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Dinu LD, Al-Zaidi QJ, Matache AG, Matei F. Improving the Efficiency of Viability-qPCR with Lactic Acid Enhancer for the Selective Detection of Live Pathogens in Foods. Foods 2024; 13:1021. [PMID: 38611327 PMCID: PMC11012224 DOI: 10.3390/foods13071021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Pathogenic Escherichia coli are the most prevalent foodborne bacteria, and their accurate detection in food samples is critical for ensuring food safety. Therefore, a quick technique named viability-qPCR (v-qPCR), which is based on the ability of a selective dye, such as propidium monoazide (PMA), to differentiate between alive and dead cells, has been developed. Despite diverse, successful applications, v-qPCR is impaired by some practical limitations, including the ability of PMA to penetrate the outer membrane of dead Gram-negative bacteria. The objective of this study is to evaluate the ability of lactic acid (LA) to improve PMA penetration and, thus, the efficiency of v-qPCR in detecting the live fraction of pathogens. The pre-treatment of E. coli ATCC 8739 cells with 10 mM LA greatly increased PMA penetration into dead cells compared to conventional PMA-qPCR assay, avoiding false positive results. The limit of detection when using LA-PMA qPCR is 1% viable cells in a mixture of dead and alive cells. The optimized LA-PMA qPCR method was reliably able to detect log 2 CFU/mL culturable E. coli in milk spiked with viable and non-viable bacteria. Lactic acid is cheap, has low toxicity, and can be used to improve the efficiency of the v-qPCR assay, which is economically interesting for larger-scale pathogen detection applications intended for food matrices.
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Affiliation(s)
- Laura-Dorina Dinu
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine, 011464 Bucharest, Romania; (Q.J.A.-Z.); (A.G.M.); (F.M.)
| | - Quthama Jasim Al-Zaidi
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine, 011464 Bucharest, Romania; (Q.J.A.-Z.); (A.G.M.); (F.M.)
| | - Adelina Georgiana Matache
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine, 011464 Bucharest, Romania; (Q.J.A.-Z.); (A.G.M.); (F.M.)
| | - Florentina Matei
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine, 011464 Bucharest, Romania; (Q.J.A.-Z.); (A.G.M.); (F.M.)
- Faculty of Food Industry and Tourism, Transilvania University of Brasov, 500015 Brasov, Romania
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2
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Dorick J, Kumar GD, Macarisin D, Andrew Widmer J, Stivers T, Dunn LL. Longitudinal Survey of Aeromonas hydrophila and Foodborne Pathogens in a Commercial Aquaponics System. J Food Prot 2024; 87:100230. [PMID: 38278488 DOI: 10.1016/j.jfp.2024.100230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024]
Abstract
Aquaponic production of fresh produce is a sustainable agricultural method becoming widely adopted, though few studies have investigated potential food safety hazards within commercial systems. A longitudinal study was conducted to isolate and quantify several foodborne pathogens from a commercial, aquaponic farm, and to elucidate their distribution throughout. The survey was conducted over 2 years on a controlled-environment farm containing Nile tilapia (Oreochromis niloticus) and lettuce (Lactuca sativa). Samples (N = 1,047) were collected bimonthly from three identical, independent systems, and included lettuce leaves, roots, fingerlings (7-126 d old), feces from mature fish (>126 d old), water, and sponge swabs collected from the tank interior surface. Most probable number of generic Escherichia coli were determined using IDEXX Colilert Quanti-Tray. Enumeration and enrichment were used to detect Shiga toxin-producing E. coli (STEC), Salmonella enterica, Listeria monocytogenes, Aeromonas spp., Aeromonas hydrophilia, and Pseudomonas aeruginosa. Generic E. coli, STEC, L. monocytogenes, and S. enterica were not detected in collected samples. P. aeruginosa was isolated from water (7/351; 1.99%), swabs (3/351; 0.85%), feces (2/108; 1.85%), and lettuce leaves (2/99; 2.02%). A. hydrophila was isolated from all sample types (623/1047; 59.50%). The incidence of A. hydrophila in water (X2 = 23.234, p < 0.001) and sponge samples (X2 = 21.352, p < 0.001) increased over time.
