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).

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.

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.

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.

Shiga toxin-producing Escherichia coli (STEC) and atypical enteropathogenic E. coli (aEPEC) in Swedish retail wheat flour.

Wheat flour has been identified as the source of multiple outbreaks of gastrointestinal disease caused by shiga toxin-producing Escherichia coli (STEC). We have investigated the presence and genomic characteristics of STEC and related atypical enteropathogenic E. coli (aEPEC) in 200 bags of Swedish-produced retail wheat flour, representing 87 products and 25 brands. Samples were enriched in modified tryptone soya broth (mTSB) and screened with real-time PCR targeting stx1, stx2 and eae, and the serogroups O157, O121 and O26. Isolation was performed by immunomagnetic separation (IMS) for suspected STEC/aEPEC O157, O121 and O26, and by screening pools of colonies for other STEC. Real-time PCR after enrichment revealed 12 % of samples to be positive for shiga toxin genes (stx1 and/or stx2) and 11 % to be positive for intimin (eae). Organic production, small-scale production or whole grain did not significantly influence shiga toxin gene presence or absence in a generalized linear mixed model analysis. Eight isolates of STEC were recovered, all of which were intimin-negative. Multiple serotype/sequence type/shiga toxin subtype combinations that have also been found in flour samples in other European countries were recovered. Most STEC types recovered were associated with sporadic cases of STEC among humans in Sweden, but no types known to have caused outbreaks or severe cases of disease (i.e. haemolytic uraemic syndrome) were found. The most common finding was O187:H28 ST200 with stx2g, with possible links to cervid hosts. Wildlife associated with crop damage is a plausible explanation for at least some of the surprisingly high frequency of STEC in wheat flour.

Control microbiológico de alimentos en la vía pública en Cuenca, Ecuador

El comercio ambulante de alimentos listos para el consumo ha crecido exponencialmente a nivel mundial. Sin embargo, la falta de condiciones óptimas de preparación y expendio de estos alimentos pueden afectar su inocuidad. El objetivo de este estudio fue evaluar la calidad microbiológica de 19 tipos de alimentos (n= 417), con y sin tratamiento térmico, expendidos en espacios públicos en Cuenca, Ecuador. Según el grupo de alimentos, se analizaron aerobios mesófilos, coliformes/Escherichia coli, mohos y levaduras, Staphylococcus aureus, Salmonella, Listeria spp., Clostridium perfringes y Vibrio parahaemolyticus. Para la identificación y recuento de los microorganismos se aplicaron normativas nacionales y, en casos de ausencia, se adoptaron normas de otros países. Como resultado, el 55,4% de las muestras se consideraron no aptas para el consumo. S. aureus fue el microorganismo patógeno presuntivo de mayor prevalencia (81,7%). El incumplimiento de las normativas fue significativamente mayor entre los alimentos sin tratamiento térmico (54,1%) en comparación con aquellos térmicamente tratados (24%) y los que combinan ingredientes con y sin tratamiento (21,9%) (p<0,001). Se destaca el alto porcentaje de incumplimiento de alimentos sin tratamiento térmico que son manipulados en su preparación, como los jugos. Además, se observó que el tratamiento térmico no garantizó la inocuidad, sugiriendo una posible recontaminación del alimento luego de su preparación hasta su expendio y consumo, por medios ambientales y/o adición de otros ingredientes contaminados. Este estudio recalca la necesidad de acciones concretas con este sector, basados principalmente en capacitación, infraestructura e inclusión, para garantizar la salud de los consumidores.

Street-vending trade in ready-to-eat foods has grown exponentially, worldwide. However, the lack of optimal conditions for the preparation and sale of these foods can affect their safety. The objective of this study was to evaluate the microbiological quality of 19 types of foods (n= 417), with and without heat treatment, sold in public spaces in Cuenca, Ecuador. According to the food group, mesophilic aerobes, coliforms/Escherichia coli, molds and yeasts, Staphylococcus aureus, Salmonella, Listeria spp., Clostridium perfringens, and Vibrio parahaemolyticus were examined. For microorganisms identification and counting, national regulations were applied and, in cases of absence, regulations from other countries were adopted. As a result, 55,4% of the samples were considered inadequate for consumption. S. aureus was the most prevalent presumptive pathogenic microorganism (81.7%). Non-compliance with regulations was significantly higher among foods without heat treatment (54.1%) compared to those heat treated (24%) and those that combine ingredients with and without treatment (21.9%) (p<0.001). The high percentage of non-compliance with foods without heat treatment that is handled for preparation, such as juices, stands out. In addition, it was observed that the heat treatment did not guarantee safety, suggesting possible food recontamination after preparation until sale and consumption, due to environmental means and/or the addition of other contaminated ingredients. This study emphasizes the need for concrete actions in this sector, mainly based on training, infrastructure, and inclusion, to guarantee consumers' health.

Data-Driven Prediction of Molecular Biotransformations in Food Fermentation.

