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Cohen PA, Jacobs B, Van Hoorde K, Vanhee C. Accuracy of Labeling of Galantamine Generic Drugs and Dietary Supplements. JAMA 2024; 331:974-976. [PMID: 38393714 PMCID: PMC10951731 DOI: 10.1001/jama.2024.0328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/10/2024] [Indexed: 02/25/2024]
Abstract
This study examines the accuracy of labeling for galantamine products formulated as both generic drugs and dietary supplements, as well as tests for contamination with microorganisms.
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Affiliation(s)
- Pieter A. Cohen
- Department of Medicine, Cambridge Health Alliance, Somerville, Massachusetts
| | - Bram Jacobs
- Department of Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | | | - Céline Vanhee
- Department of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
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2
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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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3
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Vanhee C, Jacobs B, Kamugisha A, Canfyn M, Van Der Meersch H, Ceyssens B, Deconinck E, Van Hoorde K, Willocx M. Substandard and falsified ivermectin tablets obtained for self-medication during the COVID-19 pandemic as a source of potential harm. Drug Test Anal 2023. [PMID: 38043940 DOI: 10.1002/dta.3618] [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: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 12/05/2023]
Abstract
In 2019, a global viral pandemic, due to the SARS-CoV-2 virus, broke out. Soon after, the search for a vaccine and/or antiviral medicine began. One of the candidate antiviral medicines tested was ivermectin. Although several health authorities warned the public against the use of this medicine outside clinical trials, the drug was widely used at the end of 2020 and in 2021. Simultaneously, several reports started to emerge demonstrating serious adverse effects after self-medicating with ivermectin. It stands to reason that the self-administration of substandard or falsified (SF) medicines bearing harmful quality deficiencies have contributed to this phenomenon. In order to have a better view on the nature of these harmful quality deficiencies, SF ivermectin samples, intercepted in large quantities by the Belgian regulatory agencies during the period 2021-2022, were analyzed in our official medicines control laboratory. None of the samples (n = 19) were compliant to the quality criteria applicable to medicinal products. These SF products either suffered from a systematic underdosing of the active pharmaceutical ingredient or were severely contaminated with bacteria, two of which were contaminated with known pathogens that cause gastrointestinal illness upon oral intake. In addition to the direct risks of self-medicating with such a product, the improper usage and dosage of ivermectin medication might also facilitate ivermectin tolerance or resistance in parasites. This may have detrimental consequences on a global scale, certainly as the number of newly developed active pharmaceutical ingredients that can safely be used to combat parasites is rather scarce.
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Affiliation(s)
- Celine Vanhee
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
| | - Bram Jacobs
- Service of Foodborne Pathogen, Scientific Direction of Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Angélique Kamugisha
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
| | - Michael Canfyn
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
| | | | - Bart Ceyssens
- Federal Agency for Medicine and Health Care Products, Brussels, Belgium
| | - Eric Deconinck
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
| | - Koenraad Van Hoorde
- Service of Foodborne Pathogen, Scientific Direction of Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Marie Willocx
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, 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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Bogaerts B, Fraiture MA, Huwaert A, Van Nieuwenhuysen T, Jacobs B, Van Hoorde K, De Keersmaecker SCJ, Roosens NHC, Vanneste K. Retrospective surveillance of viable Bacillus cereus group contaminations in commercial food and feed vitamin B 2 products sold on the Belgian market using whole-genome sequencing. Front Microbiol 2023; 14:1173594. [PMID: 37415815 PMCID: PMC10321352 DOI: 10.3389/fmicb.2023.1173594] [Citation(s) in RCA: 1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/01/2023] [Indexed: 07/08/2023] Open
Abstract
Bacillus cereus is a spore-forming bacterium that occurs as a contaminant in food and feed, occasionally resulting in food poisoning through the production of various toxins. In this study, we retrospectively characterized viable B. cereus sensu lato (s.l.) isolates originating from commercial vitamin B2 feed and food additives collected between 2016 and 2022 by the Belgian Federal Agency for the Safety of the Food Chain from products sold on the Belgian market. In total, 75 collected product samples were cultured on a general medium and, in case of bacterial growth, two isolates per product sample were collected and characterized using whole-genome sequencing (WGS) and subsequently characterized in terms of sequence type (ST), virulence gene profile, antimicrobial resistance (AMR) gene profile, plasmid content, and phylogenomic relationships. Viable B. cereus was identified in 18 of the 75 (24%) tested products, resulting in 36 WGS datasets, which were classified into eleven different STs, with ST165 (n = 10) and ST32 (n = 8) being the most common. All isolates carried multiple genes encoding virulence factors, including cytotoxin K-2 (52.78%) and cereulide (22.22%). Most isolates were predicted to be resistant to beta-lactam antibiotics (100%) and fosfomycin (88.89%), and a subset was predicted to be resistant to streptothricin (30.56%). Phylogenomic analysis revealed that some isolates obtained from different products were closely related or even identical indicating a likely common origin, whereas for some products the two isolates obtained did not show any close relationship to each other or other isolates found in other products. This study reveals that potentially pathogenic and drug-resistant B. cereus s.l. can be present in food and feed vitamin B2 additives that are commercially available, and that more research is warranted to assess whether their presence in these types of products poses a threat to consumers.
