1
|
Marin M, Rizzotto F, Léguillier V, Péchoux C, Borezee-Durant E, Vidic J. Naked-eye detection of Staphylococcus aureus in powdered milk and infant formula using gold nanoparticles. J Microbiol Methods 2022; 201:106578. [PMID: 36108985 DOI: 10.1016/j.mimet.2022.106578] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 12/27/2022]
Abstract
Nonspecific binding of proteins from complex food matrices is a significant challenge associated with a biosensor using gold nanoparticles (AuNPs). To overcome this, we developed an efficient EDTA chelating treatment to denature milk proteins and prevent their adsorption on AuNPs. The use of EDTA to solubilize proteins enabled a sensitive label-free apta-sensor platform for colorimetric detection of Staphylococcus aureus in milk and infant formula. In the assay, S. aureus depleted aptamers from the test solution, and the reduction of aptamers enabled aggregation of AuNPs upon salt addition, a process characterized by a color change from red to purple. Under optimized conditions, S. aureus could be visually detected within 30 min with the detection limit of 7.5 × 104 CFU/mL and 8.4 × 104 CFU/mL in milk and infant formula, respectively. The EDTA treatment provides new opportunities for monitoring milk contamination and may prove valuable for biosensor point-of-need applications.
Collapse
Affiliation(s)
- Marco Marin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Francesco Rizzotto
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Vincent Léguillier
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | | | - Elise Borezee-Durant
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Jasmina Vidic
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| |
Collapse
|
2
|
Jahansepas A, Aghazadeh M, Rezaee MA, Heidarzadeh S, Mardaneh J, Mohammadzadeh A, Pouresmaeil O. Prevalence, Antibiotic Resistance and Virulence of Enterococcus spp. Isolated from Traditional Cheese Types. Ethiop J Health Sci 2022; 32:799-808. [PMID: 35950059 PMCID: PMC9341016 DOI: 10.4314/ejhs.v32i4.17] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Indexed: 11/17/2022] Open
Abstract
Background Enterococci are naturally found in the gastrointestinal (GI) tract of animals and humans, as well as animal-derived foods and vegetables. We here aimed to determine the prevalence, antibiotic resistance, and virulence determinants of E. faecium and E. faecalis in traditional cheese in the North-west of Iran. Materials and Methods Fifty specimens of popular traditional cheese from dairy stores of Urmia and Tabriz, Iran, were collected. Identification of the genus and species of enterococci was done using molecular and phenotypic techniques. Results Forty-eight (96 %) of 50 traditional cheese samples were harboring Enterococcus spp, including Enterococcus faecalis (n= 40; 83.33 %) and E. faecium (n= 8; 16.67 %). The prevalence of enterococci ranged from 1.1×105 to 9.7×104 CFU/g, and 1.1×103 to 9.8×103 CFU/g in Urmia and Tabriz samples, respectively. Rifampicin resistance (n= 38; 79.2 %) was the most common pattern observed in the susceptibility test, which was followed by quinupristin/dalfopristin (n= 33; 68.75 %). Among E. faecalis isolates, cpd (100 %), ace (92.5 %) and gelE (87.5 %), and among E. faecium isolates, gelE (100 %) and asa1 (75 %) were found to have the most common virulence genes. Conclusion E. faecalis was the predominant species, displaying more virulence determinants. It also had high antibiotic resistance, as compared to E. faecium. The enterococci identified here commonly expressed virulence and antibiotic resistance determinants. So, it is required to improve the maintenance and production quality of traditional cheese to avoid enterococci contamination.
