High-Throughput 16S rRNA Sequencing to Assess Potentially Active Bacteria and Foodborne Pathogens: A Case Example in Ready-to-Eat Food
| Autor: | Manuel Martinez-Garcia, Lucia Maestre-Carballa, Mónica Lluesma-Gomez, Marina Mira Miralles |
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| Přispěvatelé: | Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Ecología Microbiana Molecular |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Salmonella
Health (social science) Foodborne Plant Science Vegetable Yersinia Active bacteria Microbiología lcsh:Chemical technology medicine.disease_cause Health Professions (miscellaneous) Microbiology Article 03 medical and health sciences active bacteria medicine vegetable lcsh:TP1-1185 Ready-to-eat salads bacteria Escherichia coli foodborne 030304 developmental biology 0303 health sciences Bacteria biology Pathogen 030306 microbiology Pseudomonas Lettuce biology.organism_classification 16S ribosomal RNA lettuce Aeromonas Next-generation sequencing Listeria ready-to-eat salads next-generation sequencing 16S rRNA gene Food Science pathogen |
| Zdroj: | Foods Volume 8 Issue 10 Foods, Vol 8, Iss 10, p 480 (2019) RUA. Repositorio Institucional de la Universidad de Alicante Universidad de Alicante (UA) |
| ISSN: | 2304-8158 |
| DOI: | 10.3390/foods8100480 |
| Popis: | Technologies to detect the entire bacterial diversity spectra and foodborne pathogens in food represent a fundamental advantage in the control of foodborne illness. Here, we applied high-throughput 16S rRNA sequencing of amplicons obtained by PCR and RT-PCR from extracted DNA and RNA targeting the entire bacterial community and the active bacterial fraction present in some of the most consumed and distributed ready-to-eat (RTE) salad brands in Europe. Customer demands for RTE food are increasing worldwide along with the number of associated foodborne illness and outbreaks. The total aerobic bacterial count in the analyzed samples was in the range of 2&ndash 4 × 106 CFU/g (SD ± 1.54 × 106). Culture validated methods did not detect Salmonella spp., Escherichia coli, and other fecal coliforms. 16S rRNA gene Illumina next-generation sequencing (NGS) data were congruent with these culture-based results and confirmed that these and other well-known foodborne bacterial pathogens, such as Listeria, were not detected. However, the fine-resolution of the NGS method unveiled the presence of the opportunistic pathogens Aeromonas hydrophyla and Rahnella aquatilis (relative frequency of 1.33&ndash 7.33%) that were metabolically active in addition to non-pathogenic, active members of Yersinia spp. (relative frequency of 0.0015&ndash 0.003%). The common ail and foxA marker genes of Yersinia enterocolitica were not detected by qPCR. Finally, our NGS data identified to non-pathogenic Pseudomonas spp. as the most abundant and metabolically active bacteria in the analyzed RTE salads (53&ndash 75% of bacterial abundance). Our data demonstrate the power of sequencing, in parallel, both 16S rRNA and rDNA to identify and discriminate those potentially and metabolically active bacteria and pathogens to provide a more complete view that facilitates the control of foodborne diseases, although further work should be conducted to determine the sensitivity of this method for targeting bacteria |
| Databáze: | OpenAIRE |
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