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Affiliation(s)
- Bert Bogaerts
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | - Bram Jacobs
- Foodborne Pathogens, Sciensano, Brussels, Belgium
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | | | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, 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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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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Boogaerts T, Van den Bogaert S, Van Poelvoorde LAE, El Masri D, De Roeck N, Roosens NHC, Lesenfants M, Lahousse L, Van Hoorde K, van Nuijs ALN, Delputte P. Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. Viruses 2022; 14:610. [PMID: 35337017 PMCID: PMC8953730 DOI: 10.3390/v14030610] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 02/08/2022] [Revised: 02/24/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
Since the beginning of the COVID-19 pandemic, the wastewater-based epidemiology (WBE) of SARS-CoV-2 has been used as a complementary indicator to follow up on the trends in the COVID-19 spread in Belgium and in many other countries. To further develop the use of WBE, a multiplex digital polymerase chain reaction (dPCR) assay was optimized, validated and applied for the measurement of emerging SARS-CoV-2 variants of concern (VOC) in influent wastewater (IWW) samples. Key mutations were targeted in the different VOC strains, including SΔ69/70 deletion, N501Y, SΔ241 and SΔ157. The presented bioanalytical method was able to distinguish between SARS-CoV-2 RNA originating from the wild-type and B.1.1.7, B.1.351 and B.1.617.2 variants. The dPCR assay proved to be sensitive enough to detect low concentrations of SARS-CoV-2 RNA in IWW since the limit of detection of the different targets ranged between 0.3 and 2.9 copies/µL. This developed WBE approach was applied to IWW samples originating from different Belgian locations and was able to monitor spatio-temporal changes in the presence of targeted VOC strains in the investigated communities. The present dPCR assay developments were realized to bring added-value to the current national WBE of COVID-19 by also having the spatio-temporal proportions of the VoC in presence in the wastewaters.
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Affiliation(s)
- Tim Boogaerts
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium;
| | - Siel Van den Bogaert
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (D.E.M.); (N.D.R.); (P.D.)
| | - Laura A. E. Van Poelvoorde
- Scientific Directorate of Biological Health Risks, Service Transerversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (L.A.E.V.P.); (N.H.C.R.)
| | - Diala El Masri
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (D.E.M.); (N.D.R.); (P.D.)
| | - Naomi De Roeck
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (D.E.M.); (N.D.R.); (P.D.)
| | - Nancy H. C. Roosens
- Scientific Directorate of Biological Health Risks, Service Transerversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (L.A.E.V.P.); (N.H.C.R.)
| | - Marie Lesenfants
- Scientific Directorate of Epidemiology and Public Health, Service Epidemiology of Infectious Diseases, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium;
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium;
| | - Koenraad Van Hoorde
- Scientific Directorate of Infectious Diseases in Humans, Service Foodborne Pathogens, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium;
| | | | - Peter Delputte
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (D.E.M.); (N.D.R.); (P.D.)
