Epidemiology, Virulence and Antimicrobial Resistance of Escherichia coli Isolated from Small Brazilian Farms Producers of Raw Milk Fresh Cheese.

This study aimed to identify contamination sources in raw milk and cheese on small farms in Brazil by isolating Escherichia coli at various stages of milk production and cheese manufacturing. The study targeted EAEC, EIEC, ETEC, EPEC, STEC, and ExPEC pathotypes, characterizing isolates for the presence of virulence genes, phylogroups, antimicrobial susceptibility, and phylogenetic relationships using PFGE and MLST. The presence of antimicrobial resistance genes and serogroups was also determined. Three categories of E. coli were identified: pathogenic, commensal, and ceftriaxone-resistant (ESBL) strains. Pathogenic EPEC, STEC, and ExPEC isolates were detected in milk and cheese samples. Most isolates belonged to phylogroups A and B1 and were resistant to antimicrobials such as nalidixic acid, ampicillin, kanamycin, streptomycin, sulfisoxazole, and tetracycline. Genetic analysis revealed that E. coli with identical virulence genes were present at different stages within the same farm. The most frequently identified serogroup was O18, and MLST identified ST131 associated with pathogenic isolates. The study concluded that E. coli was present at multiple points in milk collection and cheese production, with significant phylogroups and high antimicrobial resistance. These findings highlight the public health risk posed by contamination in raw milk and fresh cheese, emphasizing the need to adopt hygienic practices to control these microorganisms.

Optimization of the flow cytometry method of detection, quantification and qualification of microorganisms in carrot juice.

Fresh, unpasteurized carrot juice is a popular element of the everyday diet of many consumers, and as such the matter of the juice's microbial safety remains an important one. Imaging flow cytometry (FCM) allows a fast enumeration and determination of cells, as well as their further differentiation. However, carrot juice is a difficult food product to analyze with the use of FCM due to interference from autofluorescence and the presence of plant debris. In this research, we aimed to obtain an effective and repeatable protocol for the preparation of carrot juice samples for FCM analysis. Through experimental and software-based means we successfully determined a reliable protocol for the preparation of fresh, unpasteurized carrot juice, which consisted of a sequence of filtering, centrifugation, enzyme treatment, and finally the implementation of the Machine Learning protocol for the best result.

Foodborne Microbiological Hazards in Ghana: A Scoping Review.

Background: Foodborne diseases pose a significant public health threat, particularly in regions with poor sanitation and food handling practices. These diseases, mainly caused by microbiological hazards like bacteria, fungi, and parasites, affect millions globally. Despite the global burden, the true extent of these hazards remains underestimated, especially in low- and middle-income countries like Ghana. This study aimed to map the available literature on foodborne microbiological hazards in Ghana, providing an overview of the evidence and identifying areas where further research is needed. Method: This review followed the Preferred Reporting Items for Systematic Reviews and Meta-analysis Extension for Scoping Reviews. A detailed search was done in PubMed, Scopus, Web of Science, and Google Scholar, and articles were exported to Rayyan for screening. A three-phase screening process was used to identify relevant articles. Data from the included articles were extracted and analysed, with specific information related to food type, specific hazards, sample population, and hazard groups summarised using proportions and tables. Results: This review included 72 studies which were published between 2001 and 2023. Eighty-five percent of these studies (85%) reported on bacterial hazards, while 19%, 11%, and 6% reported on fungi, parasites, and mycotoxins, respectively. The most reported bacterial, fungal, and parasitic hazards were Escherichia coli, Aspergillus spp. and Trichuris trichiura, respectively. Aflatoxins were reported in maize, groundnut, and spices, with prevalence ranging from 61% to 100% and at levels exceeding standards set by Ghana Standards Authority and European Food Safety Authority. Conclusion: This review highlighted the spectrum of microbiological hazards in foods in Ghana. The hazards identified pose significant public health risks, particularly among vulnerable populations. It is crucial that stricter enforcement of food safety laws and improved food handling practices are implemented in the country, particularly in the informal food sector, to protect consumers.

