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Opsteegh M, Cuperus T, van Buuren C, Dam-Deisz C, van Solt-Smits C, Verhaegen B, Joeres M, Schares G, Koudela B, Egberts F, Verkleij T, van der Giessen J, Wisselink HJ. In vitro assay to determine inactivation of Toxoplasma gondii in meat samples. Int J Food Microbiol 2024; 416:110643. [PMID: 38452660 DOI: 10.1016/j.ijfoodmicro.2024.110643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/12/2024] [Accepted: 02/24/2024] [Indexed: 03/09/2024]
Abstract
Consumption of raw and undercooked meat is considered as an important source of Toxoplasma gondii infections. However, most non-heated meat products contain salt and additives, which affect T. gondii viability. It was our aim to develop an in vitro method to substitute the mouse bioassay for determining the effect of salting on T. gondii viability. Two sheep were experimentally infected by oral inoculation with 6.5 × 104 oocysts. Grinded meat samples of 50 g were prepared from heart, diaphragm, and four meat cuts. Also, pooled meat samples were either kept untreated (positive control), frozen (negative control) or supplemented with 0.6 %, 0.9 %, 1.2 % or 2.7 % NaCl. All samples were digested in pepsin-HCl solution, and digests were inoculated in duplicate onto monolayers of RK13 (a rabbit kidney cell line). Cells were maintained for up to four weeks and parasite growth was monitored by assessing Cq-values using the T. gondii qPCR on cell culture supernatant in intervals of one week and ΔCq-values determined. Additionally, 500 μL of each digest from the individual meat cuts, heart and diaphragm were inoculated in duplicate in IFNγ KO mice. Both sheep developed an antibody response and tissue samples contained similar concentrations of T. gondii DNA. From all untreated meat samples positive ΔCq-values were obtained in the in vitro assay, indicating presence and multiplication of viable parasites. This was in line with the mouse bioassay, with the exception of a negative mouse bioassay on one heart sample. Samples supplemented with 0.6 %-1.2 % NaCl showed positive ΔCq-values over time. The frozen sample and the sample supplemented with 2.7 % NaCl remained qPCR positive but with high Cq-values, which indicated no growth. In conclusion, the in vitro method has successfully been used to detect viable T. gondii in tissues of experimentally infected sheep, and a clear difference in T. gondii viability was observed between the samples supplemented with 2.7 % NaCl and those with 1.2 % NaCl or less.
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Affiliation(s)
- Marieke Opsteegh
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, the Netherlands.
| | - Tryntsje Cuperus
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, the Netherlands.
| | - Chesley van Buuren
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, the Netherlands.
| | - Cecile Dam-Deisz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, the Netherlands.
| | - Conny van Solt-Smits
- Wageningen Bioveterinary Research, Wageningen University and Research, P.O. Box 65, 8200 AB Lelystad, the Netherlands.
| | - Bavo Verhaegen
- Sciensano, Service of Foodborne Pathogens, Rue Juliette Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Maike Joeres
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, National Reference Centre for Toxoplasmosis, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Gereon Schares
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, National Reference Centre for Toxoplasmosis, Südufer 10, 17493 Greifswald-Insel Riems, Germany.
| | - Břetislav Koudela
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 61242 Brno, Czech Republic.
| | - Frans Egberts
- Dutch Meat Products Association (VNV), P.O. Box 61, 2700 AB Zoetermeer, the Netherlands.
| | - Theo Verkleij
- Wageningen Food & Biobased Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands.
| | - Joke van der Giessen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, the Netherlands.
| | - Henk J Wisselink
- Wageningen Bioveterinary Research, Wageningen University and Research, P.O. Box 65, 8200 AB Lelystad, the Netherlands.
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Bogaerts B, Van den Bossche A, Verhaegen B, Delbrassinne L, Mattheus W, Nouws S, Godfroid M, Hoffman S, Roosens NHC, De Keersmaecker SCJ, Vanneste K. Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens. J Clin Microbiol 2024:e0157623. [PMID: 38441926 DOI: 10.1128/jcm.01576-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/09/2024] [Indexed: 03/08/2024] Open
Abstract
Whole-genome sequencing has become the method of choice for bacterial outbreak investigation, with most clinical and public health laboratories currently routinely using short-read Illumina sequencing. Recently, long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which promises much lower error rates than the R9 chemistry. However, limited information is available on its performance for bacterial single-nucleotide polymorphism (SNP)-based outbreak investigation. We present an open-source workflow, Prokaryotic Awesome variant Calling Utility (PACU) (https://github.com/BioinformaticsPlatformWIV-ISP/PACU), for constructing SNP phylogenies using Illumina and/or ONT R9/R10 sequencing data. The workflow was evaluated using outbreak data sets of Shiga toxin-producing Escherichia coli and Listeria monocytogenes by comparing ONT R9 and R10 with Illumina data. The performance of each sequencing technology was evaluated not only separately but also by integrating samples sequenced by different technologies/chemistries into the same phylogenomic analysis. Additionally, the minimum sequencing time required to obtain accurate phylogenetic results using nanopore sequencing was evaluated. PACU allowed accurate identification of outbreak clusters for both species using all technologies/chemistries, but ONT R9 results deviated slightly more from the Illumina results. ONT R10 results showed trends very similar to Illumina, and we found that integrating data sets sequenced by either Illumina or ONT R10 for different isolates into the same analysis produced stable and highly accurate phylogenomic results. The resulting phylogenies for these two outbreaks stabilized after ~20 hours of sequencing for ONT R9 and ~8 hours for ONT R10. This study provides a proof of concept for using ONT R10, either in isolation or in combination with Illumina, for rapid and accurate bacterial SNP-based outbreak investigation.
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Affiliation(s)
- Bert Bogaerts
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | | | - Stéphanie Nouws
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Maxime Godfroid
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Stefan Hoffman
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Nancy H C Roosens
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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Van Poelvoorde LAE, Gobbo A, Nauwelaerts SJD, Verhaegen B, Lesenfants M, Janssens R, Hutse V, Fraiture MA, De Keersmaecker S, Herman P, Van Hoorde K, Roosens N. Development of a reverse transcriptase digital droplet polymerase chain reaction-based approach for SARS-CoV-2 variant surveillance in wastewater. Water Environ Res 2024; 96:e10999. [PMID: 38414298 DOI: 10.1002/wer.10999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/29/2024]
Abstract
An urgent need for effective surveillance strategies arose due to the global emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although vaccines and antivirals are available, concerns persist about the evolution of new variants with potentially increased infectivity, transmissibility, and immune evasion. Therefore, variant monitoring is crucial for public health decision-making. Wastewater-based surveillance has proven to be an effective tool to monitor SARS-CoV-2 variants within populations. Specific SARS-CoV-2 variants are detected and quantified in wastewater in this study using a reverse transcriptase digital droplet polymerase chain reaction (RT-ddPCR) approach. The 11 designed assays were first validated in silico using a substantial dataset of high-quality SARS-CoV-2 genomes to ensure comprehensive variant coverage. The assessment of the sensitivity and specificity with reference material showed the capability of the developed assays to reliably identify target mutations while minimizing false positives and false negatives. The applicability of the assays was evaluated using wastewater samples from a wastewater treatment plant in Ghent, Belgium. The quantification of the specific mutations linked to the variants of concern present in these samples was calculated using these assays based on the detection of single mutations, which confirms their use for real-world variant surveillance. In conclusion, this study provides an adaptable protocol to monitor SARS-CoV-2 variants in wastewater with high sensitivity and specificity. Its potential for broader application in other viral surveillance contexts highlights its added value for rapid response to emerging infectious diseases. PRACTITIONER POINTS: Robust RT-ddPCR methodology for specific SARS-CoV-2 variants of concern detection in wastewater. Rigorous validation that demonstrates high sensitivity and specificity. Demonstration of real-world applicability using wastewater samples. Valuable tool for rapid response to emerging infectious diseases.
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Affiliation(s)
| | - Andrea Gobbo
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Marie Lesenfants
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | - Raphael Janssens
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | - Veronik Hutse
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | | | | | | | | | - Nancy Roosens
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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Buytaers FE, Verhaegen B, Van Nieuwenhuysen T, Roosens NHC, Vanneste K, Marchal K, De Keersmaecker SCJ. Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling. Front Microbiol 2024; 15:1330814. [PMID: 38495515 PMCID: PMC10940517 DOI: 10.3389/fmicb.2024.1330814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
Introduction Shotgun metagenomics has previously proven effective in the investigation of foodborne outbreaks by providing rapid and comprehensive insights into the microbial contaminant. However, culture enrichment of the sample has remained a prerequisite, despite the potential impact on pathogen detection resulting from the growth competition. To circumvent the need for culture enrichment, we explored the use of adaptive sampling using various databases for a targeted nanopore sequencing, compared to shotgun metagenomics alone. Methods The adaptive sampling method was first tested on DNA of mashed potatoes mixed with DNA of a Staphylococcus aureus strain previously associated with a foodborne outbreak. The selective sequencing was used to either deplete the potato sequencing reads or enrich for the pathogen sequencing reads, and compared to a shotgun sequencing. Then, living S. aureus were spiked at 105 CFU into 25 g of mashed potatoes. Three DNA extraction kits were tested, in combination with enrichment using adaptive sampling, following whole genome amplification. After data analysis, the possibility to characterize the contaminant with the different sequencing and extraction methods, without culture enrichment, was assessed. Results Overall, the adaptive sampling outperformed the shotgun sequencing. While the use of a host removal DNA extraction kit and targeted sequencing using a database of foodborne pathogens allowed rapid detection of the pathogen, the most complete characterization was achieved when using solely a database of S. aureus combined with a conventional DNA extraction kit, enabling accurate placement of the strain on a phylogenetic tree alongside outbreak cases. Discussion This method shows great potential for strain-level analysis of foodborne outbreaks without the need for culture enrichment, thereby enabling faster investigations and facilitating precise pathogen characterization. The integration of adaptive sampling with metagenomics presents a valuable strategy for more efficient and targeted analysis of microbial communities in foodborne outbreaks, contributing to improved food safety and public health.