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Affiliation(s)
- Jennifer Dorick
- Department of Food Science and Technology, University of Georgia, Athens, GA 30602, USA
| | | | - Dumitru Macarisin
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA
| | - J Andrew Widmer
- Department of Food Science and Technology, University of Georgia, Athens, GA 30602, USA
| | - Tori Stivers
- Marine Extension and Georgia Sea Grant, University of Georgia, Peachtree City, GA 30269, USA
| | - Laurel L Dunn
- Department of Food Science and Technology, University of Georgia, Athens, GA 30602, USA.
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3
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Dinu LD, Gatea F, Roaming Israel F, Lakicevic M, Dedović N, Vamanu E. The Modulation Effect of a Fermented Bee Pollen Postbiotic on Cardiovascular Microbiota and Therapeutic Perspectives. Biomedicines 2023; 11:2712. [PMID: 37893086 PMCID: PMC10604238 DOI: 10.3390/biomedicines11102712] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Hypertension is a frequent comorbidity in patients with heart failure; therefore, blood pressure management for these patients is widely recommended in medical guidelines. Bee pollen and postbiotics that contain inactivated probiotic cells and their metabolites have emerged as promising bioactive compounds sources, and their potential role in mitigating cardiovascular (CV) risks is currently being unveiled. Therefore, this preliminary study aimed to investigate the impact of a lactic-fermented bee pollen postbiotic (FBPP) on the CV microbiota via in vitro tests. A new isolated Lactobacillus spp. strain from the digestive tract of bees was used to ferment pollen, obtaining liquid and dried atomized caps postbiotics. The modulating effects on a CV microbiota that corresponds to the pathophysiology of hypertension were investigated using microbiological methods and qPCR and correlated with the metabolic profile. Both liquid and dried FBPPs increased the number of the beneficial Lactobacillus spp. and Bifidobacterium spp. bacteria by up to 2 log/mL, while the opportunistic pathogen E. coli, which contributes to CV pathogenesis, decreased by 3 log/mL. The short-chain fatty acid (SCFA) profile revealed a significant increase in lactic (6.386 ± 0.106 g/L) and acetic (4.284 ± 0.017 g/L) acids, both with known antihypertensive effects, and the presence of isovaleric acid, which promotes a healthy gut microbiota. Understanding the impact of the FBPP on gut microbiota could lead to innovative strategies for promoting heart health and preventing cardiovascular diseases.
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Affiliation(s)
- Laura-Dorina Dinu
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine, 011464 Bucharest, Romania;
| | - Florentina Gatea
- Centre of Bioanalysis, National Institute for Biological Sciences, 060031 Bucharest, Romania;
| | - Florentina Roaming Israel
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine, 011464 Bucharest, Romania;
| | - Milena Lakicevic
- Faculty of Agriculture, University of Novi Sad, 21000 Novi Sad, Serbia; (M.L.); (N.D.)
| | - Nebojša Dedović
- Faculty of Agriculture, University of Novi Sad, 21000 Novi Sad, Serbia; (M.L.); (N.D.)
| | - Emanuel Vamanu
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine, 011464 Bucharest, Romania;
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4
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Gand M, Bloemen B, Vanneste K, Roosens NHC, De Keersmaecker SCJ. Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria. BMC Genomics 2023; 24:438. [PMID: 37537550 PMCID: PMC10401787 DOI: 10.1186/s12864-023-09537-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Oxford Nanopore Technologies (ONT) offers an accessible platform for long-read sequencing, which improves the reconstruction of genomes and helps to resolve complex genomic contexts, especially in the case of metagenome analysis. To take the best advantage of long-read sequencing, DNA extraction methods must be able to isolate pure high molecular weight (HMW) DNA from complex metagenomics samples, without introducing any bias. New methods released on the market, and protocols developed at the research level, were specifically designed for this application and need to be assessed. RESULTS In this study, with different bacterial cocktail mixes, analyzed as pure or spiked in a synthetic fecal matrix, we evaluated the performances of 6 DNA extraction methods using various cells lysis and purification techniques, from quick and easy, to more time-consuming and gentle protocols, including a portable method for on-site application. In addition to the comparison of the quality, quantity and purity of the extracted DNA, the performance obtained when doing Nanopore sequencing on a MinION flow cell was also tested. From the obtained results, the Quick-DNA HMW MagBead Kit (Zymo Research) was selected as producing the best yield of pure HMW DNA. Furthermore, this kit allowed an accurate detection, by Nanopore sequencing, of almost all the bacterial species present in a complex mock community. CONCLUSION Amongst the 6 tested methods, the Quick-DNA HMW MagBead Kit (Zymo Research) was considered as the most suitable for Nanopore sequencing and would be recommended for bacterial metagenomics studies using this technology.