Revealing the Mechanism of Aroma Production Driven by High Salt Stress in Trichomonascus ciferrii WLW.

Douchi is a Chinese traditional fermented food with a unique flavor. Methyl anthranilate (MA) plays an important role in formation of this flavor. However, the complicated relationship between the MA formation and the metabolic mechanism of the key functional microorganisms remains unclear. Here, we elucidated the response mechanism of aroma production driven by high salt stress in Trichomonascus ciferrii WLW (T. ciferrii WLW), which originates from the douchi fermentation process. The highest production of MA was obtained in a 10% NaCl environment. The enhanced expression of the key enzyme genes of the pentose phosphate pathway and shikimic acid pathway directed carbon flow toward aromatic amino acid synthesis and helped sustain an increased expression of metK to synthesize a large amount of the methyl donor S-adenosylmethionine, which promoted methyl anthranilate yield. This provides a theoretical basis for in-depth research on the applications of the flavor formation mechanisms of fermented foods.

Evaluation of the probiotic, technological, safety attributes, and GABA-producing capacity of microorganisms isolated from Iranian milk kefir beverages.

Introduction: Kefir beverage has beneficial microorganisms that have health-giving properties; therefore, they have a good potential to be probiotic. This study evaluated the probiotic potential, technological, and safety characteristics of Enterococcus faecalis, Lactococcus lactis, and Pichia fermentans isolated from traditional kefir beverages. Method: First, isolates were evaluated in terms of resistance to acid, alkali, bile salts, trypsin, and pepsin of the gastrointestinal tract. The auto-aggregation and co-aggregation ability of isolates were measured using spectrophotometry. Antimicrobial activities were assayed against important food-borne pathogens using the agar well diffusion method. Moreover, gamma-aminobutyric acid (GABA) production was investigated by thin-layer chromatography (TLC). Result: Among the isolates, P. fermentans had an 85% total survival rate, but its amount reached below 6 log CFU/ml which is considered non-resistant, and it showed the highest auto-aggregation (74.67%). Moreover, only L. lactis showed antimicrobial activity and had the highest co-aggregation with E. coli PTCC 1338 (54.33%) and L. monocytogenes ATCC 7644 (78%). Finally, an evaluation of the technological and safety characteristics of the strains showed that the strains produced GABA and were safe. Discussion: Although the isolates were not resistant to the gastrointestinal tract, their supernatant contained valuable natural compounds, including antioxidants, GABA, and antimicrobials, which can be used to produce functional foods and medicines. In addition, other approaches, such as increasing the initial number of strains, using foods as carriers of isolates, and encapsulating the isolates, can effectively increase the survivability of isolates in the gastrointestinal tract.

Use of Matrix-Assisted and Laser Desorption/Ionization Time-of-Flight Technology in the Identification of Aeromonas Strains Isolated from Retail Sushi and Sashimi.

The genus Aeromonas includes well-known pathogenic species for fishes and humans that are widely distributed in the aquatic environment and foods. Nowadays, one of the main issues related to wild Aeromonas isolates is their identification at the species level, which is challenging using classical microbiological and biomolecular methods. This study aims to test MALDI-TOF MS technology in the identification of Aeromonas strains isolated from n. 60 retail sushi and sashimi boxes using an implemented version of the SARAMIS software V4.12. A total of 43 certified Aeromonas strains were used to implement the SARAMIS database by importing the spectra obtained from their identification. The original SARAMIS version (V4.12) failed to recognize 62.79% of the certified strains, while the herein-implemented version (V4.12plus) allowed the identification of all the certified strains at least to the genus level with a match of no less than 85%. Regarding the sushi and sashimi samples, Aeromonas spp. was detected in n. 18 (30%) boxes. A total of 127 colonies were identified at the species level, with A. salmonicida detected as the most prevalent species, followed by A. bestiarum and A. caviae. Based on the results of the present study, we could speculate that MALDI-TOF technology could be a useful tool both for the food industry to monitor product contamination and for clinical purposes to make diagnoses effectively and quickly.

Salmonella in Wild Boar Meat: Prevalence and Risk Assessment in Central Italy (Umbria and Marche Region).