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9
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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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10
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Ceyssens PJ, Van den Bossche A, Phan LK, Van Hoorde K, Mattheus W. A molecular assay for rapidly distinguishing the AviPro SALMONELLA VAC T vaccine strain from wild-type field isolates. J Microbiol Methods 2021; 184:106190. [PMID: 33766608 DOI: 10.1016/j.mimet.2021.106190] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 11/17/2022]
Abstract
Rapid differentiation of the AviPro Salmonella VAC T strain from wild-type Salmonella ser. Typhimurium isolates is essential for the monitoring of veterinary isolates and targeted control actions. The distinction between the two strain types is routinely made by phenotypic antimicrobial resistance testing, but this sometime leads to ambiguous results with major economic implications. In this study, we used whole-genome sequencing to identify conserved and specific mutations in resistance and virulence genes which enable to distinguish field and vaccine strains. Based on this information, we developed and validated (n = 199) a Luminex-based assay targeting seven specific single-nucleotide polymorphisms. This molecular test is able to distinguish both Salmonella ser. Typhimurium types with 100% sensitivity and specificity within one working day.
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Affiliation(s)
| | | | - Lac Kim Phan
- Unit of Human Bacterial Diseases, Sciensano, Belgium
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11
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Biondi L, Randazzo CL, Russo N, Pino A, Natalello A, Van Hoorde K, Caggia C. Dietary Supplementation of Tannin-Extracts to Lambs: Effects on Meat Fatty Acids Composition and Stability and on Microbial Characteristics. Foods 2019; 8:E469. [PMID: 31658772 PMCID: PMC6836261 DOI: 10.3390/foods8100469] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 09/09/2019] [Revised: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 12/18/2022] Open
Abstract
Two extracts derived from plant material rich in hydrolysable (Tara, T; Caesalpinia spinosa) or condensed (Mimosa, M; Acacia mearnsii) tannins were added to lamb's diet and their effects on meat quality and on microbial population were evaluated; a diet without tannins represented the Control (C). Meat pH, vitamin E, intramuscular fat content and muscle fatty acid composition were determined. Oxidative stability and microbiological analyses were performed on meat samples after 0, 4 and 7 days of refrigerated storage. Psychrotrophic bacteria were identified through MALDI-TOF MS analysis. Regarding meat fatty acids, Tara treatment decreased the percentage of monounsaturated fatty acids. The counts of all microbial groups were similar among dietary treatments at day 0, while a significant reduction of microbial loads was observed in T-group at day 7. Pseudomonas fluorescens group count was significantly affected by T extract supplementation. The MALDI-TOF MS identification revealed the dominance of Pseudomonas fragi species in all samples while Pseudomonas lundensis, Brochothrix thermosphacta and Candida famata were revealed only in control ones. In conclusions, the tannin extract supplementation is a promising dietary strategy to preserve lamb meat quality.
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Affiliation(s)
- Luisa Biondi
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy.
| | - Cinzia L Randazzo
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy.
| | - Nunziatina Russo
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy.
| | - Alessandra Pino
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy.
| | - Antonio Natalello
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy.
| | - Koenraad Van Hoorde
- Service Foodborne Pathogens, Sciensano, B-1050 Brussels, Belgium.
- Faculty of Bioscience Engineering, Department of Biotechnology, Laboratory of Brewing Science and Technology, Ghent University, B-9000 Ghent, Belgium.
| | - Cinzia Caggia
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy.
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12
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13
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Pino A, Russo N, Van Hoorde K, De Angelis M, Sferrazzo G, Randazzo CL, Caggia C. Piacentinu Ennese PDO Cheese as Reservoir of Promising Probiotic Bacteria. Microorganisms 2019; 7:E254. [PMID: 31408976 PMCID: PMC6723934 DOI: 10.3390/microorganisms7080254] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 07/12/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 01/17/2023] Open
Abstract
Piacentinu Ennese is a protected designation of origin (PDO) cheese produced in the surrounding area of Enna (Sicily, Italy), using raw ewe's milk without the addition of any starter cultures. In the present study, the Lactobacillus population of Piacentinu Ennese PDO cheese was in vitro screened in order to select promising probiotic strains to be further used in humans. One hundred and sixty-nine lactic acid bacteria (LAB) were isolated from 90 days ripened cheeses and identified by Rep-PCR genomic fingerprinting, using the (GTG)5-primer, and by MALDI-TOF MS. One hundred and thirteen (113) isolates belonging to QPS-list species were characterized for both safety and functional properties. All tested isolates were considered safe because none showed either gelatinase, DNase, mucinase, or hemolytic activity. Tolerance to lysozyme, bile salts, and acidic conditions, along with ability to survive under simulated gastrointestinal digestion, were observed. In addition, based on antimicrobial activity against pathogens, cell surface characteristics, Caco-2 adhesion abilities, and anti-inflammatory potential, it was possible to confirm the strain-dependent functional aptitude, suggesting that Piacentinu Ennese PDO cheese may be considered a precious source of probiotic candidates.
