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van Kleef-van Koeveringe S, Matheeussen V, Schuermans A, De Koster S, Perales Selva N, Jansens H, De Coninck D, De Bruyne K, Mensaert K, Kluytmans-van den Bergh M, Kluytmans J, Goossens H, Dhaeze W, Leroux-Roels I. Epidemiology and molecular typing of multidrug-resistant bacteria in tertiary hospitals and nursing homes in Flanders, Belgium. Eur J Clin Microbiol Infect Dis 2024; 43:187-194. [PMID: 37971537 PMCID: PMC10774642 DOI: 10.1007/s10096-023-04699-2] [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: 12/14/2022] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
This study aimed to map MDRO carriage and potential transmission within and between three Flemish tertiary care hospitals and their neighbouring nursing homes. A cross-sectional MDRO prevalence survey was organized between October 2017 and February 2019. Perianal swabs were cultured for detection of MDRO. Determination of clonal relatedness based on wgMLST allelic profiles was performed. The prevalence of MDRO in Belgian hospitals and NHs is on the rise, compared to previous studies, and transmission in and between institutions is observed. These results re-emphasize the need for a healthcare network-wide infection prevention strategy in which WGS of MDRO strains can be supportive.
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Affiliation(s)
- Stefanie van Kleef-van Koeveringe
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium.
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium.
| | - Veerle Matheeussen
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Annette Schuermans
- Department of Infection Control and Epidemiology, University Hospital Leuven, Leuven, Belgium
| | - Sien De Koster
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | | | - Hilde Jansens
- Department of Infection Control, University Hospital Antwerp, Edegem, Belgium
| | - Dieter De Coninck
- bioMérieux, Augmented Diagnostics, Industrial Microbiology, Applied Maths NV, Sint-Martens-Latem, Belgium
| | - Katrien De Bruyne
- bioMérieux, Augmented Diagnostics, Industrial Microbiology, Applied Maths NV, Sint-Martens-Latem, Belgium
| | - Klaas Mensaert
- bioMérieux, Augmented Diagnostics, Industrial Microbiology, Applied Maths NV, Sint-Martens-Latem, Belgium
| | - Marjolein Kluytmans-van den Bergh
- Department of Infection Control, Amphia Hospital, Breda, The Netherlands
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
| | - Jan Kluytmans
- Microvida Laboratory for Microbiology, Amphia Hospital, Breda, and Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Herman Goossens
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Wouter Dhaeze
- Department prevention, Agentschap Zorg en Gezondheid, Leuven, Belgium
| | - Isabel Leroux-Roels
- Laboratory of Medical Microbiology, University Hospital Ghent, Ghent, Belgium
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van Kleef – van Koeveringe S, Matheeussen V, Jansens H, Perales Selva N, De Coninck D, De Bruyne K, Mensaert K, Kluytmans - van den Bergh M, Kluytmans J, Goossens H, Dhaeze W. Epidemiology and molecular typing of multidrug-resistant bacteria in day care centres in Flanders, Belgium. Epidemiol Infect 2023; 151:e156. [PMID: 37711023 PMCID: PMC10548538 DOI: 10.1017/s0950268823001528] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/16/2023] Open
Abstract
The global prevalence and spread of multidrug-resistant organisms (MDROs) represent an emerging public health threat. Day care centre (DCC) attendance is a risk factor for MDRO carriage in children and their environment. This study aimed to map the epidemiology of carriage and potential transmission of these organisms within 18 Flemish DDCs (Belgium). An MDRO prevalence survey was organised between November 2018 and February 2019 among children attending the centres. Selective chromogenic culture media were used for the detection of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E), carbapenemase-producing Enterobacterales (CPE), and vancomycin-resistant Enterococci (VRE) in faecal swabs obtained from diapers or jars (n = 448). All isolated MDROs were subjected to resistance gene sequencing. A total of 71 of 448 samples (15.8%) yielded isolates of ESBL-E with a predominance of Escherichia coli (92.2% of ESBL-E) and ESBL resistance gene blaCTX-M-15 (50.7% of ESBL coding genes in E. coli). ESBL-E prevalence varied between DCCs, ranging from 0 to 50%. Transmission, based on the clonal relatedness of ESBL-E strains, was observed. CPE was identified in only one child carrying an E. coli with an OXA-244 gene. VRE was absent from all samples. The observed prevalence of ESBL-E in Flemish DCCs is high compared with previous studies, and our findings re-emphasise the need for rigorous hygiene measures within such centres to control the further spread of MDROs in the community.