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Affiliation(s)
- Florence E. Buytaers
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Foodborne Outbreaks (NRL-FBO) and for Coagulase Positive Staphylococci (NRL-CPS), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Tom Van Nieuwenhuysen
- National Reference Laboratory for Foodborne Outbreaks (NRL-FBO) and for Coagulase Positive Staphylococci (NRL-CPS), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Information Technology, IDlab, IMEC, Ghent University, Ghent, Belgium
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Bertels X, Hanoteaux S, Janssens R, Maloux H, Verhaegen B, Delputte P, Boogaerts T, van Nuijs ALN, Brogna D, Linard C, Marescaux J, Didy C, Pype R, Roosens NHC, Van Hoorde K, Lesenfants M, Lahousse L. Time series modelling for wastewater-based epidemiology of COVID-19: A nationwide study in 40 wastewater treatment plants of Belgium, February 2021 to June 2022. Sci Total Environ 2023; 899:165603. [PMID: 37474075 DOI: 10.1016/j.scitotenv.2023.165603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 07/11/2023] [Accepted: 07/15/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Wastewater-based epidemiology (WBE) has been implemented to monitor surges of COVID-19. Yet, multiple factors impede the usefulness of WBE and quantitative adjustment may be required. AIM We aimed to model the relationship between WBE data and incident COVID-19 cases, while adjusting for confounders and autocorrelation. METHODS This nationwide WBE study includes data from 40 wastewater treatment plants (WWTPs) in Belgium (02/2021-06/2022). We applied ARIMA-based modelling to assess the effect of daily flow rate, pepper mild mottle virus (PMMoV) concentration, a measure of human faeces in wastewater, and variants (alpha, delta, and omicron strains) on SARS-CoV-2 RNA levels in wastewater. Secondly, adjusted WBE metrics at different lag times were used to predict incident COVID-19 cases. Model selection was based on AICc minimization. RESULTS In 33/40 WWTPs, RNA levels were best explained by incident cases, flow rate, and PMMoV. Flow rate and PMMoV were associated with -13.0 % (95 % prediction interval: -26.1 to +0.2 %) and +13.0 % (95 % prediction interval: +5.1 to +21.0 %) change in RNA levels per SD increase, respectively. In 38/40 WWTPs, variants did not explain variability in RNA levels independent of cases. Furthermore, our study shows that RNA levels can lead incident cases by at least one week in 15/40 WWTPs. The median population size of leading WWTPs was 85.1 % larger than that of non‑leading WWTPs. In 17/40 WWTPs, however, RNA levels did not lead or explain incident cases in addition to autocorrelation. CONCLUSION This study provides quantitative insights into key determinants of WBE, including the effects of wastewater flow rate, PMMoV, and variants. Substantial inter-WWTP variability was observed in terms of explaining incident cases. These findings are of practical importance to WBE practitioners and show that the early-warning potential of WBE is WWTP-specific and needs validation.
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Affiliation(s)
- Xander Bertels
- Department of Bioanalysis, Ghent University, 9000 Ghent, Belgium
| | - Sven Hanoteaux
- Epidemiology and Public Health, Epidemiology of Infectious Diseases, Sciensano, 1050 Brussels, Belgium
| | - Raphael Janssens
- Epidemiology and Public Health, Epidemiology of Infectious Diseases, Sciensano, 1050 Brussels, Belgium
| | - Hadrien Maloux
- Epidemiology and Public Health, Epidemiology of Infectious Diseases, Sciensano, 1050 Brussels, Belgium
| | - Bavo Verhaegen
- Infectious Diseases in Humans, Foodborne Pathogens, Sciensano, 1050 Brussels, Belgium
| | - Peter Delputte
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, 2610 Wilrijk, Belgium
| | - Tim Boogaerts
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium
| | | | - Delphine Brogna
- Institute of Life, Earth and Environment, University of Namur, 5000 Namur, Belgium
| | - Catherine Linard
- Institute of Life, Earth and Environment, University of Namur, 5000 Namur, Belgium
| | - Jonathan Marescaux
- Institute of Life, Earth and Environment, University of Namur, 5000 Namur, Belgium; E-BIOM SA, 5000 Namur, Belgium
| | - Christian Didy
- Société Publique de Gestion de l'Eau, 4800 Verviers, Belgium
| | - Rosalie Pype
- Société Publique de Gestion de l'Eau, 4800 Verviers, Belgium
| | - Nancy H C Roosens
- Biological Health Risks, Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Koenraad Van Hoorde
- Infectious Diseases in Humans, Foodborne Pathogens, Sciensano, 1050 Brussels, Belgium
| | - Marie Lesenfants
- Epidemiology and Public Health, Epidemiology of Infectious Diseases, Sciensano, 1050 Brussels, Belgium
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, 9000 Ghent, Belgium.
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Nouws S, Verhaegen B, Denayer S, Crombé F, Piérard D, Bogaerts B, Vanneste K, Marchal K, Roosens NHC, De Keersmaecker SCJ. Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices. Front Microbiol 2023; 14:1204630. [PMID: 37520372 PMCID: PMC10381951 DOI: 10.3389/fmicb.2023.1204630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Shiga toxin-producing Escherichia coli (STEC) is a gastrointestinal pathogen causing foodborne outbreaks. Whole Genome Sequencing (WGS) in STEC surveillance holds promise in outbreak prevention and confinement, in broadening STEC epidemiology and in contributing to risk assessment and source attribution. However, despite international recommendations, WGS is often restricted to assist outbreak investigation and is not yet fully implemented in food safety surveillance across all European countries, in contrast to for example in the United States. Methods In this study, WGS was retrospectively applied to isolates collected within the context of Belgian food safety surveillance and combined with data from clinical isolates to evaluate its benefits. A cross-sector WGS-based collection of 754 strains from 1998 to 2020 was analyzed. Results We confirmed that WGS in food safety surveillance allows accurate detection of genomic relationships between human cases and strains isolated from food samples, including those dispersed over time and geographical locations. Identifying these links can reveal new insights into outbreaks and direct epidemiological investigations to facilitate outbreak management. Complete WGS-based isolate characterization enabled expanding epidemiological insights related to circulating serotypes, virulence genes and antimicrobial resistance across different reservoirs. Moreover, associations between virulence genes and severe disease were determined by incorporating human metadata into the data analysis. Gaps in the surveillance system were identified and suggestions for optimization related to sample centralization, harmonizing isolation methods, and expanding sampling strategies were formulated. Discussion This study contributes to developing a representative WGS-based collection of circulating STEC strains and by illustrating its benefits, it aims to incite policymakers to support WGS uptake in food safety surveillance.
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Affiliation(s)
- Stéphanie Nouws
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- IDlab, Department of Information Technology, Ghent University—IMEC, Ghent, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC) and for Foodborne Outbreaks (NRL FBO), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Sarah Denayer
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC) and for Foodborne Outbreaks (NRL FBO), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Florence Crombé
- National Reference Centre for Shiga Toxin-Producing Escherichia coli (NRC STEC), Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Denis Piérard
- National Reference Centre for Shiga Toxin-Producing Escherichia coli (NRC STEC), Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- IDlab, Department of Information Technology, Ghent University—IMEC, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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Locus T, Lambrecht E, Peeters M, Suin V, Verhaegen B, Van Hoorde K, Lamoral S, Vanwolleghem T, Van Gucht S. Hepatitis E virus in pork meat products and exposure assessment in Belgium. Int J Food Microbiol 2023; 397:110198. [PMID: 37086528 DOI: 10.1016/j.ijfoodmicro.2023.110198] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/24/2023]
Abstract
Zoonotic hepatitis E virus (HEV) genotype 3 infections are the predominant cause of acute viral hepatitis in Europe, mostly associated with the consumption of HEV contaminated pork meat. In this study we looked at the HEV RNA positivity rate of pork meat products readily available from Belgian supermarkets and evaluated the overall HEV consumer exposure in a Belgian context. Two basic assessments were performed in a 'worst-case' scenario setting: one solely focusing on the contamination level of the product itself (ingredients and processing parameters) and another estimating the overall consumer exposure, taking into account consumption habits in Belgium. Non-thermal-processed ready-to-eat (i.e. ready for consumption without additional cooking step by consumer) pork meat products (e.g. raw dried sausages), had a high estimated HEV contamination level, while thermal-processed ready-to-eat pork meat products (e.g. pork liver pâté) had the highest overall consumer exposure estimates. Following these assessments, pork liver pâtés, raw dried hams and raw dried sausages (n = 54) were purchased from Belgian supermarkets (n = 3) and analyzed for HEV RNA by RT-PCR. In total, 31 % (n = 17) products tested positive. HEV RNA was found in 65 % of the pork liver pâtés, 15 % of raw dried hams and 0 % of raw dried sausages. Phylogenetic analysis of four isolates (all gt3c) from pork liver pâté samples showed similarities with human clinical cases from Germany and Belgium.