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Affiliation(s)
- Alessandra Pino
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy
| | - Nunziatina Russo
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy
| | - Koenraad Van Hoorde
- Department of Biotechnology, Laboratory of Brewing Science and Technology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Giuseppe Sferrazzo
- Department of Drug Sciences, Section of Biochemistry, University of Catania, 95125 Catania, Italy
| | - Cinzia Lucia Randazzo
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy.
| | - Cinzia Caggia
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy
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14
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Pino A, De Angelis M, Todaro A, Van Hoorde K, Randazzo CL, Caggia C. Fermentation of Nocellara Etnea Table Olives by Functional Starter Cultures at Different Low Salt Concentrations. Front Microbiol 2018; 9:1125. [PMID: 29922251 PMCID: PMC5996112 DOI: 10.3389/fmicb.2018.01125] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 12/21/2017] [Accepted: 05/14/2018] [Indexed: 11/13/2022] Open
Abstract
Nocellara Etnea is one of the main Sicilian cultivars traditionally used to produce both olive oil and naturally fermented table olives. In the present study, the effect of different salt concentrations on physico-chemical, microbiological, sensorial, and volatile organic compounds (VOCs) formation was evaluated in order to obtain functional Nocellara Etnea table olives. The experimental design consisted of 8 treatments as follow: fermentations at 4, 5, 6, and 8% of salt with (E1-E4 samples) and without (C1-C4 samples) the addition of starters. All the trials were carried out at room temperature (18 ± 2°C) and monitored for an overall period of 120 d. In addition, the persistence of the potential probiotic Lactobacillus paracasei N24 at the end of the process was investigated. Microbiological data revealed the dominance of lactic acid bacteria (LAB), starting from the 7th d of fermentation, and the reduction of yeasts and enterobacteria in the final product inoculated with starters. VOCs profile highlighted a high amount of aldehydes at the beginning of fermentation, which significantly decreased through the process and a concomitant increase of alcohols, acids, esters, and phenols. In particular, esters showed an occurrence percentage higher in experimental samples rather than in control ones, contributing to more pleasant flavors. Moreover, acetic acid, ethanol, and phenols, which often generate off-flavors, were negatively correlated with mesophilic bacteria and LAB. It is interesting to note that salt content did not affect the performances of starter cultures and slightly influenced the metabolome of table olives. Sensory data demonstrated significant differences among samples registering the highest overall acceptability in the experimental sample at 5% of NaCl. The persistence of the L. paracasei N24 strain in experimental samples, at the end of the process, revealed its promising perspectives as starter culture for the production of functional table olives with reduced salt content.
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Affiliation(s)
- Alessandra Pino
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Aldo Todaro
- Department of Agricultural, Food and Forest Science, University of Palermo, Palermo, Italy
| | - Koenraad Van Hoorde
- Laboratory of Brewing and Biochemistry, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Cinzia L. Randazzo
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy
| | - Cinzia Caggia
- Department of Agricultural, Food and Environment, University of Catania, Catania, Italy
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15
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Pino A, Van Hoorde K, Pitino I, Russo N, Carpino S, Caggia C, Randazzo CL. Survival of potential probiotic lactobacilli used as adjunct cultures on Pecorino Siciliano cheese ripening and passage through the gastrointestinal tract of healthy volunteers. Int J Food Microbiol 2017; 252:42-52. [PMID: 28458191 DOI: 10.1016/j.ijfoodmicro.2017.04.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 08/04/2016] [Revised: 03/02/2017] [Accepted: 04/20/2017] [Indexed: 12/01/2022]
Abstract
In the present study, two lactobacilli strains, Lactobacillus rhamnosus H25 and Lactobacillus paracasei N24, used as adjunct cultures, were evaluated for their heat resistance both with and without prior heat adaptation and for their survival, at industrial scale, during the production and ripening of the Pecorino Siciliano cheese. In addition, the viability and persistence of the lactobacilli strains after passage through the gastrointestinal tract of healthy volunteers were evaluated by using rep-PCR analysis of viable cells. Both strains exhibited good heat resistance and survival throughout cheese production and ripening, and positively influenced the physico-chemical, the microbiological and the sensorial characteristics of the final product. In addition, the molecular typing of the lactobacilli isolates, retrieved from fecal samples of healthy volunteers during and after 15 days of the experimental cheese administration, revealed a high survival of the strains, highlighting their persistence during passage into the GI tract. In conclusion, this study proposes the two adjunct cultures as potential probiotic candidate deliverable by cheese.