A survey was conducted from 2018 to 2023 to assess the presence of Salmonella in 280 hunted wild boar (carcasses after evisceration and skinning, N = 226; liver, N = 258; and fecal samples, N = 174). The overall prevalence was 2.86% (confidence interval 95%, 1.45-5.45%) with five positive samples detected in carcasses, three in the liver, and one in a fecal sample. This prevalence was in line with those found in nearby areas denoting a low number of positive samples. Positive animals were over 24 months of age and weighed, before skinning, 59.00 ± 9.11 Kg and no difference was detected in microbial loads between samples positive and negative for Salmonella (aerobic colony count of 4.59 and 4.66 log CFU/400 cm2, and Enterobacteriaceae count of 2.89 and 2.73 log CFU/400 cm2 (mean values) in positive and negative subjects, respectively). Salmonella Stanleyville was the most frequently isolated serotype. A semiquantitative risk assessment was conducted for the first time in game meat considering two products, meat cuts intended for cooking and fermented dry sausages. Only proper cooking can reduce the risk of ingestion of Salmonella to the minimum for consumers, whereas ready-to-eat dry sausages constitute risk products in terms of foodborne Salmonellosis (risk score of 64 out of 100).

Complete genome of Microbacterium plantarum CoE-159-22, isolated from traditionally produced Montenegrin cheese.

Microbacterium plantarum (M. plantarum) was recently described as a new species isolated from copper globemallow (Sphaeralcea angustifolia). Here, we report the complete genome of M. plantarum CoE-159-22, which was obtained from traditionally produced Montenegrin cheese.

Annotated whole-genome sequences of fermentative and spoilage associated Bacilli and proteobacteria autochthonous to commercial cucumber fermentation.

We report 36 whole-genome sequences, along with annotations, of fermentative (n = 12) and spoilage associated (n = 6) lactic acid bacteria, Lysinibacillus (n = 3), Streptococcus (n = 1), and Proteobacteria (n = 14) isolated from commercial cucumber fermentations. Fifty-three percent of the genome sequence assemblies consist of 1-4 contigs, and the remainder have fewer than 16.

Radio frequency inactivation of Salmonella Typhimurium and Listeria monocytogenes in skimmed and whole milk powder.

Milk powder is a convenient, shelf-stable food ingredient used in a variety of food products. However, pathogenic bacteria can be present and survive during prolonged storage, leading to outbreaks of foodborne diseases and product recalls. Radio frequency (RF) heating is a processing technology suitable for bulk treatment of milk powder, aiming at microbial inactivation. This study investigates the RF inactivation of Salmonella Typhimurium and Listeria monocytogenes in two types of milk powder; skimmed and whole milk powder. Specifically, the aims were to (i) examine the influence of the powder's composition on bacterial inactivation, (ii) evaluate the response of bacteria with different Gram properties (Gram positive and Gram negative) and (iii) verify the use of Enterococcus faecium as a surrogate for the two microorganisms for the specific RF process. In order to examine exclusively the influence of RF, a non-isothermal temperature profile was used, employing solely different RF energy levels to heat the product to the target temperatures. A log-linear model with a Bigelow-type temperature dependency was fitted to the experimental data. S. Typhimurium was less susceptible to RF treatments in comparison to L.monocytogenes, demonstrating a higher inactivation rate (k) and higher percentage of sublethal injury. A higher k was also observed for both microorganisms in the whole milk powder, indicating that the increased fat content and decreased levels of lactose and protein in the milk powder had an adverse impact on the microbial survival for both pathogens. The surrogate microorganism E. faecium successfully validated the microbial response of the two microorganisms to RF treatments. In general, a low heating rate RF-only process was successful in inactivating the two foodborne pathogens in skimmed and whole milk powder by 4 log(CFU/g).

Complete genome sequence of Heyndrickxia (Bacillus) coagulans BC99 isolated from a fecal sample of a healthy infant.