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Affiliation(s)
- Mathieu Gand
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium
| | - Bram Bloemen
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium
| | - Sigrid C J De Keersmaecker
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium.
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5
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Pakbin B, Brück WM, Brück TB, Allahyari S, Ashrafi Tamai I. A quantitative prevalence of Escherichia coliO157 in different food samples using real-time qPCR method. Food Sci Nutr 2022; 11:228-235. [PMID: 36655112 PMCID: PMC9834875 DOI: 10.1002/fsn3.3055] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/09/2022] [Accepted: 08/25/2022] [Indexed: 01/21/2023] Open
Abstract
Escherichia coli serogroup O157 is the main causative agent of several intestinal and extra-intestinal foodborne diseases in humans through consumption of low-dose contaminated foods such as milk, beef, and vegetables. To date, studies regarding the quantitative prevalence of E. coli O157 in foods are so limited. Therefore, this study aimed to evaluate the quantitative prevalence rate of E. coli serogroup O157 in raw milk (n = 144), vegetable salad (n = 174), and minced beef samples (n = 108) using the real-time qPCR SYBR green melting curve method targeting the rfbA gene. First, we evaluated the method and found a sensitive and specific qPCR assay with 1 log of CFU/ml detection limit to detect E. coli O157 (Tm = 80.3 ± 0.1°C). About 2.77%, 10.18%, and 9.19% of raw milk, minced beef, and vegetable salad samples, respectively, were contaminated with E. coli O157. Minced beef and vegetable salad samples were significantly more contaminated than raw milk samples. Population average of E. coli O157 in raw milk, minced beef, and vegetable salad samples were 2.22 ± 0.57, 3.30 ± 0.40, and 1.65 ± 0.44 log CFU/ml or gr, respectively. Significantly higher levels of population of E. coli O157 were observed in minced beef samples. Minced beef can be regarded as the main food in the transmission of this foodborne pathogen. Routine quantitative rapid monitoring is strongly suggested to be carried out to prevent foodborne diseases caused by E. coli O157.