Collapse
Affiliation(s)
- Ali Jahansepas
- Reference Laboratory, Imam Khomeini Hospital, Urmia University of Medical Sciences, Urmia, Iran
| | - Mohammad Aghazadeh
- Infectious and Tropical Diseases Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Clinical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Ahangarzadeh Rezaee
- Infectious and Tropical Diseases Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Clinical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Siamak Heidarzadeh
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Jalal Mardaneh
- Department of Microbiology, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Alireza Mohammadzadeh
- Department of Microbiology, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Omid Pouresmaeil
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
3
|
Michaux C, Hansen EE, Jenniches L, Gerovac M, Barquist L, Vogel J. Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium. Front Cell Infect Microbiol 2020; 10:600325. [PMID: 33324581 PMCID: PMC7724050 DOI: 10.3389/fcimb.2020.600325] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 10/19/2020] [Indexed: 12/19/2022] Open
Abstract
Enterococcus faecalis and faecium are two major representative clinical strains of the Enterococcus genus and are sadly notorious to be part of the top agents responsible for nosocomial infections. Despite their critical implication in worldwide public healthcare, essential and available resources such as deep transcriptome annotations remain poor, which also limits our understanding of post-transcriptional control small regulatory RNA (sRNA) functions in these bacteria. Here, using the dRNA-seq technique in combination with ANNOgesic analysis, we successfully mapped and annotated transcription start sites (TSS) of both E. faecalis V583 and E. faecium AUS0004 at single nucleotide resolution. Analyzing bacteria in late exponential phase, we capture ~40% (E. faecalis) and 43% (E. faecium) of the annotated protein-coding genes, determine 5′ and 3′ UTR (untranslated region) length, and detect instances of leaderless mRNAs. The transcriptome maps revealed sRNA candidates in both bacteria, some found in previous studies and new ones. Expression of candidate sRNAs is being confirmed under biologically relevant environmental conditions. This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. It can be accessed online at www.helmholtz-hiri.de/en/datasets/enterococcus through an instance of the genomic viewer JBrowse.
Collapse
Affiliation(s)
- Charlotte Michaux
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Elisabeth E Hansen
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Laura Jenniches
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Milan Gerovac
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| |
Collapse
|
4
|
Crucello A, Furtado MM, Chaves MDR, Sant'Ana AS. Transcriptome sequencing reveals genes and adaptation pathways in Salmonella Typhimurium inoculated in four low water activity foods. Food Microbiol 2019; 82:426-435. [PMID: 31027802 DOI: 10.1016/j.fm.2019.03.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/09/2019] [Accepted: 03/14/2019] [Indexed: 11/25/2022]
Abstract
Salmonella enterica serotypes have been reported as the agent of various outbreaks occurred after the consumption of low water activity (aw) foods. When the pathogen encounters harsh conditions, several regulatory networks are activated through dynamic differential gene expression that lead to cell survival for prolonged periods. In this work, the transcriptome of S. enterica serovar Typhimurium using RNA-Seq, after cells' inoculation in four distinct types of low aw foods (milk chocolate, powdered milk, black pepper, and dried pet food), following storage at 25 °C per 24 and 72 h was studied. The findings of this study suggest that gene regulation is influenced by the food composition mainly in the first 24 h post-inoculum, proceeded by the induction of similar genes shared among all samples. It was possible to evaluate the differences on each type of food matrix regarding the bacteria adaptation, as well as the similarities provoked by low aw. The results reveal genes that may play key roles in response to desiccation in Salmonella, as well as the pathways in which they are involved.
Collapse
Affiliation(s)
- Aline Crucello
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Marianna M Furtado
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Monyca D R Chaves
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Anderson S Sant'Ana
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil.