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Affiliation(s)
- Stefanie van Kleef – van Koeveringe
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Veerle Matheeussen
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Hilde Jansens
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium
- Department of Infection Control, University Hospital Antwerp, Edegem, Belgium
| | | | - Dieter De Coninck
- bioMérieux, Augmented Diagnostics, Industrial Microbiology, Applied Maths NV, Sint-Martens-Latem, Belgium
| | - Katrien De Bruyne
- bioMérieux, Augmented Diagnostics, Industrial Microbiology, Applied Maths NV, Sint-Martens-Latem, Belgium
| | - Klaas Mensaert
- bioMérieux, Augmented Diagnostics, Industrial Microbiology, Applied Maths NV, Sint-Martens-Latem, Belgium
| | - Marjolein Kluytmans - van den Bergh
- Department of Infection Control, Amphia Hospital, Breda, the Netherlands
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jan Kluytmans
- Microvida Laboratory for Microbiology, Amphia Hospital, Breda, and Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Herman Goossens
- Laboratory of Medical Microbiology, University Hospital Antwerp, Edegem, Belgium
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Wouter Dhaeze
- Department Prevention, Agency for Care and Health, Leuven, Belgium
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De Koster S, Ringenier M, Xavier BB, Lammens C, De Coninck D, De Bruyne K, Mensaert K, Kluytmans-van den Bergh M, Kluytmans J, Dewulf J, Goossens H. Genetic characterization of ESBL-producing and ciprofloxacin-resistant Escherichia coli from Belgian broilers and pigs. Front Microbiol 2023; 14:1150470. [PMID: 37089550 PMCID: PMC10116946 DOI: 10.3389/fmicb.2023.1150470] [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: 01/24/2023] [Accepted: 03/15/2023] [Indexed: 04/08/2023] Open
Abstract
BackgroundThe increasing number of infections caused by Escherichia coli resistant to clinically important antibiotics is a global concern for human and animal health. High overall levels of extended-spectrum beta-lactamase (ESBL)-producing and ciprofloxacin-resistant (ciproR) Escherichia coli in livestock are reported in Belgium. This cross-sectional study aimed to genotypically characterize and trace ESBL-and ciproR-E. coli of Belgian food-producing animals.MethodsA total of 798 fecal samples were collected in a stratified-random sampling design from Belgian broilers and sows. Consequently, 77 ESBL-E. coli and 84 ciproR-E. coli were sequenced using Illumina MiSeq. Minimum inhibitory concentration (MIC) for fluoroquinolones and cephalosporins were determined. Molecular in silico typing, resistance and virulence gene determination, and plasmid identification was performed. Scaffolds harboring ESBL or plasmid-mediated quinolone resistance (PMQR) genes were analyzed to detect mobile genetic elements (MGEs) and plasmid origins. Core genome allelic distances were used to determine genetic relationships among isolates.ResultsA variety of E. coli sequence types (ST) (n = 63), resistance genes and virulence profiles was detected. ST10 was the most frequently encountered ST (8.1%, n = 13). The pandemic multidrug-resistant clone ST131 was not detected. Most farms harbored more than one ESBL type, with blaCTX-M-1 (41.6% of ESBL-E. coli) being the most prevalent and blaCTX M-15 (n = 3) being the least prevalent. PMQR genes (15.5%, n = 13) played a limited role in the occurrence of ciproR-E. coli. More importantly, sequential acquisition of mutations in quinolone resistance-determining regions (QRDR) of gyrA and parC led to increasing MICs for fluoroquinolones. GyrA S83L, D87N and ParC S80I mutations were strongly associated with high-level fluoroquinolone resistance. Genetically related isolates identified within the farms or among different farms highlight transmission of resistant E. coli or the presence of a common reservoir. IncI1-I(alpha) replicon type plasmids carried different ESBL genes (blaCTX-M-1, blaCTX-M-32 and blaTEM-52C). In addition, the detection of plasmid replicons with associated insertion sequence (IS) elements and ESBL/PMQR genes in different farms and among several STs (e.g., IncI1-I(alpha)/IncX3) underline that plasmid transmission could be another important contributor to transmission of resistance in these farms.ConclusionOur findings reveal a multifaceted narrative of transmission pathways. These findings could be relevant in understanding and battling the problem of antibiotic resistance in farms.