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Affiliation(s)
- Babak Pakbin
- Institute for Life TechnologiesUniversity of Applied Sciences Western Switzerland Valais‐WallisSion 2Switzerland,Department of Chemistry, Werner Siemens Chair of Synthetic BiotechnologyTechnical University of Munich (TUM)MünchenGermany,Medical Microbiology Research CenterQazvin University of Medical SciencesQazvinIran
| | - Wolfram Manuel Brück
- Institute for Life TechnologiesUniversity of Applied Sciences Western Switzerland Valais‐WallisSion 2Switzerland
| | - Thomas B. Brück
- Department of Chemistry, Werner Siemens Chair of Synthetic BiotechnologyTechnical University of Munich (TUM)MünchenGermany
| | - Samaneh Allahyari
- Medical Microbiology Research CenterQazvin University of Medical SciencesQazvinIran
| | - Iradj Ashrafi Tamai
- Department of Microbiology and Immunology, Faculty of Veterinary MedicineUniversity of TehranTehranIran
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Timmermans M, Wattiau P, Denis O, Boland C. Colistin resistance genes mcr-1 to mcr-5, including a case of triple occurrence (mcr-1, -3 and -5), in Escherichia coli isolates from faeces of healthy pigs, cattle and poultry in Belgium, 2012-2016. Int J Antimicrob Agents 2021; 57:106350. [PMID: 33910096 DOI: 10.1016/j.ijantimicag.2021.106350] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 12/24/2022]
Abstract
Colistin is a last-resort antimicrobial used to treat infections caused by multidrug-resistant Gram-negative bacilli (MDR-GNB). The emergence of colistin resistance, particularly linked to mobile genetic elements including the mcr genes, is a major threat to the management of MDR-GNB infections. The aim of this study was to assess the presence of mcr genes in a collection of 40 colistin-resistant commensal Escherichia coli isolated from healthy pigs, cattle and poultry in Belgium between 2012 and 2016. All isolates carried at least one mcr gene. The genes mcr-1 to -5 were observed in this collection. Different replicons associated with mcr genes were identified, including IncHI2/IncHI2A associated with mcr-1, IncX4 associated with mcr-1 and mcr-2, and ColE10 associated with mcr-4. While the occurrence of multiple mcr genes in a single isolate has rarely been reported elsewhere, a triple occurrence (mcr-1, -3 and -5) was found in this study. All isolates were MDR and carried between one and nine different replicons. Seventeen different sequence types were observed among the 40 E. coli isolates. In conclusion, this study revealed the presence of a reservoir of mobile colistin resistance genes (mcr-1 to -5) observed during at least 5 years (2012-2016) in the commensal gut flora of pigs, cattle and poultry in Belgium.
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Affiliation(s)
- Michaël Timmermans
- Veterinary Bacteriology, Sciensano, Ixelles, Belgium; Faculté de médecine, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Olivier Denis
- Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium; Laboratory of Clinical Microbiology, National Reference Center for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Cécile Boland
- Veterinary Bacteriology, Sciensano, Ixelles, Belgium.
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7
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Saviñon-Flores F, Méndez E, López-Castaños M, Carabarin-Lima A, López-Castaños KA, González-Fuentes MA, Méndez-Albores A. A Review on SERS-Based Detection of Human Virus Infections: Influenza and Coronavirus. BIOSENSORS 2021; 11:66. [PMID: 33670852 PMCID: PMC7997427 DOI: 10.3390/bios11030066] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 05/05/2023]
Abstract
The diagnosis of respiratory viruses of zoonotic origin (RVsZO) such as influenza and coronaviruses in humans is crucial, because their spread and pandemic threat are the highest. Surface-enhanced Raman spectroscopy (SERS) is an analytical technique with promising impact for the point-of-care diagnosis of viruses. It has been applied to a variety of influenza A virus subtypes, such as the H1N1 and the novel coronavirus SARS-CoV-2. In this work, a review of the strategies used for the detection of RVsZO by SERS is presented. In addition, relevant information about the SERS technique, anthropozoonosis, and RVsZO is provided for a better understanding of the theme. The direct identification is based on trapping the viruses within the interstices of plasmonic nanoparticles and recording the SERS signal from gene fragments or membrane proteins. Quantitative mono- and multiplexed assays have been achieved following an indirect format through a SERS-based sandwich immunoassay. Based on this review, the development of multiplex assays that incorporate the detection of RVsZO together with their specific biomarkers and/or secondary disease biomarkers resulting from the infection progress would be desirable. These configurations could be used as a double confirmation or to evaluate the health condition of the patient.
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Affiliation(s)
- Fernanda Saviñon-Flores
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Mexico; (F.S.-F.); (E.M.); (M.A.G.-F.)
| | - Erika Méndez
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Mexico; (F.S.-F.); (E.M.); (M.A.G.-F.)
| | - Mónica López-Castaños
- Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Mexico;
| | - Alejandro Carabarin-Lima
- Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Mexico;
| | - Karen A. López-Castaños
- Centro de Química-ICUAP-Posgrado en Ciencias Ambientales, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Mexico;
| | - Miguel A. González-Fuentes
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Mexico; (F.S.-F.); (E.M.); (M.A.G.-F.)