| |
Collapse
|
5
|
Altuntop Yayla ME, Ekinci Doğan C, Sarioğlan Ş. Purification and analysis of DNA from low DNA content food samples. J Verbrauch Lebensm 2018. [DOI: 10.1007/s00003-018-1192-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
6
|
Hevia A, Delgado S, Margolles A, Sánchez B. Application of density gradient for the isolation of the fecal microbial stool component and the potential use thereof. Sci Rep 2015; 5:16807. [PMID: 26581409 PMCID: PMC4652190 DOI: 10.1038/srep16807] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 10/20/2015] [Indexed: 12/15/2022] Open
Abstract
The idea of considering the gut microbiota as a virtual human organ has led to the concept of fecal microbiota transplantation (FMT), which has recently been extremely successful in the treatment of cases of recurrent Clostridium difficile infection. Administration of safe, viable, and representative fecal microbiota is crucial for FMT. To our knowledge, suitable techniques and systematic conditions for separating the fecal microbiota from stool samples have not been thoroughly investigated. In this work we show the potential to separate stool microorganisms from the rest of fecal material using a procedure with a Nycodenz® density gradient, yielding 1010 viable bacteria per two grams of feces. This procedure did not affect the original microbiota composition in terms of viability, distribution and proportions, as assessed by a phylogenetic metagenomic approach. Obtaining the fecal microbiota by concentration and separation of the microorganisms from the rest of the stool components would allow the standardization of its recovery and its long-term preservation. FMT or similar microbiota restoration therapies could be used for the treatment of several disorders, or even for aesthetic purposes, so the method described in our work may contribute to the setting of the basis for the development of safe and standardized products.
Collapse
Affiliation(s)
- Arancha Hevia
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Susana Delgado
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| |
Collapse
|
7
|
Tang S, Orsi RH, den Bakker HC, Wiedmann M, Boor KJ, Bergholz TM. Transcriptomic Analysis of the Adaptation of Listeria monocytogenes to Growth on Vacuum-Packed Cold Smoked Salmon. Appl Environ Microbiol 2015; 81:6812-24. [PMID: 26209664 PMCID: PMC4561693 DOI: 10.1128/aem.01752-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/16/2015] [Indexed: 01/26/2023] Open
Abstract
The foodborne pathogen Listeria monocytogenes is able to survive and grow in ready-to-eat foods, in which it is likely to experience a number of environmental stresses due to refrigerated storage and the physicochemical properties of the food. Little is known about the specific molecular mechanisms underlying survival and growth of L. monocytogenes under different complex conditions on/in specific food matrices. Transcriptome sequencing (RNA-seq) was used to understand the transcriptional landscape of L. monocytogenes strain H7858 grown on cold smoked salmon (CSS; water phase salt, 4.65%; pH 6.1) relative to that in modified brain heart infusion broth (MBHIB; water phase salt, 4.65%; pH 6.1) at 7°C. Significant differential transcription of 149 genes was observed (false-discovery rate [FDR], <0.05; fold change, ≥2.5), and 88 and 61 genes were up- and downregulated, respectively, in H7858 grown on CSS relative to the genes in H7858 grown in MBHIB. In spite of these differences in transcriptomes under these two conditions, growth parameters for L. monocytogenes were not significantly different between CSS and MBHIB, indicating that the transcriptomic differences reflect how L. monocytogenes is able to facilitate growth under these different conditions. Differential expression analysis and Gene Ontology enrichment analysis indicated that genes encoding proteins involved in cobalamin biosynthesis as well as ethanolamine and 1,2-propanediol utilization have significantly higher transcript levels in H7858 grown on CSS than in that grown in MBHIB. Our data identify specific transcriptional profiles of L. monocytogenes growing on vacuum-packaged CSS, which may provide targets for the development of novel and improved strategies to control L. monocytogenes growth on this ready-to-eat food.
Collapse
Affiliation(s)
- Silin Tang
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Renato H Orsi
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Henk C den Bakker
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Kathryn J Boor
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Teresa M Bergholz
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| |
Collapse
|
8
|
Innocenti N, Golumbeanu M, Fouquier d'Hérouël A, Lacoux C, Bonnin RA, Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E. Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis. RNA (NEW YORK, N.Y.) 2015; 21:1018-30. [PMID: 25737579 PMCID: PMC4408782 DOI: 10.1261/rna.048470.114] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/22/2014] [Indexed: 05/21/2023]
Abstract
Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5' RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search retrieved canonical features of SigA- and SigN-dependent promoters preceding transcription start sites mapped. We discovered 85 novel putative regulatory RNAs, small- and antisense RNAs, and 72 transcriptional antisense organizations. Presented data constitute a significant insight into bacterial RNA landscapes and a step toward the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.
