized dairy products that have not been exposed to post-processing contamination, advances in knowledge of bacterial populations most commonly associated with post-processing contamination in dairy foods has led to questions regarding the utility of coliforms as indicators of unsanitary conditions for dairy products. For example, Pseudomonas spp. frequently contaminate dairy products after pasteurization, yet they are not detected by coliform tests. This review will address the role that coliforms play in raw and finished dairy products, their sources and the future of this diverse group as indicator organisms in dairy products.