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Affiliation(s)
- Alessandra Pino
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Santa Sofia 98, 95123 Catania, Italy
| | - Koenraad Van Hoorde
- Laboratory of Brewing and Biochemistry, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, 9000 Gent, Belgium
| | - Iole Pitino
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Santa Sofia 98, 95123 Catania, Italy
| | - Nunziatina Russo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Santa Sofia 98, 95123 Catania, Italy
| | - Stefania Carpino
- CoRFiLaC, Regione Siciliana, S.P. 25 Km 5 Ragusa Mare, 97100 Ragusa, Italy
| | - Cinzia Caggia
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Santa Sofia 98, 95123 Catania, Italy.
| | - Cinzia L Randazzo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Santa Sofia 98, 95123 Catania, Italy
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16
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Hamet MF, Londero A, Medrano M, Vercammen E, Van Hoorde K, Garrote GL, Huys G, Vandamme P, Abraham AG. Application of culture-dependent and culture-independent methods for the identification of Lactobacillus kefiranofaciens in microbial consortia present in kefir grains. Food Microbiol 2013; 36:327-34. [DOI: 10.1016/j.fm.2013.06.022] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 06/11/2013] [Accepted: 06/29/2013] [Indexed: 01/28/2023]
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17
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De Bel A, Van Hoorde K, Wybo I, Vandoorslaer K, Echahidi F, De Brandt E, Schumann P, Ieven M, Soetens O, Piérard D, Vandamme P. Staphylococcus
jettensis sp. nov., a coagulase-negative staphylococcal species isolated from human clinical specimens. Int J Syst Evol Microbiol 2013; 63:3250-3256. [DOI: 10.1099/ijs.0.044438-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eight coagulase-negative, novobiocin-susceptible staphylococcal strains were isolated from human clinical specimens at two different Belgian medical facilities. All strains were non-motile, Gram-stain-positive, catalase-positive cocci. DNA G+C content, peptidoglycan type, menaquinone pattern, the presence of teichoic acid and cellular fatty acid composition were in agreement with the characteristics of species of the genus
Staphylococcus
. Sequencing of the 16S rRNA gene and four housekeeping genes (dnaJ, tuf, gap and rpoB) demonstrated that these strains constitute a separate taxon within the genus
Staphylococcus
. Less than 41 % DNA–DNA hybridization with the most closely related species of the genus
Staphylococcus
(
Staphylococcus haemolyticus
,
Staphylococcus hominis
and
Staphlococcus lugdunensis
) was observed. Key biochemical characteristics that allowed these bacteria to be distinguished from their nearest phylogenetic neighbours are arginine dihydrolase positivity, ornithine decarboxylase negativity and inability to produce acid aerobically from d-mannose, α-lactose and turanose. Acid is produced aerobically from trehalose. Based on these results, a novel species of the genus
Staphylococcus
is described and named
Staphylococcus
jettensis sp. nov. The type strain is SEQ110T ( = LMG 26879T = CCUG 62657T = DSM 26618T).