| | - Alia Méndez-Albores
- Centro de Química-ICUAP-Posgrado en Ciencias Ambientales, Benemérita Universidad Autónoma de Puebla, 72570 Puebla, Mexico;
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Baldo V, Salogni C, Giovannini S, D'Incau M, Boniotti MB, Birbes L, Pitozzi A, Formenti N, Grassi A, Pasquali P, Alborali GL. Pathogenicity of Shiga Toxin Type 2e Escherichia coli in Pig Colibacillosis. Front Vet Sci 2020; 7:545818. [PMID: 33062659 PMCID: PMC7530191 DOI: 10.3389/fvets.2020.545818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/12/2020] [Indexed: 11/24/2022] Open
Abstract
Shiga toxin type 2e (Stx2e) Escherichia coli is the causative factor of diarrhea and edema in swine. The aims of this study were to determine the prevalence of Stx2e-producing E. coli isolates and to characterize isolates from clinical cases of pig colibacillosis and healthy swine. During the 11 years of the study (2006–2017), a total of 233 Stx2e-producing isolates were detected−230 out of 2,060 (11.16%) E. coli isolated from diseased pigs and 3 out of 171 (1.75%) from healthy swine. Stx2e-producing isolates were indeed more present in clinical colibacillosis cases than in healthy pigs (p = 0.0002). The predominant serogroup was O139 (79.82%) and the most common fimbrial factor present in these isolates was F18 (177 isolates), followed by F6 (5 isolates). The enterotoxins LTI, STa, and STb were detected in 10.43, 41.73, and 48.26% of the isolates, respectively. The predominant virotypes F18-Stx2e and -STa-STb-Stx2e were similarly present in weaners (33.33 and 35.52%) and finishers (38.30 and 25.53%). Among isolates from diseased pigs, O139 and F18 were the more frequently identified serogroup and virulence factor, respectively. Of the tested 230 Stx2e-producing isolates isolated from diseased pigs, 29 (12.60%) harbored genes encoding ESBL, particularly TEM (79.30%), CTX-M1 (17.20%), and CMY-2 (3.40%). Antimicrobial resistance to tetracycline was the most common characteristic (98.25%), followed by ampicillin (93.91%), cephalotin (90.43%) and trimethoprim/sulfamethoxazole (82.17%). Our results showed that Stx2e-producing E. coli were more frequently associated with clinical forms of colibacillosis, with minimal probability to isolate these isolates from healthy pigs.
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Affiliation(s)
- Valentina Baldo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Cristian Salogni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Stefano Giovannini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Mario D'Incau
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Maria Beatrice Boniotti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Laura Birbes
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Alessandra Pitozzi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Nicoletta Formenti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Andrea Grassi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Paolo Pasquali
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Giovanni Loris Alborali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
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9
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Saltykova A, Buytaers FE, Denayer S, Verhaegen B, Piérard D, Roosens NHC, Marchal K, De Keersmaecker SCJ. Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study. Int J Mol Sci 2020; 21:E5688. [PMID: 32784459 PMCID: PMC7460976 DOI: 10.3390/ijms21165688] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
Culture-independent diagnostics, such as metagenomic shotgun sequencing of food samples, could not only reduce the turnaround time of samples in an outbreak investigation, but also allow the detection of multi-species and multi-strain outbreaks. For successful foodborne outbreak investigation using a metagenomic approach, it is, however, necessary to bioinformatically separate the genomes of individual strains, including strains belonging to the same species, present in a microbial community, which has up until now not been demonstrated for this application. The current work shows the feasibility of strain-level metagenomics of enriched food matrix samples making use of data analysis tools that classify reads against a sequence database. It includes a brief comparison of two database-based read classification tools, Sigma and Sparse, using a mock community obtained by in vitro spiking minced meat with a Shiga toxin-producing Escherichia coli (STEC) isolate originating from a described outbreak. The more optimal tool Sigma was further evaluated using in silico simulated metagenomic data to explore the possibilities and limitations of this data analysis approach. The performed analysis allowed us to link the pathogenic strains from food samples to human isolates previously collected during the same outbreak, demonstrating that the metagenomic approach could be applied for the rapid source tracking of foodborne outbreaks. To our knowledge, this is the first study demonstrating a data analysis approach for detailed characterization and phylogenetic placement of multiple bacterial strains of one species from shotgun metagenomic WGS data of an enriched food sample.