This study reports the complete genome sequence of Heyndrickxia (Bacillus) coagulans BC99, a promising human probiotic strain isolated from the fecal sample of a healthy infant in Hailaer Inner Mongolia. The genome sequence of BC99 contains a 3,655,496-bp circular chromosome with a GC content of 46.23%. Genome annotation predicted 3,273 protein-coding genes.

Circular genomes of two bacterial strains capable of growing in a CO2-containing atmosphere.

The bacterial strains Brochothrix thermosphacta DH-B18 and Rathayibacter sp. DH-RSZ4 were isolated from raw sausage and escalope samples and grown in a CO2-rich modified atmosphere. Here, we present both circular genomes obtained by nanopore sequencing.

Pathogenic microorganism monitoring in the food processing of school canteens / 中国学校卫生

Objective@#To analyze the key control points of pathogenic microbial contamination during the food processing of school canteens, so as to provide a basis for effectively preventing the occurrence of campus food safety incidents.@*Methods@#In March 2023, 10 school canteens from Zhengzhou City, Henan Province were selected by convenient sampling method. A total of 300 samples were collected from the storage equipment of raw materials, production tools, staff hands, infrastructure, dining utensils and other facilities in the school canteens during the food processing process.The rapid detection method of foodborne pathogens based on isothermal multiple selfmatchinginitiated amplification (IMSA) technology was used to analyze the possible risk of pathogenic microorganism contamination. Fisher exact probability method was applied for the statistical analysis.@*Results@#Among the 300 samples collected, pathogenic microorganisms including Staphylococcus aureus, Salmonella and Listeria monocytogenes were detected in 5 samples, distributed in the food preparation utensils such as cutting boards, operating tables, knives and staff hands, while no pathogenic microorganisms were detected in dining utensils, raw material storage equipment and canteen infrastructure.There was no statistically significant difference between the IMSA rapid detection method and the national standard method for testing Staphylococcus aureus, Salmonella and Listeria monocytogenes(P>0.05). Compared to international method, the positive coincidence of pathogenic microorganism detected by IMSA rapid inspection system was 83.3%(5/6), the negative coincidence was 100%(n=294), and the overall consistency rate was 99.7%.@*Conclusions@#The key control points of pathogenic microbial contamination in the food processing process of school canteens mainly are the utensils in the food production process, such as cutting boards, operating tables, knives and staff hands in the food processing process of the school canteen, which could be accurately identified by the rapid detection method of pathogenic microorganism established based on IMSA technology. The quality and efficiency campus food safety supervision should be promoted to prevent the food safety events in school canteen.

Traditional marketed meats as a reservoir of multidrug-resistant Escherichia coli.

This study aimed to analyze Escherichia coli from marketed meat samples in Peru. Sixty-six E. coli isolates were recovered from 21 meat samples (14 chicken, 7 beef), and antimicrobial resistance levels and the presence of mechanisms of antibiotic resistance, as well as clonal relationships and phylogeny of colistin-resistant isolates, were established. High levels of antimicrobial resistance were detected, with 93.9% of isolates being multi-drug resistant (MDR) and 76.2% of samples possessing colistin-resistant E. coli; of these, 6 samples from 6 chicken samples presenting mcr-1-producer E. coli. Colistin-resistant isolates were classified into 22 clonal groups, while phylogroup A (15 isolates) was the most common. Extended-spectrum ß-lactamase- and pAmpC-producing E. coli were found in 18 and 8 samples respectively, with blaCTX-M-55 (28 isolates; 16 samples) and blaCIT (8 isolates; 7 samples) being the most common of each type. Additionally, blaCTX-M-15, blaCTX-M-65, blaSHV-27, blaOXA-5/10-like, blaDHA, blaEBC and narrow-spectrum blaTEM were detected. In addition, 5 blaCTX-M remained unidentified, and no sought ESBL-encoding gene was detected in other 6 ESBL-producer isolates. The tetA, tetE and tetX genes were found in tigecycline-resistant isolates. This study highlights the presence of MDR E. coli in Peruvian food-chain. The high relevance of CTX-M-55, the dissemination through the food-chain of pAmpC, as well as the high frequency of unrelated colistin-resistant isolates is reported.