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Affiliation(s)
- Tatjana Locus
- Sciensano, Infectious Diseases in Humans, Viral Diseases, Engelandstraat 642, 1180 Ukkel, Belgium; ILVO, Flemish Research Institute for Agriculture, Fisheries and Food, Technology and Food Unit, Brusselsesteenweg 370, 9090 Melle, Belgium; University of Antwerp, Laboratory of Experimental Medicine and Pediatrics, Viral Hepatitis Research Group, Drie Eikenstraat 655, 2650 Edegem, Belgium
| | - Ellen Lambrecht
- ILVO, Flemish Research Institute for Agriculture, Fisheries and Food, Technology and Food Unit, Brusselsesteenweg 370, 9090 Melle, Belgium
| | - Michael Peeters
- Sciensano, Infectious Diseases in Humans, Viral Diseases, Engelandstraat 642, 1180 Ukkel, Belgium
| | - Vanessa Suin
- Sciensano, Infectious Diseases in Humans, Viral Diseases, Engelandstraat 642, 1180 Ukkel, Belgium
| | - Bavo Verhaegen
- Sciensano, Infectious Diseases in Humans, Foodborne Pathogens, Juliette Wytsmanstraat 14, 1050 Elsene, Belgium
| | - Koenraad Van Hoorde
- Sciensano, Infectious Diseases in Humans, Foodborne Pathogens, Juliette Wytsmanstraat 14, 1050 Elsene, Belgium
| | - Sophie Lamoral
- Sciensano, Infectious Diseases in Humans, Viral Diseases, Engelandstraat 642, 1180 Ukkel, Belgium
| | - Thomas Vanwolleghem
- University of Antwerp, Laboratory of Experimental Medicine and Pediatrics, Viral Hepatitis Research Group, Drie Eikenstraat 655, 2650 Edegem, Belgium
| | - Steven Van Gucht
- Sciensano, Infectious Diseases in Humans, Viral Diseases, Engelandstraat 642, 1180 Ukkel, Belgium.
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8
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Van Poelvoorde LAE, Picalausa C, Gobbo A, Verhaegen B, Lesenfants M, Herman P, Van Hoorde K, Roosens NHC. Development of a Droplet Digital PCR to Monitor SARS-CoV-2 Omicron Variant BA.2 in Wastewater Samples. Microorganisms 2023; 11:microorganisms11030729. [PMID: 36985302 PMCID: PMC10059707 DOI: 10.3390/microorganisms11030729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Wastewater-based surveillance can be used as a complementary method to other SARS-CoV-2 surveillance systems. It allows the emergence and spread of infections and SARS-CoV-2 variants to be monitored in time and place. This study presents an RT-ddPCR method that targets the T19I amino acid mutation in the spike protein of the SARS-CoV-2 genomes, which is specific to the BA.2 variant (omicron). The T19I assay was evaluated both in silico and in vitro for its inclusivity, sensitivity, and specificity. Moreover, wastewater samples were used as a proof of concept to monitor and quantify the emergence of the BA.2 variant from January until May 2022 in the Brussels-Capital Region which covers a population of more than 1.2 million inhabitants. The in silico analysis showed that more than 99% of the BA.2 genomes could be characterized using the T19I assay. Subsequently, the sensitivity and specificity of the T19I assay were successfully experimentally evaluated. Thanks to our specific method design, the positive signal from the mutant probe and wild-type probe of the T19I assay was measured and the proportion of genomes with the T19I mutation, characteristic of the BA.2 mutant, compared to the entire SARS-CoV-2 population was calculated. The applicability of the proposed RT-ddPCR method was evaluated to monitor and quantify the emergence of the BA.2 variant over time. To validate this assay as a proof of concept, the measurement of the proportion of a specific circulating variant with genomes containing the T19I mutation in comparison to the total viral population was carried out in wastewater samples from wastewater treatment plants in the Brussels-Capital Region in the winter and spring of 2022. This emergence and proportional increase in BA.2 genomes correspond to what was observed in the surveillance using respiratory samples; however, the emergence was observed slightly earlier, which suggests that wastewater sampling could be an early warning system and could be an interesting alternative to extensive human testing.
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Affiliation(s)
| | - Corinne Picalausa
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Andrea Gobbo
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | | | - Marie Lesenfants
- Epidemiology of Infectious Diseases, Sciensano, 1050 Brussels, Belgium
| | | | | | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
- Correspondence:
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9
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Buytaers FE, Verhaegen B, Gand M, D’aes J, Vanneste K, Roosens NHC, Marchal K, Denayer S, De Keersmaecker SCJ. Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study. Foods 2022; 11:foods11213348. [PMID: 36359961 PMCID: PMC9654790 DOI: 10.3390/foods11213348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/11/2022] [Accepted: 10/22/2022] [Indexed: 12/02/2022] Open
Abstract
In this proof-of-concept study on food contaminated with norovirus, we investigated the feasibility of metagenomics as a new method to obtain the whole genome sequence of the virus and perform strain level characterization but also relate to human cases in order to resolve foodborne outbreaks. We tested several preparation methods to determine if a more open sequencing approach, i.e., shotgun metagenomics, or a more targeted approach, including hybrid capture, was the most appropriate. The genetic material was sequenced using Oxford Nanopore technologies with or without adaptive sampling, and the data were analyzed with an in-house bioinformatics workflow. We showed that a viral genome sequence could be obtained for phylogenetic analysis with shotgun metagenomics if the contamination load was sufficiently high or after hybrid capture for lower contamination. Relatedness to human cases goes well beyond the results obtained with the current qPCR methods. This workflow was also tested on a publicly available dataset of food spiked with norovirus and hepatitis A virus. This allowed us to prove that we could detect even fewer genome copies and two viruses present in a sample using shotgun metagenomics. We share the lessons learnt on the satisfactory and unsatisfactory results in an attempt to advance the field.
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Affiliation(s)
- Florence E. Buytaers
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory (NRL) for Food-Borne Outbreaks and NRL Food-Borne Viruses, Food-Borne Pathogens, Sciensano, 1050 Brussels, Belgium
| | - Mathieu Gand
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Jolien D’aes
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Department of Information Technology, IDlab, IMEC, Ghent University, 9052 Ghent, Belgium
| | - Sarah Denayer
- National Reference Laboratory (NRL) for Food-Borne Outbreaks and NRL Food-Borne Viruses, Food-Borne Pathogens, Sciensano, 1050 Brussels, Belgium
| | - Sigrid C. J. De Keersmaecker
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
- Correspondence: ; Tel.: +32-2-642-5257
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10
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Nouws S, Bogaerts B, Verhaegen B, Denayer S, Laeremans L, Marchal K, Roosens NHC, Vanneste K, De Keersmaecker SCJ. Whole Genome Sequencing Provides an Added Value to the Investigation of Staphylococcal Food Poisoning Outbreaks. Front Microbiol 2021; 12:750278. [PMID: 34795649 PMCID: PMC8593433 DOI: 10.3389/fmicb.2021.750278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022] Open
Abstract
Through staphylococcal enterotoxin (SE) production, Staphylococcus aureus is a common cause of food poisoning. Detection of staphylococcal food poisoning (SFP) is mostly performed using immunoassays, which, however, only detect five of 27 SEs described to date. Polymerase chain reactions are, therefore, frequently used in complement to identify a bigger arsenal of SE at the gene level (se) but are labor-intensive. Complete se profiling of isolates from different sources, i.e., food and human cases, is, however, important to provide an indication of their potential link within foodborne outbreak investigation. In addition to complete se gene profiling, relatedness between isolates is determined with more certainty using pulsed-field gel electrophoresis, Staphylococcus protein A gene typing and other methods, but these are shown to lack resolution. We evaluated how whole genome sequencing (WGS) can offer a solution to these shortcomings. By WGS analysis of a selection of S. aureus isolates, including some belonging to a confirmed foodborne outbreak, its added value as the ultimate multiplexing method was demonstrated. In contrast to PCR-based se gene detection for which primers are sometimes shown to be non-specific, WGS enabled complete se gene profiling with high performance, provided that a database containing reference sequences for all se genes was constructed and employed. The custom compiled database and applied parameters were made publicly available in an online user-friendly interface. As an all-in-one approach with high resolution, WGS additionally allowed inferring correct isolate relationships. The different DNA extraction kits that were tested affected neither se gene profiling nor relatedness determination, which is interesting for data sharing during SFP outbreak investigation. Although confirming the production of enterotoxins remains important for SFP investigation, we delivered a proof-of-concept that WGS is a valid alternative and/or complementary tool for outbreak investigation.