Collapse
Affiliation(s)
- Nicolas Innocenti
- Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Monica Golumbeanu
- Department of Biosystems Science and Engineering, ETH Zürich, CH-4058, Basel, Switzerland SIB Swiss Institute of Bioinformatics, University of Basel, CH-4056, Basel, Switzerland
| | - Aymeric Fouquier d'Hérouël
- Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Caroline Lacoux
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Rémy A Bonnin
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS, UMR8621, F-91405, Orsay, France
| | - Sean P Kennedy
- INRA, MetaGenoPolis US1367, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Françoise Wessner
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Pascale Serror
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Philippe Bouloc
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS, UMR8621, F-91405, Orsay, France
| | - Francis Repoila
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Erik Aurell
- Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden Department of Information and Computer Science, Aalto University, FI-02150 Espoo, Finland
| |
Collapse
|
9
|
Rodríguez A, Werning ML, Rodríguez M, Bermúdez E, Córdoba JJ. Quantitative real-time PCR method with internal amplification control to quantify cyclopiazonic acid producing molds in foods. Food Microbiol 2012; 32:397-405. [DOI: 10.1016/j.fm.2012.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 07/26/2012] [Accepted: 08/05/2012] [Indexed: 11/25/2022]
|
10
|
Jamet E, Akary E, Poisson MA, Chamba JF, Bertrand X, Serror P. Prevalence and characterization of antibiotic resistant Enterococcus faecalis in French cheeses. Food Microbiol 2012; 31:191-8. [DOI: 10.1016/j.fm.2012.03.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 02/17/2012] [Accepted: 03/19/2012] [Indexed: 11/28/2022]
|
11
|
Marcobal A, De las Rivas B, Landete JM, Tabera L, Muñoz R. Tyramine and phenylethylamine biosynthesis by food bacteria. Crit Rev Food Sci Nutr 2012; 52:448-67. [PMID: 22369263 DOI: 10.1080/10408398.2010.500545] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Tyramine poisoning is caused by the ingestion of food containing high levels of tyramine, a biogenic amine. Any foods containing free tyrosine are subject to tyramine formation if poor sanitation and low quality foods are used or if the food is subject to temperature abuse or extended storage time. Tyramine is generated by decarboxylation of the tyrosine through tyrosine decarboxylase (TDC) enzymes derived from the bacteria present in the food. Bacterial TDC have been only unequivocally identified and characterized in Gram-positive bacteria, especially in lactic acid bacteria. Pyridoxal phosphate (PLP)-dependent TDC encoding genes (tyrDC) appeared flanked by a similar genetic organization in several species of lactic acid bacteria, suggesting a common origin by a single mobile genetic element. Bacterial TDC are also able to decarboxylate phenylalanine to produce phenylethylamine (PEA), another biogenic amine. The molecular knowledge of the genes involved in tyramine production has led to the development of molecular methods for the detection of bacteria able to produce tyramine and PEA. These rapid and simple methods could be used for the analysis of the ability to form tyramine by bacteria in order to evaluate the potential risk of tyramine biosynthesis in food products.