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Affiliation(s)
- Sien De Koster
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
| | - Moniek Ringenier
- Veterinary Epidemiology Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Hospital Outbreak Support Team-HOST, ZNA Middelheim, Antwerp, Belgium
- Hospital Outbreak Support Team-HOST, GZA Ziekenhuizen, Wilrijk, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
| | | | | | | | - Marjolein Kluytmans-van den Bergh
- Department of Infection Control, Amphia Hospital, Breda, Netherlands
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, University of Utrecht, CG Utrecht, Netherlands
- Amphia Academy Infectious Disease Foundation, Amphia Hospital, CK Breda, Netherlands
| | - Jan Kluytmans
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, University of Utrecht, CG Utrecht, Netherlands
- Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands
| | - Jeroen Dewulf
- Veterinary Epidemiology Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
- *Correspondence: Herman Goossens,
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Brandão RD, Mensaert K, López‐Perolio I, Tserpelis D, Xenakis M, Lattimore V, Walker LC, Kvist A, Vega A, Gutiérrez‐Enríquez S, Díez O, de la Hoya M, Spurdle AB, De Meyer T, Blok MJ. Targeted RNA-seq successfully identifies normal and pathogenic splicing events in breast/ovarian cancer susceptibility and Lynch syndrome genes. Int J Cancer 2019; 145:401-414. [PMID: 30623411 PMCID: PMC6635756 DOI: 10.1002/ijc.32114] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 07/24/2018] [Revised: 11/27/2018] [Accepted: 12/12/2018] [Indexed: 12/21/2022]
Abstract
A subset of genetic variants found through screening of patients with hereditary breast and ovarian cancer syndrome (HBOC) and Lynch syndrome impact RNA splicing. Through target enrichment of the transcriptome, it is possible to perform deep-sequencing and to identify the different and even rare mRNA isoforms. A targeted RNA-seq approach was used to analyse the naturally-occurring splicing events for a panel of 8 breast and/or ovarian cancer susceptibility genes (BRCA1, BRCA2, RAD51C, RAD51D, PTEN, STK11, CDH1, TP53), 3 Lynch syndrome genes (MLH1, MSH2, MSH6) and the fanconi anaemia SLX4 gene, in which monoallelic mutations were found in non-BRCA families. For BRCA1, BRCA2, RAD51C and RAD51D the results were validated by capillary electrophoresis and were compared to a non-targeted RNA-seq approach. We also compared splicing events from lymphoblastoid cell-lines with those from breast and ovarian fimbriae tissues. The potential of targeted RNA-seq to detect pathogenic changes in RNA-splicing was validated by the inclusion of samples with previously well characterized BRCA1/2 genetic variants. In our study, we update the catalogue of normal splicing events for BRCA1/2, provide an extensive catalogue of normal RAD51C and RAD51D alternative splicing, and list splicing events found for eight other genes. Additionally, we show that our approach allowed the identification of aberrant splicing events due to the presence of BRCA1/2 genetic variants and distinguished between complete and partial splicing events. In conclusion, targeted-RNA-seq can be very useful to classify variants based on their putative pathogenic impact on splicing.