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Affiliation(s)
- Stéphanie Nouws
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium.,IDLab, Department of Information Technology, Ghent University - IMEC, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium.,IDLab, Department of Information Technology, Ghent University - IMEC, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Foodborne Outbreaks (NRL-FBO) and for Coagulase Positive Staphylococci (NRL-CPS), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Sarah Denayer
- National Reference Laboratory for Foodborne Outbreaks (NRL-FBO) and for Coagulase Positive Staphylococci (NRL-CPS), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Lasse Laeremans
- Organic Contaminants and Additives, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- IDLab, Department of Information Technology, Ghent University - IMEC, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
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11
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Van Poelvoorde LAE, Gand M, Fraiture MA, De Keersmaecker SCJ, Verhaegen B, Van Hoorde K, Cay AB, Balmelle N, Herman P, Roosens N. Strategy to Develop and Evaluate a Multiplex RT-ddPCR in Response to SARS-CoV-2 Genomic Evolution. Curr Issues Mol Biol 2021; 43:1937-1949. [PMID: 34889894 PMCID: PMC8928932 DOI: 10.3390/cimb43030134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022] Open
Abstract
The worldwide emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since 2019 has highlighted the importance of rapid and reliable diagnostic testing to prevent and control the viral transmission. However, inaccurate results may occur due to false negatives (FN) caused by polymorphisms or point mutations related to the virus evolution and compromise the accuracy of the diagnostic tests. Therefore, PCR-based SARS-CoV-2 diagnostics should be evaluated and evolve together with the rapidly increasing number of new variants appearing around the world. However, even by using a large collection of samples, laboratories are not able to test a representative collection of samples that deals with the same level of diversity that is continuously evolving worldwide. In the present study, we proposed a methodology based on an in silico and in vitro analysis. First, we used all information offered by available whole-genome sequencing data for SARS-CoV-2 for the selection of the two PCR assays targeting two different regions in the genome, and to monitor the possible impact of virus evolution on the specificity of the primers and probes of the PCR assays during and after the development of the assays. Besides this first essential in silico evaluation, a minimal set of testing was proposed to generate experimental evidence on the method performance, such as specificity, sensitivity and applicability. Therefore, a duplex reverse-transcription droplet digital PCR (RT-ddPCR) method was evaluated in silico by using 154 489 whole-genome sequences of SARS-CoV-2 strains that were representative for the circulating strains around the world. The RT-ddPCR platform was selected as it presented several advantages to detect and quantify SARS-CoV-2 RNA in clinical samples and wastewater. Next, the assays were successfully experimentally evaluated for their sensitivity and specificity. A preliminary evaluation of the applicability of the developed method was performed using both clinical and wastewater samples.
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Affiliation(s)
- Laura A. E. Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Mathieu Gand
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Marie-Alice Fraiture
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Sigrid C. J. De Keersmaecker
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Bavo Verhaegen
- Food Pathogens, Sciensano, 1050 Brussels, Belgium; (B.V.); (K.V.H.)
| | | | - Ann Brigitte Cay
- Enzootic, Vector-Borne and Bee Diseases, Sciensano, 1180 Brussels, Belgium; (A.B.C.); (N.B.)
| | - Nadège Balmelle
- Enzootic, Vector-Borne and Bee Diseases, Sciensano, 1180 Brussels, Belgium; (A.B.C.); (N.B.)
| | - Philippe Herman
- Expertise and Service Provision, Sciensano, 1050 Brussels, Belgium;
| | - Nancy Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
- Correspondence:
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12
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Buytaers FE, Saltykova A, Denayer S, Verhaegen B, Vanneste K, Roosens NHC, Piérard D, Marchal K, De Keersmaecker SCJ. Towards Real-Time and Affordable Strain-Level Metagenomics-Based Foodborne Outbreak Investigations Using Oxford Nanopore Sequencing Technologies. Front Microbiol 2021; 12:738284. [PMID: 34803953 PMCID: PMC8602914 DOI: 10.3389/fmicb.2021.738284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/13/2021] [Indexed: 11/18/2022] Open
Abstract
The current routine laboratory practices to investigate food samples in case of foodborne outbreaks still rely on attempts to isolate the pathogen in order to characterize it. We present in this study a proof of concept using Shiga toxin-producing Escherichia coli spiked food samples for a strain-level metagenomics foodborne outbreak investigation method using the MinION and Flongle flow cells from Oxford Nanopore Technologies, and we compared this to Illumina short-read-based metagenomics. After 12 h of MinION sequencing, strain-level characterization could be achieved, linking the food containing a pathogen to the related human isolate of the affected patient, by means of a single-nucleotide polymorphism (SNP)-based phylogeny. The inferred strain harbored the same virulence genes as the spiked isolate and could be serotyped. This was achieved by applying a bioinformatics method on the long reads using reference-based classification. The same result could be obtained after 24-h sequencing on the more recent lower output Flongle flow cell, on an extract treated with eukaryotic host DNA removal. Moreover, an alternative approach based on in silico DNA walking allowed to obtain rapid confirmation of the presence of a putative pathogen in the food sample. The DNA fragment harboring characteristic virulence genes could be matched to the E. coli genus after sequencing only 1 h with the MinION, 1 h with the Flongle if using a host DNA removal extraction, or 5 h with the Flongle with a classical DNA extraction. This paves the way towards the use of metagenomics as a rapid, simple, one-step method for foodborne pathogen detection and for fast outbreak investigation that can be implemented in routine laboratories on samples prepared with the current standard practices.
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Affiliation(s)
- Florence E. Buytaers
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Assia Saltykova
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Sarah Denayer
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, 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), Brussels, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Information Technology, IDlab, IMEC, Ghent University, Ghent, Belgium
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13
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Buytaers FE, Saltykova A, Mattheus W, Verhaegen B, Roosens NHC, Vanneste K, Laisnez V, Hammami N, Pochet B, Cantaert V, Marchal K, Denayer S, De Keersmaecker SC. Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak. Microb Genom 2021; 7:000547. [PMID: 33826490 PMCID: PMC8208685 DOI: 10.1099/mgen.0.000547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/23/2021] [Indexed: 02/04/2023] Open
Abstract
Food-borne outbreak investigation currently relies on the time-consuming and challenging bacterial isolation from food, to be able to link food-derived strains to more easily obtained isolates from infected people. When no food isolate can be obtained, the source of the outbreak cannot be unambiguously determined. Shotgun metagenomics approaches applied to the food samples could circumvent this need for isolation from the suspected source, but require downstream strain-level data analysis to be able to accurately link to the human isolate. Until now, this approach has not yet been applied outside research settings to analyse real food-borne outbreak samples. In September 2019, a Salmonella outbreak occurred in a hotel school in Bruges, Belgium, affecting over 200 students and teachers. Following standard procedures, the Belgian National Reference Center for human salmonellosis and the National Reference Laboratory for Salmonella in food and feed used conventional analysis based on isolation, serotyping and MLVA (multilocus variable number tandem repeat analysis) comparison, followed by whole-genome sequencing, to confirm the source of the contamination over 2 weeks after receipt of the sample, which was freshly prepared tartar sauce in a meal cooked at the school. Our team used this outbreak as a case study to deliver a proof of concept for a short-read strain-level shotgun metagenomics approach for source tracking. We received two suspect food samples: the full meal and some freshly made tartar sauce served with this meal, requiring the use of raw eggs. After analysis, we could prove, without isolation, that Salmonella was present in both samples, and we obtained an inferred genome of a Salmonella enterica subsp. enterica serovar Enteritidis that could be linked back to the human isolates of the outbreak in a phylogenetic tree. These metagenomics-derived outbreak strains were separated from sporadic cases as well as from another outbreak circulating in Europe at the same time period. This is, to our knowledge, the first Salmonella food-borne outbreak investigation uniquely linking the food source using a metagenomics approach and this in a fast time frame.
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Affiliation(s)
- Florence E. Buytaers
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Assia Saltykova
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Wesley Mattheus
- National Reference Center for Salmonella and Shigella spp., Sciensano, Brussels, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Salmonella and Food-Borne Infections, Food-Borne Pathogens, Sciensano, Brussels, Belgium
| | | | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Brigitte Pochet
- Federal Agency for the Security of the Food Chain, Brussels, Belgium
| | - Vera Cantaert
- Federal Agency for the Security of the Food Chain, Brussels, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Information Technology, IDlab, IMEC, Ghent University, Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Sarah Denayer
- National Reference Laboratory for Salmonella and Food-Borne Infections, Food-Borne Pathogens, Sciensano, Brussels, Belgium
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Bogaerts B, Nouws S, Verhaegen B, Denayer S, Van Braekel J, Winand R, Fu Q, Crombé F, Piérard D, Marchal K, Roosens NHC, De Keersmaecker SCJ, Vanneste K. Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods. Microb Genom 2021; 7:mgen000531. [PMID: 33656437 PMCID: PMC8190621 DOI: 10.1099/mgen.0.000531] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Whole genome sequencing (WGS) enables complete characterization of bacterial pathogenic isolates at single nucleotide resolution, making it the ultimate tool for routine surveillance and outbreak investigation. The lack of standardization, and the variation regarding bioinformatics workflows and parameters, however, complicates interoperability among (inter)national laboratories. We present a validation strategy applied to a bioinformatics workflow for Illumina data that performs complete characterization of Shiga toxin-producing Escherichia coli (STEC) isolates including antimicrobial resistance prediction, virulence gene detection, serotype prediction, plasmid replicon detection and sequence typing. The workflow supports three commonly used bioinformatics approaches for the detection of genes and alleles: alignment with blast+, kmer-based read mapping with KMA, and direct read mapping with SRST2. A collection of 131 STEC isolates collected from food and human sources, extensively characterized with conventional molecular methods, was used as a validation dataset. Using a validation strategy specifically adopted to WGS, we demonstrated high performance with repeatability, reproducibility, accuracy, precision, sensitivity and specificity above 95 % for the majority of all assays. The WGS workflow is publicly available as a 'push-button' pipeline at https://galaxy.sciensano.be. Our validation strategy and accompanying reference dataset consisting of both conventional and WGS data can be used for characterizing the performance of various bioinformatics workflows and assays, facilitating interoperability between laboratories with different WGS and bioinformatics set-ups.