Collapse
Affiliation(s)
- Angela Marcobal
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición, ICTAN-CSIC, Madrid, Spain
| | | | | | | | | |
Collapse
|
12
|
A comparative study of DNA extraction methods to be used in real-time PCR based quantification of ochratoxin A-producing molds in food products. Food Control 2012. [DOI: 10.1016/j.foodcont.2011.12.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
13
|
Transcriptome sequencing of Salmonella enterica serovar Enteritidis under desiccation and starvation stress in peanut oil. Food Microbiol 2011; 30:311-5. [PMID: 22265317 DOI: 10.1016/j.fm.2011.11.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 10/07/2011] [Accepted: 11/02/2011] [Indexed: 11/21/2022]
Abstract
It is well recognized that Salmonella can survive long-term starvation and desiccation stresses and contaminate foods that have intermediate to low water activities; however, little is known about the specific molecular mechanisms underlying its survival and persistence in low water activity foods. In this study, we used the RNA-seq approach to compare the transcriptomes (27-33 million 36-bp reads per sample) of a Salmonella enterica subsp. enteric serovar Enteritidis strain ATCC BAA-1045 after inoculation in peanut oil (water activity 0.30) for 72 h, 216 h and 528 h to those grown in Luria-Bertani (LB) broth for 12 h and 312 h. Our results showed that desiccated Salmonella cells in peanut oil were in a physiologically dormant state with <5% of its genome being transcribed compared to 78% in LB broth. Among the few detected transcripts in peanut oil, genes involved in heat and cold shock response, DNA protection and regulatory functions likely play roles in cross protecting Salmonella from desiccation and starvation stresses. In addition, non-coding RNAs may also play roles in Salmonella desiccation stress response. This is the first report of using RNA-seq technology in characterizing bacterial transcriptomes in a food matrix.
Collapse
|
14
|
Rodríguez A, Córdoba JJ, Werning ML, Andrade MJ, Rodríguez M. Duplex real-time PCR method with internal amplification control for quantification of verrucosidin producing molds in dry-ripened foods. Int J Food Microbiol 2011; 153:85-91. [PMID: 22119450 DOI: 10.1016/j.ijfoodmicro.2011.10.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/06/2011] [Accepted: 10/25/2011] [Indexed: 11/28/2022]
Abstract
Verrucosidin, which is a tremorgenic mycotoxin responsible for neurological diseases, has been detected in different dry-ripened foods as consequence of the growth of toxigenic molds. To improve food safety, the presence of verrucosidin producing molds in these kind foods should be quantified. The aim of this study was to design a duplex real-time PCR (qPCR) protocol based on TaqMan methodology with an internal amplification control (IAC). Eleven verrucosidin producing and 11 non producing strains belonging to different species often reported in food products were used. Verrucosidin production was tested by micellar electrokinetic capillary electrophoresis (MECE) and high-pressure liquid chromatography-mass spectrometry (HPLC-MS). A primer pair (VerF1/VerR1) and a TaqMan probe (Verprobe) were designed from the SVr1 probe sequence of a verrucosidin producing Penicillium polonicum. The conserved regions of the β-tubulin gene were used to design primers (TubF1/TubR1) and probe (Tubprobe) of the non-competitive IAC. The functionality of the developed method was demonstrated by the high linear relationship of the standard curves which relating Ct values and DNA template of the tested verrucosidin producers using the verrucosidin and IAC primers. The ability to quantify verrucosidin producers of the developed TaqMan assay in all artificially inoculated food samples was successful, with a minimum detection limit of 1 log cfu per gram of food. This qPCR protocol including an IAC could be very useful to quantify verrucosidin producing molds in dry-ripened foods avoiding false negative results. This method should be proposed to monitor the target molds in HACCP programs to prevent the risk of verrucosidin formation and consequently avoid its presence in the food chain.
Collapse
Affiliation(s)
- Alicia Rodríguez
- Food Hygiene and Safety, Faculty of Veterinary Science, University of Extremadura, Avda. de Universidad, s/n. 10003-Cáceres, Spain
| | | | | | | | | |
Collapse
|
15
|
Method enabling gene expression studies of pathogens in a complex food matrix. Appl Environ Microbiol 2011; 77:8456-8. [PMID: 21984236 DOI: 10.1128/aem.05471-11] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe a simple method for stabilizing and extracting high-quality prokaryotic RNA from meat. Heat and salt stress of Escherichia coli and Salmonella spp. in minced meat reproducibly induced dnaK and otsB expression, respectively, as observed by quantitative reverse transcription-PCR (>5-fold relative changes). Thus, the method is applicable in studies of bacterial gene expression in a meat matrix.