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Affiliation(s)
- Rita D. Brandão
- Department of Clinical GeneticsMaastricht University Medical Centre+, GROW‐ School for Oncology and Developmental BiologyMaastrichtThe Netherlands
| | - Klaas Mensaert
- Department of Data Analysis and Mathematical Modelling and Bioinformatics Institute Ghent N2NGhent UniversityGhentBelgium
| | - Irene López‐Perolio
- Molecular Oncology Laboratory CIBERONCHospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Demis Tserpelis
- Department of Clinical GeneticsMaastricht University Medical Centre+, GROW‐ School for Oncology and Developmental BiologyMaastrichtThe Netherlands
| | - Markos Xenakis
- Department of Clinical GeneticsMaastricht University Medical Centre+, GROW‐ School for Oncology and Developmental BiologyMaastrichtThe Netherlands
- Department of Data Science and Knowledge EngineeringMaastricht UniversityMaastrichtThe Netherlands
| | - Vanessa Lattimore
- Department of Pathology and Biomedical ScienceUniversity of OtagoChristchurchNew Zealand
| | - Logan C. Walker
- Department of Pathology and Biomedical ScienceUniversity of OtagoChristchurchNew Zealand
| | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical SciencesLund UniversityLundSweden
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica‐Servicio Galgo de SaúdeGrupo de Medicina Xenómica‐USC, CIBERER, IDISSantiago de CompostelaSpain
| | | | - Orland Díez
- Oncogenetics GroupVall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- Area of Clinical and Molecular GeneticsUniversity Hospital of Vall d'HebronBarcelonaSpain
| | | | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONCHospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling and Bioinformatics Institute Ghent N2NGhent UniversityGhentBelgium
- CRIG (Cancer Research Institute Ghent)Ghent UniversityGhentBelgium
| | - Marinus J. Blok
- Department of Clinical GeneticsMaastricht University Medical Centre+, GROW‐ School for Oncology and Developmental BiologyMaastrichtThe Netherlands
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Coussement L, Bolca S, Van Criekinge W, Trooskens G, Mensaert K, Poels K, Roche N, Blondeel P, Godderis L, Depypere H, De Meyer T. Exploratory analysis of the human breast DNA methylation profile upon soymilk exposure. Sci Rep 2018; 8:13617. [PMID: 30206342 PMCID: PMC6133922 DOI: 10.1038/s41598-018-31767-x] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/24/2018] [Indexed: 12/17/2022] Open
Abstract
Upon soy consumption, isoflavone metabolites attain bioactive concentrations in breast tissue possibly affecting health. Though in vitro epigenetic activity of soy metabolites has been described, the in vivo impact on the epigenome is largely unknown. Therefore, in this case-control study, the breast glandular tissue DNA methylome was explored in women undergoing an aesthetic breast reduction. After a run-in phase, 10 generally healthy Belgian or Dutch women received soymilk for 5 days. MethylCap-seq methylation profiles were compared with those of 10 matched controls. Isoflavones and their microbial metabolites were quantified in urine, serum, and glandular breast tissue (liquid chromatography-mass spectrometry) and 17β-estradiol in glandular breast tissue (immunoassay). Global DNA methylation levels were obtained for 6 cases and 5 controls using liquid chromatography-mass spectrometry. Although lower MethylCap-seq coverages were observed, mass spectrometry results and computational LINE-1 methylation analysis did not provide evidence supporting global methylation alterations upon treatment. At a false discovery rate of 0.05, no differentially methylated loci were identified. Moreover, a set of previously identified loci was specifically tested, but earlier reported results could not be validated. In conclusion, after a 5-day soymilk treatment, no major general epigenetic reprogramming in breast tissue could be found in this exploratory study.