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Affiliation(s)
- Bert Bogaerts
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Stéphanie Nouws
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Shiga toxin-producing Escherichia coli (NRL STEC), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Sarah Denayer
- National Reference Laboratory for Shiga toxin-producing Escherichia coli (NRL STEC), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Julien Van Braekel
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Raf Winand
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Qiang Fu
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Florence Crombé
- National Reference Center for Shiga toxin-producing Escherichia coli (NRC STEC), Brussels, Belgium
| | - Denis Piérard
- National Reference Center for Shiga toxin-producing Escherichia coli (NRC STEC), Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria, South-Africa
| | | | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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15
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Nouws S, Bogaerts B, Verhaegen B, Denayer S, Piérard D, Marchal K, Roosens NHC, Vanneste K, De Keersmaecker SCJ. Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates. Sci Rep 2020; 10:14649. [PMID: 32887913 PMCID: PMC7474065 DOI: 10.1038/s41598-020-71207-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 08/11/2020] [Indexed: 01/28/2023] Open
Abstract
Whole genome sequencing (WGS) has proven to be the ultimate tool for bacterial isolate characterization and relatedness determination. However, standardized and harmonized workflows, e.g. for DNA extraction, are required to ensure robust and exchangeable WGS data. Data sharing between (inter)national laboratories is essential to support foodborne pathogen control, including outbreak investigation. This study evaluated eight commercial DNA preparation kits for their potential influence on: (i) DNA quality for Nextera XT library preparation; (ii) MiSeq sequencing (data quality, read mapping against plasmid and chromosome references); and (iii) WGS data analysis, i.e. isolate characterization (serotyping, virulence and antimicrobial resistance genotyping) and phylogenetic relatedness (core genome multilocus sequence typing and single nucleotide polymorphism analysis). Shiga toxin-producing Escherichia coli (STEC) was selected as a case study. Overall, data quality and inferred phylogenetic relationships between isolates were not affected by the DNA extraction kit choice, irrespective of the presence of confounding factors such as EDTA in DNA solution buffers. Nevertheless, completeness of STEC characterization was, although not substantially, influenced by the plasmid extraction performance of the kits, especially when using Nextera XT library preparation. This study contributes to addressing the WGS challenges of standardizing protocols to support data portability and to enable full exploitation of its potential.
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Affiliation(s)
- Stéphanie Nouws
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium.,Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium.,Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL-STEC), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Sarah Denayer
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL-STEC), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, National Reference Center for Shiga Toxin-Producing Escherichia coli (NRC-STEC), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Nouws S, Bogaerts B, Verhaegen B, Denayer S, Crombé F, De Rauw K, Piérard D, Marchal K, Vanneste K, Roosens NHC, De Keersmaecker SCJ. The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country. Foods 2020; 9:E1030. [PMID: 32752159 PMCID: PMC7466227 DOI: 10.3390/foods9081030] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/21/2022] Open
Abstract
Gradually, conventional methods for foodborne pathogen typing are replaced by whole genome sequencing (WGS). Despite studies describing the overall benefits, National Reference Laboratories of smaller countries often show slower uptake of WGS, mainly because of significant investments required to generate and analyze data of a limited amount of samples. To facilitate this process and incite policy makers to support its implementation, a Shiga toxin-producing Escherichia coli (STEC) O157:H7 (stx1+, stx2+, eae+) outbreak (2012) and a STEC O157:H7 (stx2+, eae+) outbreak (2013) were retrospectively analyzed using WGS and compared with their conventional investigations. The corresponding results were obtained, with WGS delivering even more information, e.g., on virulence and antimicrobial resistance genotypes. Besides a universal, all-in-one workflow with less hands-on-time (five versus seven actual working days for WGS versus conventional), WGS-based cgMLST-typing demonstrated increased resolution. This enabled an accurate cluster definition, which remained unsolved for the 2013 outbreak, partly due to scarce epidemiological linking with the suspect source. Moreover, it allowed detecting two and one earlier circulating STEC O157:H7 (stx1+, stx2+, eae+) and STEC O157:H7 (stx2+, eae+) strains as closely related to the 2012 and 2013 outbreaks, respectively, which might have further directed epidemiological investigation initially. Although some bottlenecks concerning centralized data-sharing, sampling strategies, and perceived costs should be considered, we delivered a proof-of-concept that even in smaller countries, WGS offers benefits for outbreak investigation, if a sufficient budget is available to ensure its implementation in surveillance. Indeed, applying a database with background isolates is critical in interpreting isolate relationships to outbreaks, and leveraging the true benefit of WGS in outbreak investigation and/or prevention.
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Affiliation(s)
- Stéphanie Nouws
- Department of Expertise and service provision, Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.N.); (B.B.); (K.V.); (N.H.C.R.)
- Department of Information Technology, IDLab, imec, Ghent University, 9052 Ghent, Belgium;
| | - Bert Bogaerts
- Department of Expertise and service provision, Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.N.); (B.B.); (K.V.); (N.H.C.R.)
- Department of Information Technology, IDLab, imec, Ghent University, 9052 Ghent, Belgium;
| | - Bavo Verhaegen
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL-STEC), National Reference Laboratory for Foodborne Outbreaks (NRL-FBO), Department of Infectious diseases in humans, Foodborne Pathogens, Sciensano, 1050 Brussels, Belgium; (B.V.); (S.D.)
| | - Sarah Denayer
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL-STEC), National Reference Laboratory for Foodborne Outbreaks (NRL-FBO), Department of Infectious diseases in humans, Foodborne Pathogens, Sciensano, 1050 Brussels, Belgium; (B.V.); (S.D.)
| | - Florence Crombé
- Department of Microbiology and Infection Control, National Reference Center for Shiga Toxin-Producing Escherichia coli (NRC-STEC), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium; (F.C.); (K.D.R.); (D.P.)
| | - Klara De Rauw
- Department of Microbiology and Infection Control, National Reference Center for Shiga Toxin-Producing Escherichia coli (NRC-STEC), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium; (F.C.); (K.D.R.); (D.P.)
| | - Denis Piérard
- Department of Microbiology and Infection Control, National Reference Center for Shiga Toxin-Producing Escherichia coli (NRC-STEC), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium; (F.C.); (K.D.R.); (D.P.)
| | - Kathleen Marchal
- Department of Information Technology, IDLab, imec, Ghent University, 9052 Ghent, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria 0083, South Africa
| | - Kevin Vanneste
- Department of Expertise and service provision, Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.N.); (B.B.); (K.V.); (N.H.C.R.)
| | - Nancy H. C. Roosens
- Department of Expertise and service provision, Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.N.); (B.B.); (K.V.); (N.H.C.R.)
| | - Sigrid C. J. De Keersmaecker
- Department of Expertise and service provision, Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.N.); (B.B.); (K.V.); (N.H.C.R.)
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19
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Garcia-Graells C, Berbers B, Verhaegen B, Vanneste K, Marchal K, Roosens NHC, Botteldoorn N, De Keersmaecker SCJ. First detection of a plasmid located carbapenem resistant bla VIM-1 gene in E. coli isolated from meat products at retail in Belgium in 2015. Int J Food Microbiol 2020; 324:108624. [PMID: 32302878 DOI: 10.1016/j.ijfoodmicro.2020.108624] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/25/2020] [Accepted: 03/29/2020] [Indexed: 11/24/2022]
Abstract
Carbapenemase-producing Enterobacteriaceae (CPE) confer resistance to antibiotics that are of critical importance to human medicine. There have only been a few reported cases of CPEs in the European food chain. We report the first detection of a carbapenemase-producing Escherichia coli (ST 5869) in the Belgian food chain. Our aim was to characterize the origin of the carbapenem resistance in the E. coli isolate. The isolate was detected during the screening of 178 minced pork samples and was shown to contain the carbapenemase gene blaVIM-1 by PCR and Sanger sequencing. Whole genome short and long read sequencing (MiSeq and MinION) was performed to characterize the isolate. With a hybrid assembly we reconstructed a 190,205 bp IncA/C2 plasmid containing blaVIM-1 (S15FP06257_p), in addition to other critically important resistance genes. This plasmid showed only low similarity to plasmids containing blaVIM-1 previously reported in Germany. Moreover, no sequences existed in the NCBI nucleotide database that completely covered S15FP06257_p. Analysis of the blaVIM-1 gene cassette demonstrated that it likely originated from an integron of a Klebsiella plasmid reported previously in a clinical isolate in Europe, suggesting that the meat could have been contaminated by human handling in one of the steps of the food chain. This study shows the relevance of fully reconstructing plasmids to characterize their genetic content and to allow source attribution. This is especially important in view of the potential risk of antimicrobial resistance gene transmission through mobile elements as was reported here for the of public health concern blaVIM-1.