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Affiliation(s)
- Assia Saltykova
- Transversal Activities in Applied Genomics (TAG), Sciensano, 1050 Brussels, Belgium
- IDLab, Department of Information Technology, Ghent University, IMEC, 9052 Ghent, Belgium
| | - Florence E Buytaers
- Transversal Activities in Applied Genomics (TAG), Sciensano, 1050 Brussels, Belgium
- IDLab, Department of Information Technology, Ghent University, IMEC, 9052 Ghent, Belgium
| | - Sarah Denayer
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC), Foodborne Pathogens, Sciensano, 1050 Brussels, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC), Foodborne Pathogens, Sciensano, 1050 Brussels, Belgium
| | - Denis Piérard
- National Reference Center for Shiga Toxin-Producing Escherichia coli (NRC STEC), Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics (TAG), Sciensano, 1050 Brussels, Belgium
| | - Kathleen Marchal
- IDLab, Department of Information Technology, Ghent University, IMEC, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria 0083, South Africa
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10
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Buytaers FE, Saltykova A, Denayer S, Verhaegen B, Vanneste K, Roosens NHC, Piérard D, Marchal K, De Keersmaecker SCJ. A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine. Microorganisms 2020; 8:E1191. [PMID: 32764329 PMCID: PMC7463776 DOI: 10.3390/microorganisms8081191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 12/13/2022] Open
Abstract
The management of a foodborne outbreak depends on the rapid and accurate identification of the responsible food source. Conventional methods based on isolation of the pathogen from the food matrix and target-specific real-time polymerase chain reactions (qPCRs) are used in routine. In recent years, the use of whole genome sequencing (WGS) of bacterial isolates has proven its value to collect relevant information for strain characterization as well as tracing the origin of the contamination by linking the food isolate with the patient's isolate with high resolution. However, the isolation of a bacterial pathogen from food matrices is often time-consuming and not always successful. Therefore, we aimed to improve outbreak investigation by developing a method that can be implemented in reference laboratories to characterize the pathogen in the food vehicle without its prior isolation and link it back to human cases. We tested and validated a shotgun metagenomics approach by spiking food pathogens in specific food matrices using the Shiga toxin-producing Escherichia coli (STEC) as a case study. Different DNA extraction kits and enrichment procedures were investigated to obtain the most practical workflow. We demonstrated the feasibility of shotgun metagenomics to obtain the same information as in ISO/TS 13136:2012 and WGS of the isolate in parallel by inferring the genome of the contaminant and characterizing it in a shorter timeframe. This was achieved in food samples containing different E. coli strains, including a combination of different STEC strains. For the first time, we also managed to link individual strains from a food product to isolates from human cases, demonstrating the power of shotgun metagenomics for rapid outbreak investigation and source tracking.
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Affiliation(s)
- Florence E. Buytaers
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (F.E.B.); (A.S.); (K.V.); (N.H.C.R.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9000 Ghent, Belgium;
| | - Assia Saltykova
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (F.E.B.); (A.S.); (K.V.); (N.H.C.R.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9000 Ghent, Belgium;
| | - Sarah Denayer
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC), Foodborne Pathogens, Sciensano, 1050 Brussels, Belgium; (S.D.); (B.V.)
| | - Bavo Verhaegen
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC), Foodborne Pathogens, Sciensano, 1050 Brussels, Belgium; (S.D.); (B.V.)
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (F.E.B.); (A.S.); (K.V.); (N.H.C.R.)
| | - Nancy H. C. Roosens
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (F.E.B.); (A.S.); (K.V.); (N.H.C.R.)
| | - Denis Piérard
- National Reference Center for Shiga Toxin-Producing Escherichia coli (NRC STEC), Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium;
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9000 Ghent, Belgium;
- Department of Information Technology, IDlab, IMEC, Ghent University, 9000 Ghent, Belgium
- Department of Genetics, University of Pretoria, 0001 Pretoria, South Africa
| | - Sigrid C. J. De Keersmaecker
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (F.E.B.); (A.S.); (K.V.); (N.H.C.R.)