Computational analysis of carboxylesterase genes and proteins in non-pathogenic food bacterium Alicyclobacillus acidocaldarius: insights from proteogenomics.

Over recent years, Alicyclobacillus acidocaldarius, a Gram-positive nonpathogenic rod-shaped thermo-acid-tolerant bacterium, has posed numerous challenges for the fruit juice industry. However, the bacterium's unique characteristics, particularly its nonpathogenic and thermophilic capabilities, offer significant opportunities for genetic exploration by biotechnologists. This study presents the computational proteogenomics report on the carboxylesterase (CE) enzyme in A. acidocaldarius, shedding light on structural and evolutional of CEs from this bacterium. Our analysis revealed that the average molecular weight of CEs in A. acidocaldarius was 41 kDa, with an isoelectric point around 5. The amino acid composition favored negative amino acids over positive ones. The aliphatic index and hydropathicity were approximately 88 and - 0.15, respectively. While the protein sequence showed no disulfide bonds in the CEs' structure, the presence of Cys amino acids was observed in the structure of CEs. Phylogenetic analysis presented more than 99% similarity between CEs, indicating their close evolutionary relationship. By applying homology modeling, the 3-dimensional structural models of the carboxylesterase were constructed, which with the help of structural conservation and solvent accessibility analysis highlighted key residues and regions responsible for enzyme stability and conformation. The specific patterns presented the total solvent accessibility of less than 25 (Å2) was in considerable position as well as Gly residues were noticeably have high accessibility to solvent in all structures. Ala was the more frequent amino acids in the conserved-SASA of carboxylesterases. Furthermore, unsupervised agglomerative hierarchical clustering based on solvent accessibility feature successfully clustered and even distinguished this enzyme from proteases from the same genome. These findings contribute to a deeper understanding of the nonpathogenic A. acidocaldarius carboxylesterase and its potential applications in biotechnology. Additionally, structural analysis of CEs would help to address potential solutions in fruit juice industry with utilization of computational structural biology.

Microbiological contamination present in enteral tube feeding prepared in hospitals and/or at home: a systematic review.

CONTEXT: The safety of enteral formulas is important to restore and maintain the health of patients. OBJECTIVE: A systematic review of the literature was conducted to assess the microbiological contamination present in enteral tube feeding prepared in hospitals and/or at home. DATA SOURCES: A systematic search was conducted of the Medline, Scopus, BVS, CAPES/MEC, Embase, Science Direct, and SciELO databases and gray literature. DATA EXTRACTION: Eligible studies that analyzed the contamination of enteral formulas manipulated in hospitals and/or at home were selected; a quality assessment tool was used. DATA ANALYSIS: Twenty-three studies evaluated 1099 enteral formulations. Of these, 44.67% of enteral formulas (n = 491) exceeded the acceptable bacterial count. Samples of homemade enteral formulation preparations (86.03%; n = 191) had the highest bacterial counts, followed by mixed preparations (79.72%; n = 59), and commercial formulas (30.01%; n = 241). The number of samples of enteral formulations that exceeded the bacterial count at home was 70.79% (n = 160 at the hospital was 37.91% (n = 331). Total coliforms (82.68%; n = 406) and mesophilic aerobes (79.22%; n = 389) were the most common microorganisms. Samples with bacterial pathogens were also identified, with Bacillus cereus (4.07%; n = 20) and Listeria monocytogenes (3.66%; n = 18) being the most prevalent. CONCLUSIONS: A high number of samples of enteral formulations exceeded the bacterial count, but the risk to patient's health when consuming enteral tube feeding prepared in hospitals or at home may be low. This is because the bacteria present in the samples are not considered potential causes of disease but rather indicators of hygiene conditions. SYSTEMATIC REVIEW REGISTRATION: PROSPERO registration no. CRD42022367573.

Analysis of the Effect of Various Potential Antimicrobial Agents on the Quality of the Unpasteurized Carrot Juice.