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Affiliation(s)
| | - Bas Berbers
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium; Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
| | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Nancy H C Roosens
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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20
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Gisbert Algaba I, Verhaegen B, Murat JB, Coucke W, Mercier A, Cox E, Dorny P, Dierick K, De Craeye S. Molecular Study of Toxoplasma gondii Isolates Originating from Humans and Organic Pigs in Belgium. Foodborne Pathog Dis 2020; 17:316-321. [PMID: 31905293 DOI: 10.1089/fpd.2019.2675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Toxoplasma gondii is a worldwide prevalent, zoonotic parasite of major importance for public health, which can infect any warm-blooded animal species, including humans. Humans can get infected by consumption of meat from a chronically infected animal, by ingestion of sporulated oocysts (resulting from the sexual replication in felids), via contaminated water, soil, or vegetables, and by vertical transmission via the placenta. Infection through meat consumption is estimated to be one of the main sources of human toxoplasmosis cases in developed countries, and more specifically pork is considered to be responsible for 41% of foodborne human toxoplasmosis cases in the United States. To better assess the role of pork as a source of T. gondii infection in humans in Belgium, parasites were isolated from pigs to compare with human clinical isolates in a molecular epidemiological study. A positive result was obtained by magnetic capture-quantitative polymerase chain reaction for T. gondii in 14 out of the 92 hearts sampled during 2016 and 2017 from pigs raised in organic farms. From 9 of these 14 samples, parasites were isolated by mouse bioassay, demonstrating the presence of viable T. gondii in animals intended for human consumption. When genotyped and compared with 15 human isolates obtained during 2015 and 2016, a highly related structured population was demonstrated. Overall, these findings demonstrate the presence of infectious T. gondii in pigs intended for human consumption. Therefore, a potential transmission of T. gondii strains from pigs to humans could occur. However, both species could also be infected via a common source of infection such as oocysts. Furthermore, Belgium does not have an official surveillance program for T. gondii in human cases or food-producing animals; as a consequence, the detection of the infection source of a patient is very rare. Overall, this study reinforces the identification of pork as a potential risk for the consumers.
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Affiliation(s)
| | - Bavo Verhaegen
- Scientific Service Food-Borne Pathogens, Sciensano, Brussels, Belgium
| | | | | | | | - Eric Cox
- Ghent University Faculty of Veterinary Medicine, Merelbeke, Belgium
| | - Pierre Dorny
- Ghent University Faculty of Veterinary Medicine, Merelbeke, Belgium
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21
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Drali R, Deriet A, Verhaegen B, De Keersmaecker SCJ, Botteldoorn N, Vanneste K, Roosens NHC, Mouffok F. Whole-genome sequencing of Listeria monocytogenes serotype 4b isolated from ready-to-eat lentil salad in Algiers, Algeria. New Microbes New Infect 2019; 33:100628. [PMID: 31908783 PMCID: PMC6939032 DOI: 10.1016/j.nmni.2019.100628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 11/13/2019] [Indexed: 11/10/2022] Open
Abstract
Listeria monocytogenes is a Gram-positive food-borne pathogen causing a serious threat for public health. Here we announce the whole genome sequence (3 011 693 bp) of Listeria monocytogenes serotype 4b, isolated from ready-to-eat lentil salad in Algiers and belonging to sequence type 2, lineage I and clonal complex 2.
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Affiliation(s)
- R Drali
- Plateforme Génomique-Bioinformatique, Institut Pasteur d'Algérie, Alger, Algeria
| | - A Deriet
- Laboratoire de Bactériologie des Aliments, Eaux et Environnement, Institut Pasteur d'Algérie, Alger, Algeria
| | - B Verhaegen
- Sciensano, Service Food-Borne Pathogens, Brussels, Belgium
| | | | - N Botteldoorn
- Sciensano, Service Food-Borne Pathogens, Brussels, Belgium
| | - K Vanneste
- Sciensano, Transversal Activities in Applied Genomics, Brussels, Belgium
| | - N H C Roosens
- Sciensano, Transversal Activities in Applied Genomics, Brussels, Belgium
| | - F Mouffok
- Laboratoire de Bactériologie des Aliments, Eaux et Environnement, Institut Pasteur d'Algérie, Alger, Algeria
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22
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Rahman M, Devriendt B, Gisbert Algaba I, Verhaegen B, Dorny P, Dierick K, Cox E. QuilA-Adjuvanted T. gondii Lysate Antigens Trigger Robust Antibody and IFNγ + T Cell Responses in Pigs Leading to Reduction in Parasite DNA in Tissues Upon Challenge Infection. Front Immunol 2019; 10:2223. [PMID: 31620134 PMCID: PMC6763570 DOI: 10.3389/fimmu.2019.02223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/02/2019] [Indexed: 12/22/2022] Open
Abstract
Toxoplasma gondii is an intracellular parasite of all mammals and birds, responsible for toxoplasmosis. In healthy individuals T. gondii infections mostly remain asymptomatic, however this parasite causes severe morbidity and mortality in immunocompromised patients and congenital toxoplasmosis in pregnant women. The consumption of raw or undercooked pork is considered as an important risk factor to develop toxoplasmosis in humans. Since effective therapeutic interventions to treat toxoplasmosis are scarce, vaccination of meat producing animals may prevent T. gondii transmission to humans. Here, we evaluated the elicited immune responses and the efficacy of a potential vaccine candidate, generated by size fractionation of T. gondii lysate proteins, to reduce the parasite burden in tissues from experimentally T. gondii infected pigs as compared to vaccination with total lysate antigens (TLA). Our results show that both the vaccine candidate and the TLA immunization elicited strong serum IgG responses and elevated percentages of CD4+CD8+IFNγ+ T cells in T. gondii infected pigs. However, the TLA vaccine induced the strongest immune response and reduced the parasite DNA load below the detection limit in brain and skeletal muscle tissue in most animals. These findings might inform the development of novel vaccines to prevent T. gondii infections in livestock species and humans.
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Affiliation(s)
- Mizanur Rahman
- Laboratory of Immunology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Bert Devriendt
- Laboratory of Immunology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Ignacio Gisbert Algaba
- Sciensano, National Reference Center for Toxoplasmosis, Scientific Institute of Public Health, Communicable and Infectious Diseases, Brussels, Belgium
| | - Bavo Verhaegen
- Sciensano, National Reference Center for Toxoplasmosis, Scientific Institute of Public Health, Communicable and Infectious Diseases, Brussels, Belgium
| | - Pierre Dorny
- Department of Biomedical Sciences, Institute for Tropical Medicine, Antwerp, Belgium
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Katelijne Dierick
- Sciensano, National Reference Center for Toxoplasmosis, Scientific Institute of Public Health, Communicable and Infectious Diseases, Brussels, Belgium
| | - Eric Cox
- Laboratory of Immunology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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23
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Deriet A, Berrazeg M, De Keersmaecker SCJ, Botteldoorn N, Vanneste K, Verhaegen B, Roosens NHC, Mouffok F, Drali R. Whole-Genome Sequencing of Six Strains of Salmonella enterica Isolated from Imported Meat in Algeria. Microbiol Resour Announc 2019; 8:e00615-19. [PMID: 31467095 PMCID: PMC6715865 DOI: 10.1128/mra.00615-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/13/2019] [Indexed: 11/26/2022] Open
Abstract
Nontyphoidal Salmonella (NTS) is one of the main causes of foodborne disease worldwide. In this report, we announce the first whole-genome sequencing of six strains of Salmonella enterica isolated from imported meat in Algeria. The genome sizes ranged from 4,601,209 to 4,958,962 bp. Antimicrobial resistance (AMR) genes, plasmids, and virulence factors were detected.
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Affiliation(s)
- A Deriet
- Unité environnement, Laboratoire de Bactériologie des Aliments, Eaux et Environnement, Institut Pasteur d'Algérie, Alger, Algeria
| | - M Berrazeg
- Laboratoire de Microbiologie, Institut Pasteur d'Algérie, Antenne d'Oran, Oran, Algeria
- Département de Biologie, Faculté des Sciences de la Nature et de la Vie, Université d'Oran 1, Oran, Algeria
| | | | - N Botteldoorn
- Sciensano, Service Food Borne Pathogens, Brussels, Belgium
| | - K Vanneste
- Sciensano, Transversal Activities in Applied Genomics, Brussels, Belgium
| | - B Verhaegen
- Sciensano, Service Food Borne Pathogens, Brussels, Belgium
| | - N H C Roosens
- Sciensano, Transversal Activities in Applied Genomics, Brussels, Belgium
| | - F Mouffok
- Unité environnement, Laboratoire de Bactériologie des Aliments, Eaux et Environnement, Institut Pasteur d'Algérie, Alger, Algeria
| | - R Drali
- Unité environnement, Laboratoire de Bactériologie des Aliments, Eaux et Environnement, Institut Pasteur d'Algérie, Alger, Algeria
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24
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Gisbert Algaba I, Verhaegen B, Jennes M, Rahman M, Coucke W, Cox E, Dorny P, Dierick K, De Craeye S. Pork as a source of transmission of Toxoplasma gondii to humans: a parasite burden study in pig tissues after infection with different strains of Toxoplasma gondii as a function of time and different parasite stages. Int J Parasitol 2018; 48:555-560. [PMID: 29625125 DOI: 10.1016/j.ijpara.2017.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/14/2017] [Accepted: 12/19/2017] [Indexed: 10/17/2022]
Abstract
Toxoplasma gondii is an ubiquitous apicomplexan parasite which can infect any warm-blooded animal including humans. Humans and carnivores/omnivores can also become infected by consumption of raw or undercooked infected meat containing muscle cysts. This route of transmission is considered to account for at least 30% of human toxoplasmosis cases. To better assess the role of pork as a source of infection for humans, the parasite burden resulting from experimental infection with different parasite stages and different strains of T. gondii during the acute and chronic phases was studied. The parasite burden in different tissues was measured with a ISO 17025 validated Magnetic Capture-quantitative PCR. A high burden of infection was found in heart and lungs during the acute phase of infection and heart and brain were identified as the most parasitised tissues during the chronic phase of infection, independent of the parasite stage and the strain used. Remarkably, a higher parasite burden was measured in different tissues following infection with oocysts of a type II strain compared with a tissue cyst infection with three strains of either type II or a type I/II. However, these results could have been affected by the use of different strains and euthanasia time points. The parasite burden resulting from a tissue cyst infection was not significantly different between the two strains.