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Rotundo L, Amagliani G, Carloni E, Omiccioli E, Magnani M, Paoli G. Evaluation of PCR-based methods for the identification of enteroaggregative hemorrhagic Escherichia coli in sprouts. Int J Food Microbiol 2019; 291:59-64. [DOI: 10.1016/j.ijfoodmicro.2018.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 11/27/2022]
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12
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Wang JB, Gu Y, Zhang MX, Yang S, Wang Y, Wang W, Li XR, Zhao YT, Wang HT. High expression of type I inositol 1,4,5-trisphosphate receptor in the kidney of rats with hepatorenal syndrome. World J Gastroenterol 2018; 24:3273-3280. [PMID: 30090007 PMCID: PMC6079285 DOI: 10.3748/wjg.v24.i29.3273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/19/2018] [Accepted: 06/27/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To detect the expression of type I inositol 1,4,5-trisphosphate receptor (IP3RI) in the kidney of rats with hepatorenal syndrome (HRS). METHODS One hundred and twenty-five Sprague-Dawley rats were randomly divided into four groups to receive an intravenous injection of D-galactosamine (D-GalN) plus lipopolysaccharide (LPS; group G/L, n = 50), D-GalN alone (group G, n = 25), LPS alone (group L, n = 25), and normal saline (group NS, n = 25), respectively. At 3, 6, 9, 12, and 24 h after injection, blood, liver, and kidney samples were collected. Hematoxylin-eosin staining of liver tissue was performed to assess hepatocyte necrosis. Electron microscopy was used to observe ultrastructural changes in the kidney. Western blot analysis and real-time PCR were performed to detect the expression of IP3RI protein and mRNA in the kidney, respectively. RESULTS Hepatocyte necrosis was aggravated gradually, which was most significant at 12 h after treatment with D-galactosamine/lipopolysaccharide, and was characterized by massive hepatocyte necrosis. At the same time, serum levels of biochemical indicators including liver and kidney function indexes were all significantly changed. The structure of the renal glomerulus and tubules was normal at all time points. Western blot analysis indicated that IP3RI protein expression began to rise at 3 h (P < 0.05) and peaked at 12 h (P < 0.01). Real-time PCR demonstrated that IP3RI mRNA expression began to rise at 3 h (P < 0.05) and peaked at 9 h (P < 0.01). CONCLUSION IP3RI protein expression is increased in the kidney of HRS rats, and may be regulated at the transcriptional level.
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MESH Headings
- Animals
- Disease Models, Animal
- Galactosamine/toxicity
- Hepatocytes/pathology
- Hepatorenal Syndrome/chemically induced
- Hepatorenal Syndrome/pathology
- Humans
- Inositol 1,4,5-Trisphosphate Receptors/genetics
- Inositol 1,4,5-Trisphosphate Receptors/metabolism
- Kidney/blood supply
- Kidney/cytology
- Kidney/pathology
- Kidney/ultrastructure
- Lipopolysaccharides/toxicity
- Liver/cytology
- Liver/drug effects
- Liver/pathology
- Male
- Microscopy, Electron
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/pathology
- Myocytes, Smooth Muscle/ultrastructure
- Necrosis
- RNA, Messenger/metabolism
- Rats
- Rats, Sprague-Dawley
- Specific Pathogen-Free Organisms
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Affiliation(s)
- Jing-Bo Wang
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Ye Gu
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Ming-Xiang Zhang
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Shun Yang
- Liaoning Cancer Hospital & Institute, Shenyang 110042, Liaoning Province, China
| | - Yan Wang
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Wei Wang
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Xi-Ran Li
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Yi-Tong Zhao
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Hai-Tao Wang
- Department of General Surgery, the Second Affiliated Hospital of Shenyang Medical College, Shenyang 110002, Liaoning Province, China
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