Collapse
|
16
|
Ndoye B, Rasolofo EA, LaPointe G, Roy D. A review of the molecular approaches to investigate the diversity and activity of cheese microbiota. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s13594-011-0031-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
17
|
Yvon M, Gitton C, Chambellon E, Bergot G, Monnet V. The initial efficiency of the proteolytic system of Lactococcus lactis strains determines their responses to a cheese environment. Int Dairy J 2011. [DOI: 10.1016/j.idairyj.2010.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
18
|
Fouquier d'Hérouel A, Wessner F, Halpern D, Ly-Vu J, Kennedy SP, Serror P, Aurell E, Repoila F. A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis. Nucleic Acids Res 2011; 39:e46. [PMID: 21266481 PMCID: PMC3074167 DOI: 10.1093/nar/gkr012] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enterococcus faecalis is a commensal bacterium and a major opportunistic human pathogen. In this study, we combined in silico predictions with a novel 5′RACE-derivative method coined ‘5′tagRACE’, to perform the first search for non-coding RNAs (ncRNAs) encoded on the E. faecalis chromosome. We used the 5′tagRACE to simultaneously probe and characterize primary transcripts, and demonstrate here the simplicity, the reliability and the sensitivity of the method. The 5′tagRACE is complementary to tiling arrays or RNA-sequencing methods, and is also directly applicable to deep RNA sequencing and should significantly improve functional studies of bacterial RNA landscapes. From 45 selected loci of the E. faecalis chromosome, we discovered and mapped 29 novel ncRNAs, 10 putative novel mRNAs and 16 antisense transcriptional organizations. We describe in more detail the oxygen-dependent expression of one ncRNA located in an E. faecalis pathogenicity island, the existence of an ncRNA that is antisense to the ncRNA modulator of the RNA polymerase, SsrS and provide evidences for the functional interplay between two distinct toxin–antitoxin modules.
Collapse
|
19
|
Fratamico PM, Wang S, Yan X, Zhang W, Li Y. Differential Gene Expression of E. coli O157:H7 in Ground Beef Extract Compared to Tryptic Soy Broth. J Food Sci 2011; 76:M79-87. [DOI: 10.1111/j.1750-3841.2010.01952.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
20
|
Tool for quantification of staphylococcal enterotoxin gene expression in cheese. Appl Environ Microbiol 2010; 76:1367-74. [PMID: 20061456 DOI: 10.1128/aem.01736-09] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cheese is a complex and dynamic microbial ecosystem characterized by the presence of a large variety of bacteria, yeasts, and molds. Some microorganisms, including species of lactobacilli or lactococci, are known to contribute to the organoleptic quality of cheeses, whereas the presence of other microorganisms may lead to spoilage or constitute a health risk. Staphylococcus aureus is recognized worldwide as an important food-borne pathogen, owing to the production of enterotoxins in food matrices. In order to study enterotoxin gene expression during cheese manufacture, we developed an efficient procedure to recover total RNA from cheese and applied a robust strategy to study gene expression by reverse transcription-quantitative PCR (RT-qPCR). This method yielded pure preparations of undegraded RNA suitable for RT-qPCR. To normalize RT-qPCR data, expression of 10 potential reference genes was investigated during S. aureus growth in milk and in cheese. The three most stably expressed reference genes during cheese manufacture were ftsZ, pta, and gyrB, and these were used as internal controls for RT-qPCR of the genes sea and sed, encoding staphylococcal enterotoxins A and D, respectively. Expression of these staphylococcal enterotoxin genes was monitored during the first 72 h of the cheese-making process, and mRNA data were correlated with enterotoxin production.
Collapse
|
21
|
Affiliation(s)
- Roland J Siezen
- Kluyver Centre for Genomics of Industrial Fermentation, TI Food and Nutrition, Wageningen, The Netherlands.
| | | |
Collapse
|