Food Microbial Pathogen Detection and Analysis Using DNA Microarray Technologies

Culture-based methods used for microbial detection and identification are simple to use, relatively inexpensive, and sensitive. However, culture-based methods are too time-consuming for high-throughput testing and too tedious for analysis of samples with multiple organisms and provide little clinical information regarding the pathogen (e.g., antibiotic resistance genes, virulence factors, or strain subtype). DNA-based methods, such as polymerase chain reaction (PCR), overcome some these limitations since they are generally faster and can provide more information than culture-based methods. One limitation of traditional PCR-based methods is that they are normally limited to the analysis of a single pathogen, a small group of related pathogens, or a small number of relevant genes. Microarray technology enables a significant expansion of the capability of DNA-based methods in terms of the number of DNA sequences that can be analyzed simultaneously, enabling molecular identification and characterization of multiple pathogens and many genes in a single array assay. Microarray analysis of microbial pathogens has potential uses in research, food safety, medical, agricultural, regulatory, public health, and industrial settings. In this article, we describe the main technical elements of microarray technology and the application and potential use of DNA microarrays for food microbial analysis

Evolutionary and functional patterns of shared gene neighbourhood in fungi

Gene clusters comprise genomically co-localized and potentially co-regulated genes that tend to be conserved across species. In eukaryotes, multiple examples of metabolic gene clusters are known, particularly among fungi and plants. However, little is known about how gene clustering patterns vary among taxa or with respect to functional roles. Furthermore, mechanisms of the formation, maintenance and evolution of gene clusters remain unknown. We surveyed 341 fungal genomes to discover gene clusters shared by different species, independently of their functions. We inferred 12,120 cluster families, which comprised roughly one third of the gene space and were enriched in genes associated with diverse cellular functions. Additionally, most clusters did not encode transcription factors, suggesting that they are regulated distally. We used phylogenomics to characterize the evolutionary history of these clusters. We found that most clusters originated once and were transmitted vertically, coupled to differential loss. However, convergent evolution-that is, independent appearance of the same cluster-was more prevalent than anticipated. Finally, horizontal gene transfer of entire clusters was somewhat restricted, with the exception of those associated with secondary metabolism. Altogether, our results provide insights on the evolution of gene clustering as well as a broad catalogue of evolutionarily conserved gene clusters whose function remains to be elucidated.The T.G. group acknowledges support from the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) for the EMBL partnership, and grants ‘Centro de Excelencia Severo Ochoa 2013-2017’ SEV-2012-0208 and BFU2015-67107 cofounded by European Regional Development Fund (ERDF); from the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857, and a grant from the European Union’s Horizon 2020 research and innovation programme under grant agreement ERC-2016-724173 the Marie Sklodowska-Curie grant agreement H2020-MSCA-ITN-2014-64209

The prevalence and molecular typing of Clostridium perfringens in ground beef and sheep meats

This study was aimed at the investigation of the prevalence of Clostridium perfringens in ground beef and sheep meats and to detect the cpa, cpb, etx, iA, cpe and cpb2 toxin genes by multiplex PCR. Obtained from retail markets and butchers, 100 ground meat samples, 50 of which were beef and 50 of which were sheep meat samples, were examined. Out of the 50 ground beef samples 48 (96 %) and out of the 50 ground sheep meat samples 44 (88 %) were contaminated with C. perfringens. According to microscopic examination and the results of biochemical tests, 262 positive isolates obtained from these samples were identified as C. perfringens. Multiplex PCR results demonstrated that, out of the 262 isolates, 203 (77.4 %) possessed only the cpa gene (type A), while 20 (7.6 %) carried the cpa and cpb2 toxin genes (type A-cpb2), and 6 (2.2 %) the cpa and cpe toxin genes (type A-cpe). Furthermore, it was determined that, out of the 262 C. perfringens isolates, 4 (1.5 %), 10 (3.8 %) and 19 (7.2 %) were of the types B, C and D, respectively.Dicle University [DUBAP/10-VF-83]The present study was supported by the Dicle University Research Fund (DUBAP/10-VF-83). We thank Senay Ercelik and Zulkuf Emre Papatya for their excellent laboratory assistance