Fermentation products, together with food components, determine the sense, nutrition, and safety of fermented foods. Traditional methods of fermentation product identification are time-consuming and cumbersome, which cannot meet the increasing need for the identification of the extensive bioactive metabolites produced during food fermentation. Hence, we propose a data-driven integrated platform (FFExplorer, http://www.rxnfinder.org/ffexplorer/) based on machine learning and data on 2,192,862 microbial sequence-encoded enzymes for computational prediction of fermentation products. Using FFExplorer, we explained the mechanism behind the disappearance of spicy taste during pepper fermentation and evaluated the detoxification effects of microbial fermentation for common food contaminants. FFExplorer will provide a valuable reference for inferring bioactive "dark matter" in fermented foods and exploring the application potential of microorganisms.

Phenolic Compounds in Bacterial Inactivation: A Perspective from Brazil.

Phenolic compounds are natural substances that are produced through the secondary metabolism of plants, fungi, and bacteria, in addition to being produced by chemical synthesis. These compounds have anti-inflammatory, antioxidant, and antimicrobial properties, among others. In this way, Brazil represents one of the most promising countries regarding phenolic compounds since it has a heterogeneous flora, with the presence of six distinct biomes (Cerrado, Amazon, Atlantic Forest, Caatinga, Pantanal, and Pampa). Recently, several studies have pointed to an era of antimicrobial resistance due to the unrestricted and large-scale use of antibiotics, which led to the emergence of some survival mechanisms of bacteria to these compounds. Therefore, the use of natural substances with antimicrobial action can help combat these resistant pathogens and represent a natural alternative that may be useful in animal nutrition for direct application in food and can be used in human nutrition to promote health. Therefore, this study aimed to (i) evaluate the phenolic compounds with antimicrobial properties isolated from plants present in Brazil, (ii) discuss the compounds across different classes (flavonoids, xanthones, coumarins, phenolic acids, and others), and (iii) address the structure-activity relationship of phenolic compounds that lead to antimicrobial action.

Longitudinal Study of Lactococcus Phages in a Canadian Cheese Factory.

The presence of virulent phages is closely monitored during cheese manufacturing, as these bacterial viruses can significantly slow down the milk fermentation process and lead to low-quality cheeses. From 2001 to 2020, whey samples from cheddar cheese production in a Canadian factory were monitored for the presence of virulent phages capable of infecting proprietary strains of Lactococcus cremoris and Lactococcus lactis used in starter cultures. Phages were successfully isolated from 932 whey samples using standard plaque assays and several industrial Lactococcus strains as hosts. A multiplex PCR assay assigned 97% of these phage isolates to the Skunavirus genus, 2% to the P335 group, and 1% to the Ceduovirus genus. DNA restriction profiles and a multilocus sequence typing (MLST) scheme distinguished at least 241 unique lactococcal phages from these isolates. While most phages were isolated only once, 93 of them (out of 241, 39%) were isolated multiple times. Phage GL7 was isolated 132 times from 2006 to 2020, demonstrating that phages can persist in a cheese factory for long periods of time. Phylogenetic analysis of MLST sequences showed that phages could be clustered based on their bacterial hosts rather than their year of isolation. Host range analysis showed that Skunavirus phages exhibited a very narrow host range, whereas some Ceduovirus and P335 phages had a broader host range. Overall, the host range information was useful in improving the starter culture rotation by identifying phage-unrelated strains and helped mitigating the risk of fermentation failure due to virulent phages. IMPORTANCE Although lactococcal phages have been observed in cheese production settings for almost a century, few longitudinal studies have been performed. This 20-year study describes the close monitoring of dairy lactococcal phages in a cheddar cheese factory. Routine monitoring was conducted by factory staff, and when whey samples were found to inhibit industrial starter cultures under laboratory conditions, they were sent to an academic research laboratory for phage isolation and characterization. This led to a collection of at least 241 unique lactococcal phages, which were characterized through PCR typing and MLST profiling. Phages of the Skunavirus genus were by far the most dominant. Most phages lysed a small subset of the Lactococcus strains. These findings guided the industrial partner in adapting the starter culture schedule by using phage-unrelated strains in starter cultures and removing some strains from the starter rotation. This phage control strategy could be adapted for other large-scale bacterial fermentation processes.

Prevalence and Antibiotic Resistance Phenotypes of Pseudomonas spp. in Fresh Fish Fillets.

In fresh fish products, excessive loads of Pseudomonas can lead to their rapid spoilage. It is wise for Food Business Operators (FBOs) to consider its presence both in whole and prepared fish products. With the current study, we aimed to quantify Pseudomonas spp. in fresh fillets of Salmo salar, Gadus morhua and Pleuronectes platessa. For all three fish species, we detected loads of presumptive Pseudomonas no lower than 104-105 cfu/g in more than 50% of the samples. We isolated 55 strains of presumptive Pseudomonas and carried out their biochemical identification; 67.27% of the isolates were actually Pseudomonas. These data confirm that fresh fish fillets are normally contaminated with Pseudomonas spp. and the FBOs should add it as a "process hygiene criterion" according to EC Regulation n.2073/2005. Furthermore, in food hygiene, it is worth evaluating the prevalence of antimicrobial resistance. A total of 37 Pseudomonas strains were tested against 15 antimicrobials, and they all were identified as being resistant to at least one antimicrobial, mainly penicillin G, ampicillin, amoxicillin, tetracycline, erythromycin, vancomycin, clindamycin and trimethoprim. As many as 76.47% of Pseudomonas fluorescens isolates were multi-drug resistant. Our results confirm that Pseudomonas is becoming increasingly resistant to antimicrobials and thus should be continuously monitored in foods.