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Affiliation(s)
- Ignacio Gisbert Algaba
- Scientific Institute of Public Health, Communicable and Infectious Diseases, National Reference Center for Toxoplasmosis, 1050 Brussels, Belgium.
| | - Bavo Verhaegen
- Scientific Institute of Public Health, Communicable and Infectious Diseases, National Reference Center for Toxoplasmosis, 1050 Brussels, Belgium
| | - Malgorzata Jennes
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Mizanur Rahman
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Wim Coucke
- Scientific Institute of Public Health, Quality of Medical Laboratories, 1050 Brussels, Belgium
| | - Eric Cox
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Pierre Dorny
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Department of Biomedical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Katelijne Dierick
- Scientific Institute of Public Health, Communicable and Infectious Diseases, National Reference Center for Toxoplasmosis, 1050 Brussels, Belgium
| | - Stéphane De Craeye
- Scientific Institute of Public Health, Communicable and Infectious Diseases, National Reference Center for Toxoplasmosis, 1050 Brussels, Belgium
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25
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Verhaegen B, De Reu K, De Zutter L, Verstraete K, Heyndrickx M, Van Coillie E. Comparison of Droplet Digital PCR and qPCR for the Quantification of Shiga Toxin-Producing Escherichia coli in Bovine Feces. Toxins (Basel) 2016; 8:E157. [PMID: 27213452 PMCID: PMC4885071 DOI: 10.3390/toxins8050157] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/21/2016] [Accepted: 05/10/2016] [Indexed: 12/31/2022] Open
Abstract
Cattle are considered to be the main reservoir for Shiga toxin-producing Escherichia coli (STEC) and are often the direct or indirect source of STEC outbreaks in humans. Accurate measurement of the concentration of shed STEC in cattle feces could be a key answer to questions concerning transmission of STEC, contamination sources and efficiency of treatments at farm level. Infected animals can be identified and the contamination level quantified by real-time quantitative PCR (qPCR), which has its specific limitations. Droplet digital PCR (ddPCR) has been proposed as a method to overcome many of the drawbacks of qPCR. This end-point amplification PCR is capable of absolute quantification independent from any reference material and is less prone to PCR inhibition than qPCR. In this study, the qPCR-based protocol described by Verstraete et al. (2014) for Shiga toxin genes stx1 and stx2 and the intimin gene eae quantification was optimized for ddPCR analysis. The properties of ddPCR and qPCR using two different mastermixes (EMM: TaqMan(®) Environmental Master Mix 2.0; UMM: TaqMan(®) Universal PCR Master Mix) were evaluated, using standard curves and both artificial and natural contaminated cattle fecal samples. In addition, the susceptibility of these assays to PCR-inhibitors was investigated. Evaluation of the standard curves and both artificial and natural contaminated cattle fecal samples suggested a very good agreement between qPCR using EMM and ddPCR. Furthermore, similar sensitivities and no PCR inhibition were recorded for both assays. On the other hand, qPCR using UMM was clearly prone to PCR inhibition. In conclusion, the ddPCR technique shows potential for the accurate absolute quantification of STEC on the farms, without relying on standardized reference material.
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Affiliation(s)
- Bavo Verhaegen
- Institute of Agriculture and Fishery Research (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, Melle 9090, Belgium.
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke 9820, Belgium.
| | - Koen De Reu
- Institute of Agriculture and Fishery Research (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, Melle 9090, Belgium.
| | - Lieven De Zutter
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke 9820, Belgium.
| | - Karen Verstraete
- Institute of Agriculture and Fishery Research (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, Melle 9090, Belgium.
| | - Marc Heyndrickx
- Institute of Agriculture and Fishery Research (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, Melle 9090, Belgium.
- Department of Pathology, Faculty of Veterinary Medicine, Bacteriology and Poultry Diseases, Ghent University; Salisburylaan 133, Merelbeke 9820, Belgium.
| | - Els Van Coillie
- Institute of Agriculture and Fishery Research (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, Melle 9090, Belgium.
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Verhaegen B, Van Damme I, Heyndrickx M, Botteldoorn N, Elhadidy M, Verstraete K, Dierick K, Denayer S, De Zutter L, De Reu K. Evaluation of detection methods for non-O157 Shiga toxin-producing Escherichia coli from food. Int J Food Microbiol 2016; 219:64-70. [PMID: 26736066 DOI: 10.1016/j.ijfoodmicro.2015.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/15/2015] [Accepted: 12/18/2015] [Indexed: 01/09/2023]
Abstract
Shiga toxin-producing Escherichia coli (STEC) remains a major foodborne pathogen of concern across the globe. Rapid detection and isolation of this pathogen is of great importance for public health reasons. In this study the detection and isolation of four non-O157 STEC strains (O26, O103, O111, O145) from different artificially contaminated matrices, namely ground (minced) beef, cattle carcass swab, lettuce mix and sprouted soy beans, were evaluated. Low amounts of STEC were used (0.25-1.40 cfu/g) to spike the samples. All samples were enriched in parallel in Buffered Peptone Water (BPW) and Brila broth. After enrichment, detection was performed using real-time PCR (qPCR), and isolation using two chromogenic agar media, CHROMagar™ STEC and ChromID™ EHEC. Inoculation on the agar media was performed either directly after enrichment or after the use of an acid treatment procedure. Furthermore, the use of this procedure was also tested on naturally contaminated food products, using 150 stx-positive samples. Although the qPCR Cycle Threshold (Ct) values were lower after enrichment in Brila broth, no significant differences in recovery were observed between both enrichment broths. Both agar media were equally suitable for the isolation of STEC, although a significantly higher recovery was obtained when using both agar media in parallel. For samples with a Ct value above 25, an acid treatment step prior to isolation ensured a significant improvement in the recovery of STEC due to the reduction in background microbiota. This acid treatment procedure proved especially useful for the isolation of STEC from sprouted soy bean samples.
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Affiliation(s)
- Bavo Verhaegen
- Institute for Agriculture and Fisheries Research (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090 Melle, Belgium; Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Inge Van Damme
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Marc Heyndrickx
- Institute for Agriculture and Fisheries Research (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090 Melle, Belgium; Ghent University, Faculty of Veterinary Medicine, Department of Pathology, Bacteriology and Poultry Diseases, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Nadine Botteldoorn
- Foodborne Pathogens, Scientific Institute of Public Health, Juliettte Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Mohamed Elhadidy
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Karen Verstraete
- Institute for Agriculture and Fisheries Research (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090 Melle, Belgium
| | - Katelijne Dierick
- Foodborne Pathogens, Scientific Institute of Public Health, Juliettte Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Sarah Denayer
- Foodborne Pathogens, Scientific Institute of Public Health, Juliettte Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Lieven De Zutter
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Koen De Reu
- Institute for Agriculture and Fisheries Research (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090 Melle, Belgium.
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Verhaegen B, De Reu K, Heyndrickx M, Van Damme I, De Zutter L. Growth of Stressed Strains of Four Non-O157 Shiga Toxin-Producing Escherichia coli Serogroups in Five Enrichment Broths. J Food Prot 2015; 78:1960-6. [PMID: 26555518 DOI: 10.4315/0362-028x.jfp-15-019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The purpose of this study was to evaluate (i) the behavior of several strains of non-O157 Shiga toxin-producing Escherichia coli (STEC) serogroups (O26, O103, O111, and O145) exposed to different stress conditions and (ii) the growth dynamics of stressed and nonstressed non-O157 STEC cells in five enrichment media. STEC strains were exposed to acid, cold, and freeze stresses. Lethal and sublethal injuries were determined by plating in parallel on selective and nonselective agar media. Freeze stress (8 days, 20°C) caused the most lethal (95.3% ± 2.5%) injury, as well as the most sublethal (89.1% ± 8.8%) injury in the surviving population. Growth of stressed and nonstressed pure cultures of non-O157 STEC on modified tryptic soy broth, buffered peptone water (BPW), BPW with sodium pyruvate, Brila, and STEC enrichment broth (SEB) was determined using total viable counts. To compare growth capacities, growth after 7 and 24 h of enrichment was measured; lag phases and maximum growth rates were also calculated. In general, growth on BPW resulted in a short lag phase followed by a high maximum growth rate during the enrichment of all tested strains when using all three stress types. Furthermore, BPW ensured the highest STEC count after 7 h of growth. Supplementing the medium with sodium pyruvate did not improve the growth dynamics. The two selective media, Brila and SEB, were less efficient than BPW, but Brila's enrichment performance was remarkably better than that of SEB. This study shows that irrespective of the effect of background flora, BPW is still recommended for resuscitation of non-O157 STEC.