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Affiliation(s)
- Annelies De Bel
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Koenraad Van Hoorde
- Faculty of Applied Bioscience Engineering, University College Ghent, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Fedoua Echahidi
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Evie De Brandt
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Braunschweig, Germany
| | - Margareta Ieven
- Laboratory of Microbiology, Universitair Ziekenhuis Antwerpen, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Oriane Soetens
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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18
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Nguyen DTL, Cnockaert M, Van Hoorde K, De Brandt E, Snauwaert I, Snauwaert C, De Vuyst L, Le BT, Vandamme P. Lactobacillus porcinae sp. nov., isolated from traditional Vietnamese nem chua. Int J Syst Evol Microbiol 2013; 63:1754-1759. [DOI: 10.1099/ijs.0.044123-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A species diversity study of lactic acid bacteria occurring in traditional Vietnamese nem chua yielded an isolate, LMG 26767T, that could not be assigned to a species with a validly published name. The isolate was initially investigated by 16S rRNA gene sequence analysis, which revealed that it belonged to the genus
Lactobacillus
, with
Lactobacillus manihotivorans
and
Lactobacillus camelliae
as the closest relatives (98.9 % and 96.9 % gene sequence similarity to the type strains, respectively). Comparative (GTG)5-PCR genomic fingerprinting confirmed the unique taxonomic status of the novel strain. DNA–DNA hybridization experiments, DNA G+C content determination, sequence analysis of the phenylalanyl-tRNA synthase (pheS) gene, and physiological and biochemical characterization demonstrated that strain LMG 26767T represents a novel species, for which the name Lactobacillus porcinae sp. nov. is proposed; the type strain is LMG 26767T ( = CCUG 62266T). Biochemically, L. porcinae can be distinguished from
L. manihotivorans
and
L. camelliae
by its carbohydrate fermentation profile, absence of growth at 45 °C, and production of d- and l-lactate as end products of glucose metabolism.
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Affiliation(s)
- Doan Thi Lam Nguyen
- Department of Biochemistry and Food Biotechnology, Faculty of Food Science and Technology, Hanoi University of Agriculture, Trauquy – Gialam, Hanoi, Vietnam
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Gent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Gent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Koenraad Van Hoorde
- Faculty of Applied Bioscience Engineering, University College Gent, Schoonmeersstraat 52, 9000 Gent, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Gent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Evie De Brandt
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Gent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Isabel Snauwaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Gent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Cindy Snauwaert
- BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Gent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Binh Thanh Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Gent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
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19
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Nguyen DTL, Van Hoorde K, Cnockaert M, De Brandt E, Aerts M, Binh Thanh L, Vandamme P. A description of the lactic acid bacteria microbiota associated with the production of traditional fermented vegetables in Vietnam. Int J Food Microbiol 2013; 163:19-27. [DOI: 10.1016/j.ijfoodmicro.2013.01.024] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 12/11/2012] [Accepted: 01/22/2013] [Indexed: 11/28/2022]
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20
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Nguyen DTL, Van Hoorde K, Cnockaert M, De Brandt E, De Bruyne K, Le BT, Vandamme P. A culture-dependent and -independent approach for the identification of lactic acid bacteria associated with the production of nem chua, a Vietnamese fermented meat product. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.09.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Hoefman S, Van Hoorde K, Boon N, Vandamme P, De Vos P, Heylen K. Survival or revival: long-term preservation induces a reversible viable but non-culturable state in methane-oxidizing bacteria. PLoS One 2012; 7:e34196. [PMID: 22539945 PMCID: PMC3335116 DOI: 10.1371/journal.pone.0034196] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 02/23/2012] [Indexed: 11/18/2022] Open
Abstract
Knowledge on long-term preservation of micro-organisms is limited and research in the field is scarce despite its importance for microbial biodiversity and biotechnological innovation. Preservation of fastidious organisms such as methane-oxidizing bacteria (MOB) has proven difficult. Most MOB do not survive lyophilization and only some can be cryopreserved successfully for short periods. A large-scale study was designed for a diverse set of MOB applying fifteen cryopreservation or lyophilization conditions. After three, six and twelve months of preservation, the viability (via live-dead flow cytometry) and culturability (via most-probable number analysis and plating) of the cells were assessed. All strains could be cryopreserved without a significant loss in culturability using 1% trehalose in 10-fold diluted TSB (TT) as preservation medium and 5% DMSO as cryoprotectant. Several other cryopreservation and lyophilization conditions, all of which involved the use of TT medium, also allowed successful preservation but showed a considerable loss in culturability. We demonstrate here that most of these non-culturables survived preservation according to viability assessment indicating that preservation induces a viable but non-culturable (VBNC) state in a significant fraction of cells. Since this state is reversible, these findings have major implications shifting the emphasis from survival to revival of cells in a preservation protocol. We showed that MOB cells could be significantly resuscitated from the VBNC state using the TT preservation medium.