Short shelf-life and poor microbial quality of minimally processed foods of plant origin pose a serious problem for the food industry. Novel techniques of minimal treatment combined with disinfection are being researched, and, for fresh juice, the addition of antimicrobial agents appears to be a promising route. In this research, fresh, nonfiltered, unpasteurized carrot juice was mixed with four potential antimicrobials (bourbon vanilla extract, peppermint extract, cannabidiol oil, and grapefruit extract). All four variants and the reference pure carrot juice were analyzed for metapopulational changes, microbial changes, and physicochemical changes. The potential antimicrobials used in the research have improved the overall microbial quality of carrot juice across 4 days of storage. However, it is important to notice that each of the four agents had a different spectrum of effectiveness towards the groups identified in the microflora of carrot juice. Additionally, the antimicrobials have increased the diversity of the carrot juice microbiome but did not prevent the occurrence of pathogenic bacteria. In conclusion, the use of antimicrobial agents such as essential oils or their derivatives may be a promising way of improving the microbial quality and prolonging the shelf-life of minimally processed foods, such as fresh juices, but the technique requires further research.

Microbiological Assessment of White Button Mushrooms with an Edible Film Coating.

The development of edible coatings incorporating bioextracts from mushrooms native to Portuguese forests aims to enhance the value of the endogenous forest and mycological resources by harnessing their potential as a source of antimicrobial and antioxidant compounds. Edible coatings represent an important pathway to decreasing food waste and contributing to implementing a circular bioeconomy. The coating should result in product valorization through improved preservation/conservation, increased shelf life, as well as enhancement of its antioxidant and enzymatic properties. To evaluate the effectiveness of an edible coating on fungal food matrices, a 14-day shelf-life study was conducted, wherein both coated and untreated mushrooms were examined under controlled storage temperatures of 4 °C and 9.3 °C. Agaricus bisporus was chosen as the food matrix for its bioeconomy significance, and Pleurotus eryngii was selected for the preparation of the food-based coating due to its profile of bioactive compounds. Microbiological analysis and physicochemical monitoring were conducted on the food matrices and the coating. Coated mushrooms had less mass loss and color change, and had better texture after 14 days. Microbiological analysis revealed that the coating had no antimicrobial activity. Overall, the coating improved the shelf life of the coated mushrooms but had less effect on the microbial community.

Salmonella detection with LAMP and qPCR and identification of serovars of interest by multiplex qPCR in poultry carcasses.

Salmonella is present in the poultry production chain and is a major challenge in terms of food safety and animal health. The early Salmonella detection is one of the main tools to control and prevent the transmission of this pathogen. Microbiological isolation and serotyping to identify and differentiate Salmonella serovars are laborious processes, time-consuming, and expensive. Therefore, molecular diagnostic methods can be rapid and efficient alternatives to the detection of this pathogen. Thus, the aim herein was to standardize and evaluate the use of loop-mediated isothermal amplification (LAMP) in comparison with real-time PCR (qPCR) for detection of Salmonella associated with a multiplex qPCR for simultaneous identification and differentiation of S. Enteritidis, S. Typhimurium, S. Pullorum, and S. Gallinarum. The LAMP, qPCR, and multiplex qPCR assays were comparable in specificity. The three techniques were evaluated for specificity for 16 different serovars of Salmonella and for 37 strains of the serovars of interest. The limit of detection and the efficiency of the LAMP, qPCR, and multiplex qPCR reactions were determined. The techniques were applied to 33 samples of chicken carcasses and compared to the results of conventional microbiology for validation. As results, LAMP was specific in the detection of different Salmonella serovars but presented lower limit of detection ranging from 101 to 104 CFU/reaction. In comparison, qPCR could detect less cells (100 to 102 CFU/reaction), reaching equal specificity and better repeatability in the assays. The qPCR multiplexing for identification of the different serovars also showed good specificity, with the detection threshold between entre 101 and 102 CFU/reaction. The results obtained in the analyses on poultry carcasses suggested a correspondence between the results obtained in molecular methods and in conventional microbiology. Thus, the proposed assays are promising for the diagnosis of Salmonella in poultry carcasses, already proved to be faster and more efficient than conventional diagnostics techniques, being of great interest for poultry production, animal, and public health.