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The recent advances in molecular biology, such as the advent of next-generation sequencing (NGS) platforms, have paved the way to new exciting tools which rapidly transform food microbiology. Nowadays, NGS methods such as 16S rDNA/rRNA metagenomics or amplicon sequencing are used for the taxonomic profiling of the food microbial communities. Although 16S rDNA/rRNA NGS-based microbial data are not suited for the investigation of the functional potential of the identified operational taxonomic units as compared to shotgun metagenomics, advances in the bioinformatics discipline allow now the performance of such studies. In this paper, a bioinformatics workflow is described integrating predictive metagenomics profiling with specific application to food microbiology data. Bioinformatics tools pertinent to each sub-module of the pipeline are suggested as well. The published 16S rDNA/rRNA amplicon data originated from an Italian Grana-type cheese, using an NGS platform, was employed to demonstrate the predictive metagenomics profiling approach. The pipeline identified the microbial community and the changes that occurred in the microbial profile during manufacture of the food product studied (taxonomic profiling). The workflow also indicated significant changes in the functional profiling of the community. The tool may help to investigate the functional potential, alterations, and interactions of a microbial community. The proposed workflow may also find an application in the investigation of the ecology of foodborne pathogens encountered in various food products. [ABSTRACT FROM AUTHOR]

The aim of this study was to assess serotype prevalence and biodiversity of Listeria monocytogenes strains isolated from diverse food products, i.e., minced pork, fruits, and vegetables. Three hundred twenty-six samples previously purchased from supermarkets and street markets within the Athens area were studied for L. monocytogenes prevalence. A total of 121 strains were isolated from the 36 samples that were positive for L. monocytogenes. Serotyping was performed with multiplex PCR, and biodiversity was assessed with random amplified polymorphic DNA (RAPD) PCR analysis using M13, UBC155, and HLWL85 as primers and with repetitive element palindromic (rep) PCR analysis using (GTG)5 as the primer. The majority (17 of 22) of the contaminated minced pork samples contained strains identified as serotype 1/2a, either alone or in combination with strains belonging to serotypes 1/2b, 4a, 4c, or 4ab. However, all L. monocytogenes isolates from fruits and vegetables belonged to serotype 4b. Rep-PCR provided better differentiation of the isolates than did RAPD PCR and resulted in discrimination of the isolates into a larger number of unique profiles. Complete differentiation was achieved only with the combination of these subtyping techniques. [ABSTRACT FROM AUTHOR]

The aim of this study was to assess the microbiological quality and the ability of Listeria monocytogenes and Salmonella enterica serovar Typhimurium strains to survive during storage at 4 °C of all available brand names of brined pickles and some in-bulk ones, in the district of Athens. None of the samples could be characterized as heavily contaminated. The microbial populations detected could be due to inadequacy of packaging, regarding the ones available in-bulk and improper thermal treatment in the case of the canned ones. Moreover, the ability of both pathogens to survive for 5 days at 4 °C, in some products, has been exhibited. [ABSTRACT FROM AUTHOR]

Listeria monocytogenes poses a serious threat to public health, and the majority of cases of human listeriosis are associated with contaminated food. Reliable microbiological testing is needed for effective control of this pathogen by the food industry and competent authorities. The aim of this study was to determine the performance of three culture media commonly used for detecting L. monocytogenes in foods. Minced pork meat samples (n = 100) were subjected to microbiological testing for L. monocytogene according to Intemational Organization for Standardization methods 11290-1:1996 and 11290-2:1998 using PALCAM, ALOA, and RAPID'L.mono culture media in parallel. Presence of the pathogen was confirmed by conducting biochemical and molecular tests on the presumptive L. monocytogenes colonies. Performance attributes of sensitivity, specificity, positive and negative predictive values, positive and negative likelihood ratios, diagnostic odds ratios, error odds ratios, receiving operating characteristic (ROC) curve, and area under this curve were calculated from the presence-absence microbiological test results by combining the results obtained from the culture media and confirmative tests. PALCAM had the best performance in terms of positive predictive value (i.e., a positive result indicates high probability of L. monocytogenes presence) but not in terms of sensitivity (i.e., the ability of the medium to detect the pathogen when present). RAPID'L.mono was the most sensitive medium. None of the culture media were perfect for detecting L. monocytogenes in minced pork meat alone. The pathogen was detected in 16, 19, and 26% (apparent prevalence) of the samples by PALCAM, ALOA, and RAPID'L.mono, respectively, although the true prevalence of the pathogen was 22%. These findings indicate that the use of a single culture medium may lead to erroneous determination of the prevalence of L. monocytogenes. [ABSTRACT FROM AUTHOR]

Abstract: The objective of this study was to estimate the test accuracy measures (classification probabilities [CPs], predictive values [PVs], likelihood ratios [LRs] and area under receiving operating characteristic curve [AUC]) of three different culture-dependent methods, commonly used during routine analysis for the detection of the foodborne pathogen Listeria monocytogenes, from a Bayesian perspective. Data from a previous study by Andritsos et al. (2010) were used to define measures of accuracy for the diagnostic tests. Samples of minced pork meat obtained from local markets were tested for L. monocytogenes presence by parallel testing using selective media (PALCAM, ALOA and RAPID''L.mono). Dirichlet distribution, which is the multivariate expression of a Beta distribution, was used to analyze the data. Bayesian analysis determines characteristics of the posterior distribution from available prior information. Results showed that all methods were best at ruling in L. monocytogenes presence than ruling it out. PALCAM seemed to have better performance based on positive PV, positive LR and AUC, but it was not so sensitive as RAPID''L.mono was. Results also showed that none of the media were perfect in detecting L. monocytogenes, i.e. sensitivity and specificity equal to one. Besides, the problem of observing zero counts may be overcome by applying Bayesian analysis, making the determination of a test performance feasible. [Copyright &y& Elsevier]

In recent years and with the significant advancements in instrumentation for molecular biology methods, the focus of food microbiologists, dealing with pathogenic microorganisms in foods, is shifting. Scientists specifically aim at elucidating the effect that the food composition, as well as the commonly employed preservation/storage techniques throughout the food chain, have on the virulence of pathogens. Quantitative PCR and microarrays are, nowadays, powerful tools used for such determinations. The application of these approaches for the determination of the gene expression in situ, is a new field of research for food microbiologists and provides new information regarding virulence potential of foodborne pathogens. [ABSTRACT FROM AUTHOR]

The aim of the present study was to assess the expression of key virulence genes, during growth of a Listeria monocytogenes isolate in liquid medium, on melon and rocket at different temperatures and time. For that purpose, BHI broth, rocket and melon were inoculated at 7.0–7.5 log CFU mL −1 or g −1 and stored at 4, 10 and 30 °C. Sampling took place upon inoculation and after 0.5, 6 and 24 h of incubation. The RNA was stabilized and the expression of hly , plcA , plcB , sigB , inlA , inlB , inlC , inlJ , lmo2672 and lmo2470 was assessed by RT-qPCR. The results obtained were summarized into two observations; the first one referring to the interactive effect of incubation temperature and type of substrate and the second one to the effect of time on gene expression. Regarding the latter, nearly all genes were regulated upon inoculation and exhibited differential expression in the subsequent sampling times indicating the existence of additional regulatory mechanisms yet to be explored. [ABSTRACT FROM AUTHOR]