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Affiliation(s)
- Sven Hoefman
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Koenraad Van Hoorde
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- Faculty of Applied Bioscience Engineering, University College Ghent, Gent, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology, Ghent University, Gent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Paul De Vos
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- BCCM/LMG Bacteria Collection, Gent, Belgium
| | - Kim Heylen
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
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22
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Zaluga J, Heylen K, Van Hoorde K, Hoste B, Van Vaerenbergh J, Maes M, De Vos P. GyrB sequence analysis and MALDI-TOF MS as identification tools for plant pathogenic Clavibacter. Syst Appl Microbiol 2011; 34:400-7. [PMID: 21802235 DOI: 10.1016/j.syapm.2011.05.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 05/02/2011] [Accepted: 05/06/2011] [Indexed: 11/30/2022]
Abstract
The bacterial genus Clavibacter has only one species, Clavibacter michiganensis, containing five subspecies. All five are plant pathogens, among which three are recognized as quarantine pests (mentioned on the EPPO A2 list). Prevention of their introduction and epidemic outbreaks requires a reliable and accurate identification. Currently, identification of these bacteria is time consuming and often problematic, mainly because of cross-reactions with other plant-associated bacteria in immunological tests and false-negative results in PCR detection methods. Furthermore, distinguishing closely related subspecies is not straightforward. This study aimed at evaluating the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and a fragment of the gyrB sequence for the reliable and fast identification of the Clavibacter subspecies. Amplification and sequencing of gyrB using a single primer set had sufficient resolution and specificity to identify each subspecies based on both sequence similarities in cluster analyses and specific signatures within the sequences. All five subspecies also generated distinct and reproducible MALDI-TOF MS profiles, with unique and specific ion peaks for each subspecies, which could be used as biomarkers for identification. Results from both methods were in agreement and were able to distinguish the five Clavibacter subspecies from each other and from representatives of closely related Rathayibacter, Leifsonia or Curtobacterium species. Our study suggests that proteomic analysis using MALDI-TOF MS and gyrB sequence are powerful diagnostic tools for the accurate identification of Clavibacter plant pathogens.
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Affiliation(s)
- Joanna Zaluga
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
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23
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Ghyselinck J, Van Hoorde K, Hoste B, Heylen K, De Vos P. Evaluation of MALDI-TOF MS as a tool for high-throughput dereplication. J Microbiol Methods 2011; 86:327-36. [PMID: 21699925 DOI: 10.1016/j.mimet.2011.06.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 05/31/2011] [Accepted: 06/05/2011] [Indexed: 10/18/2022]
Abstract
The present study examined the suitability of matrix assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for the rapid grouping of bacterial isolates, i.e. dereplication. Dereplication is important in large-scale isolation campaigns and screening programs since it can significantly reduce labor intensity, time and costs in further downstream analyses. Still, current dereplication techniques are time consuming and costly. MALDI-TOF MS is an attractive tool since it performs fast and cheap analyses with the potential of automation. However, its taxonomic resolution for a broad diversity of bacteria remains largely unknown. To verify the suitability of MALDI-TOF MS for dereplication, a total of 249 unidentified bacterial isolates retrieved from the rhizosphere of potato plants, were analyzed with both MALDI-TOF MS and repetitive element sequence based polymerase chain reaction (rep-PCR). The latter technique was used as a benchmark. Cluster analysis and inspection of the profiles showed that for 204 isolates (82%) the taxonomic resolution of both techniques was comparable, while for 45 isolates (18%) one of both techniques had a higher taxonomic resolution. Additionally, 16S rRNA gene sequence analysis was performed on all members of each delineated cluster to gain insight in the identity and sequence similarity between members in each cluster. MALDI-TOF MS proved to have higher reproducibility than rep-PCR and seemed to be more promising with respect to high-throughput analyses, automation, and time and cost efficiency. Its taxonomic resolution was situated at the species to strain level. The present study demonstrated that MALDI-TOF MS is a powerful tool for dereplication.
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Affiliation(s)
- Jonas Ghyselinck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium.