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Affiliation(s)
- Bavo Verhaegen
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; Institute for Agricultural and Fisheries Research (ILVO), Technology and Science Food Unit, Brusselsesteenweg 370, 9090 Melle, Belgium
| | - Koen De Reu
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Science Food Unit, Brusselsesteenweg 370, 9090 Melle, Belgium.
| | - Marc Heyndrickx
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Science Food Unit, Brusselsesteenweg 370, 9090 Melle, Belgium. Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Inge Van Damme
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Lieven De Zutter
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
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Verhaegen B, De Reu K, Heyndrickx M, De Zutter L. Comparison of Six Chromogenic Agar Media for the Isolation of a Broad Variety of Non-O157 Shigatoxin-Producing Escherichia coli (STEC) Serogroups. Int J Environ Res Public Health 2015; 12:6965-78. [PMID: 26090610 PMCID: PMC4483743 DOI: 10.3390/ijerph120606965] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/02/2015] [Accepted: 06/11/2015] [Indexed: 11/16/2022]
Abstract
The isolation of non-O157 STEC from food samples has proved to be challenging. The selection of a suitable selective isolation agar remains problematic. The purpose of this study was to qualitatively and quantitatively evaluate six chromogenic agar media for the isolation of STEC: Tryptone Bile X-glucuronide agar (TBX), Rainbow® Agar O157 (RB), Rapid E. coli O157:H7 (RE), Modified MacConkey Agar (mMac), CHROMagarTM STEC (Chr ST) and chromIDTM EHEC (Chr ID). During this study, 45 E. coli strains were used, including 39 STEC strains belonging to 16 different O serogroups and 6 non-STEC E. coli. All E. coli strains were able to grow on TBX and RB, whereas one STEC strain was unable to grow on Chr ID and a number of other STEC strains did not grow on mMac, CHROMagar STEC and Rapid E. coli O157:H7. However, only the latter three agars were selective enough to completely inhibit the growth of the non-STEC E. coli. Our conclusion was that paired use of a more selective agar such as CHROMagar STEC together with a less selective agar like TBX or Chr ID might be the best solution for isolating non-O157 STEC from food.
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Affiliation(s)
- Bavo Verhaegen
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090 Melle, Belgium.
- Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - Koen De Reu
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090 Melle, Belgium.
| | - Marc Heyndrickx
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090 Melle, Belgium.
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - Lieven De Zutter
- Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
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Seliwiorstow T, Baré J, Verhaegen B, Uyttendaele M, de Zutter L. Evaluation of a new chromogenic medium for direct enumeration of Campylobacter in poultry meat samples. J Food Prot 2014; 77:2111-4. [PMID: 25474058 DOI: 10.4315/0362-028x.jfp-14-237] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The present study was conducted to compare Campylobacter counts obtained by three selective media: modified charcoal cefoperazonedeoxycholate agar (mCCDA), Campy Food agar (CFA), and a novel agar RAPID' Campylobacter agar. Analysis of 12 artificially and 36 naturally contaminated samples indicated no significant differences in Campylobacter counts obtained with all three selective media. Lin's concordance correlation coefficient (CCC) and the Bland-Altman plot revealed a high level of agreement between Campylobacter counts when evaluating RAPID versus mCCDA and CFA plates. RAPID agar was the only medium tested that could effectively suppress the growth of the background microflora with naturally contaminated samples. Results of this study clearly indicated that RAPID agar is highly selective without loss of sensitivity for recovering Campylobacter. Results obtained are in agreement with those for other commonly used media; therefore, RAPID medium is suitable for Campylobacter enumeration in poultry meat samples.
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Affiliation(s)
- Tomasz Seliwiorstow
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - Julie Baré
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Bavo Verhaegen
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Mieke Uyttendaele
- Department of Food Safety and Food Quality, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Lieven de Zutter
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
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Elhadidy M, Elkhatib WF, Elfadl EAA, Verstraete K, Denayer S, Barbau-Piednoir E, De Zutter L, Verhaegen B, De Rauw K, Piérard D, De Reu K, Heyndrickx M. Genetic diversity of Shiga toxin-producing Escherichia coli O157 : H7 recovered from human and food sources. Microbiology (Reading) 2014; 161:112-119. [PMID: 25411313 DOI: 10.1099/mic.0.083063-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The aim of this study was to identify an epidemiological association between Shiga toxin-producing Escherichia coli O157 : H7 strains associated with human infection and with food sources. Frequency distributions of different genetic markers of E. coli O157 : H7 strains recovered from human and food sources were compared using molecular assays to identify E. coli O157 : H7 genotypes associated with variation in pathogenic potential and host specificity. Genotypic characterization included: lineage-specific polymorphism assay (LSPA-6), clade typing, tir (A255T) polymorphism, Shiga toxin-encoding bacteriophage insertion site analysis and variant analysis of Shiga toxin 2 gene (stx2a and stx2c) and antiterminator Q genes (Q933 and Q21). The intermediate lineage (LI/II) dominated among both food and human strains. Compared to other clades, clades 7 and 8 were more frequent among food and human strains, respectively. The tir (255T) polymorphism occurred more frequently among human strains than food strains. Q21 and Q933 + Q21 were found at significantly higher frequencies among food and human strains, respectively. Moreover, stx2a and stx2a+c were detected at significantly higher frequencies among human strains compared to food strains. Bivariate analysis revealed significant concordance (P<0.05) between the LSPA-6 assay and the other typing methods. Multivariable regression analysis suggested that tir (255T) was the most distinctive genotype that can be used to detect bacterial clones with potential risk for human illness from food sources. This study supported previous reports of the existence of diversity in genetic markers among different isolation sources by including E. coli O157 : H7 strains from both food and human sources. This might enable tracking genotypes with potential risk for human illness from food sources.
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Affiliation(s)
- Mohamed Elhadidy
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Walid F Elkhatib
- Department of Pharmacy Practice, School of Pharmacy, Hampton University, Kittrell Hall Hampton, VA 23668, USA.,Department of Microbiology & Immunology, Faculty of Pharmacy, Ain Shams University, African Union Organization St Abbassia, Cairo 11566, Egypt
| | - Eman A Abo Elfadl
- Department of Animal Husbandry and Development of Animal Wealth, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Karen Verstraete
- Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, Melle 9090, Belgium
| | - Sarah Denayer
- Foodborne Pathogens, Scientific Institute of Public Health, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Elodie Barbau-Piednoir
- Foodborne Pathogens, Scientific Institute of Public Health, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Lieven De Zutter
- Department of Veterinary Public Health and Food Safety, Ghent University, Salisburylaan 133, Merelbeke 9820, Belgium
| | - Bavo Verhaegen
- Department of Veterinary Public Health and Food Safety, Ghent University, Salisburylaan 133, Merelbeke 9820, Belgium.,Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, Melle 9090, Belgium
| | - Klara De Rauw
- UZ Brussels, Department of Microbiology, Belgian VTEC Reference Lab, Laarbeeklaan 101 - 1090 Brussels, Belgium
| | - Denis Piérard
- UZ Brussels, Department of Microbiology, Belgian VTEC Reference Lab, Laarbeeklaan 101 - 1090 Brussels, Belgium
| | - Koen De Reu
- Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, Melle 9090, Belgium
| | - Marc Heyndrickx
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Salisburylaan 133, Merelbeke 9820, Belgium.,Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, Melle 9090, Belgium
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Verhaegen B, Rekecki A, Decostere A, Van den Broeck W. Knelpunten in aquacultuur: enkele risicovolle aspecten van de vroege levensstadia van de vis. VLAAMS DIERGEN TIJDS 2012. [DOI: 10.21825/vdt.v81i2.18359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aquacultuur is een zeer snel groeiende sector, maar er zijn nog talrijke knelpunten bij het opkweken van larven (larvicultuur) en van adulte vissen. Veel van deze knelpunten zijn van nutritionele aard. Het voedingsregime is nog vaak onvoldoende afgesteld op de behoeften van specifieke vissoorten waardoor uithongering een grote invloed blijft hebben. Deze problemen kunnen opgelost worden door de ontwikkeling van het gastro-intestinale stelsel per vissoort in kaart te brengen. Parameters, zoals de enterocytenhoogte, de aanwezigheid van supranucleaire vacuoles in de enterocyten en ‘the point of no return’ kunnen als maatstaf gebruikt worden om uithongering te monitoren en te voorkomen. Aan de hand van deze gegevens kan een optimaal voedingsregime met rotiferen (radardiertjes), Artemia (pekelkreeftjes) en Copepoda (eenoogkreeftjes) uitgewerkt worden.
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Vekemans M, Verhaegen B. [Survey of the number of voluntary pregnancy interruptions practiced in Belgium in 1985]. Rev Med Brux 1987; 8:21-5. [PMID: 3563180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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