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De Jonghe V, Coorevits A, Van Hoorde K, Messens W, Van Landschoot A, De Vos P, Heyndrickx M. Influence of storage conditions on the growth of Pseudomonas species in refrigerated raw milk. Appl Environ Microbiol 2011; 77:460-70. [PMID: 21115713 PMCID: PMC3020527 DOI: 10.1128/aem.00521-10] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 10/31/2010] [Indexed: 11/20/2022] Open
Abstract
The refrigerated storage of raw milk throughout the dairy chain prior to heat treatment creates selective conditions for growth of psychrotolerant bacteria. These bacteria, mainly belonging to the genus Pseudomonas, are capable of producing thermoresistant extracellular proteases and lipases, which can cause spoilage and structural defects in pasteurized and ultra-high-temperature-treated milk (products). To map the influence of refrigerated storage on the growth of these pseudomonads, milk samples were taken after the first milking turn and incubated laboratory scale at temperatures simulating optimal and suboptimal preprocessing storage conditions. The outgrowth of Pseudomonas members was monitored over time by means of cultivation-independent denaturing gradient gel electrophoresis (DGGE). Isolates were identified by a polyphasic approach. These incubations revealed that outgrowth of Pseudomonas members occurred from the beginning of the dairy chain (farm tank) under both optimal and suboptimal storage conditions. An even greater risk for outgrowth, as indicated by a vast increase of about 2 log CFU per ml raw milk, existed downstream in the chain, especially when raw milk was stored under suboptimal conditions. This difference in Pseudomonas outgrowth between optimal and suboptimal storage was already statistically significant within the farm tank. The predominant taxa were identified as Pseudomonas gessardii, Pseudomonas gessardii-like, Pseudomonas fluorescens-like, Pseudomonas lundensis, Pseudomonas fragi, and Pseudomonas fragi-like. Those taxa show an important spoilage potential as determined on elective media for proteolysis and lipolysis.
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Affiliation(s)
- Valerie De Jonghe
- Institute for Agricultural and Fisheries Research (ILVO), Technology & Food Science Unit, Brusselsesteenweg 370, 9090 Melle, Belgium.
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Van Hoorde K, Heyndrickx M, Vandamme P, Huys G. Influence of pasteurization, brining conditions and production environment on the microbiota of artisan Gouda-type cheeses. Food Microbiol 2010; 27:425-33. [DOI: 10.1016/j.fm.2009.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 12/03/2009] [Accepted: 12/04/2009] [Indexed: 11/17/2022]
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Van Hoorde K, Vandamme P, Huys G. Molecular identification and typing of lactic acid bacteria associated with the production of two artisanal raw milk cheeses. ACTA ACUST UNITED AC 2008. [DOI: 10.1051/dst:2008011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Van Hoorde K, Verstraete T, Vandamme P, Huys G. Diversity of lactic acid bacteria in two Flemish artisan raw milk Gouda-type cheeses. Food Microbiol 2008; 25:929-35. [PMID: 18721684 DOI: 10.1016/j.fm.2008.06.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 06/18/2008] [Accepted: 06/19/2008] [Indexed: 10/21/2022]
Abstract
PCR-denaturing gradient gel electrophoresis (PCR-DGGE) was used to study the diversity of lactic acid bacteria (LAB) in two Flemish artisan raw milk Gouda-type cheeses. In parallel, conventional culturing was performed. Isolates were identified using (GTG)(5)-PCR and sequence analysis of 16S rRNA and pheS genes. Discriminant analysis revealed some differences in overall LAB diversity between the two batches and between the two cheeses. Within each batch, the diversity of 8- and 12-week-old cheeses was relatively similar. Conventional isolation mainly revealed the presence of Lactobacillus paracasei, Lactobacillus plantarum, Lactobacillus brevis, Lactobacillus rhamnosus and Pediococcus pentosaceus. PCR-DGGE revealed the presence of three species of which no isolates were recovered, i.e. Enterococcus faecalis, Lactobacillus parabuchneri and Lactobacillus gallinarum. Conversely, not all isolated bacteria were detected by PCR-DGGE. We recommend the integrated use of culture-dependent and -independent approaches to maximally encompass the taxonomic spectrum of LAB occurring in Gouda-type and other cheeses.
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Affiliation(s)
- Koenraad Van Hoorde
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium.
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