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Affiliation(s)
- Louis Coussement
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Belgium, Coupure Links 653, B-9000, Ghent, Belgium
| | - Selin Bolca
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Belgium, Coupure Links 653, B-9000, Ghent, Belgium
| | - Wim Van Criekinge
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Belgium, Coupure Links 653, B-9000, Ghent, Belgium.,Bioinformatics Institute Ghent: from Nucleotides 2 Networks (BIG-N2N), Ghent University, Belgium, Ghent University - VIB, Technologiepark 927, B-9052, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University (Hospital), Belgium, Ghent University Hospital MRB, Corneel Heymanslaan 10, B-9000, Ghent, Belgium
| | - Geert Trooskens
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Belgium, Coupure Links 653, B-9000, Ghent, Belgium
| | - Klaas Mensaert
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Belgium, Coupure Links 653, B-9000, Ghent, Belgium
| | - Katrien Poels
- Department of Public Health and Primary Care, Centre for Environment and Health, KU Leuven, Belgium, Kapucijnenvoer 35 blok d, box 7001, B-3000, Leuven, Belgium
| | - Nathalie Roche
- Department of Plastic and Reconstructive Surgery, Ghent University Hospital, Belgium, University Hospital 2K12 IC, De Pintelaan 185, B-9000, Ghent, Belgium
| | - Phillip Blondeel
- Department of Plastic and Reconstructive Surgery, Ghent University Hospital, Belgium, University Hospital 2K12 IC, De Pintelaan 185, B-9000, Ghent, Belgium
| | - Lode Godderis
- Department of Public Health and Primary Care, Centre for Environment and Health, KU Leuven, Belgium, Kapucijnenvoer 35 blok d, box 7001, B-3000, Leuven, Belgium
| | - Herman Depypere
- Department of Uro-Gynaecology, Ghent University Hospital, Belgium, Corneel Heymanslaan 10, P3, B-9000, Ghent, Belgium
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Belgium, Coupure Links 653, B-9000, Ghent, Belgium. .,Bioinformatics Institute Ghent: from Nucleotides 2 Networks (BIG-N2N), Ghent University, Belgium, Ghent University - VIB, Technologiepark 927, B-9052, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent University (Hospital), Belgium, Ghent University Hospital MRB, Corneel Heymanslaan 10, B-9000, Ghent, Belgium.
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Mensaert K, Van Criekinge W, Thas O, Schuuring E, Steenbergen RDM, Wisman GBA, De Meyer T. Mining for viral fragments in methylation enriched sequencing data. Front Genet 2015; 6:16. [PMID: 25699076 PMCID: PMC4316777 DOI: 10.3389/fgene.2015.00016] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 01/13/2015] [Indexed: 12/26/2022] Open
Abstract
Most next generation sequencing experiments generate more data than is usable for the experimental set up. For example, methyl-CpG binding domain (MBD) affinity purification based sequencing is often used for DNA-methylation profiling, but up to 30% of the sequenced fragments cannot be mapped uniquely to the reference genome. Here we present and evaluate a methodology for the identification of viruses in these otherwise unused paired-end MBD-seq data. Viral detection is accomplished by mapping non-reference alignable reads to a comprehensive set of viral genomes. As viruses play an important role in epigenetics and cancer development, 92 (pre)malignant and benign samples, originating from two different collections of cervical samples and related cell lines, were used in this study. These samples include primary carcinomas (n = 22), low- and high-grade cervical intraepithelial neoplasia (CIN1 and CIN2/3 - n = 2/n = 30) and normal tissue (n = 20), as well as control samples (n = 17). Viruses that were detected include phages, adenoviruses, herpesviridae and HPV. HPV, which causes virtually all cervical cancers, was identified in 95% of the carcinomas, 100% of the CIN2/3 samples, both CIN1 samples and in 55% of the normal samples. Comparing the amount of mapped fragments on HPV for each HPV-infected sample yielded a significant difference between normal samples and carcinomas or CIN2/3 samples (adjusted p-values resp. <10(-5), <10(-5)), reflecting different viral loads and/or methylation degrees in non-normal samples. Fragments originating from different HPV types could be distinguished and were independently validated by PCR-based assays in 71% of the detections. In conclusion, although limited by the a priori knowledge of viral reference genome sequences, the proposed methodology can provide a first confined but substantial insight into the presence, concentration and types of methylated viral sequences in MBD-seq data at low additional cost.
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Affiliation(s)
- Klaas Mensaert
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University Ghent, Belgium
| | - Wim Van Criekinge
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University Ghent, Belgium ; Department of Pathology, VU University Medical Center Amsterdam, Netherlands
| | - Olivier Thas
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University Ghent, Belgium
| | - Ed Schuuring
- Department of Pathology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen Groningen, Netherlands
| | | | - G Bea A Wisman
- Department of Gynecologic Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen Groningen, Netherlands
| | - Tim De Meyer
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University Ghent, Belgium
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7
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Steyaert S, Van Criekinge W, De Paepe A, Denil S, Mensaert K, Vandepitte K, Vanden Berghe W, Trooskens G, De Meyer T. SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data. Nucleic Acids Res 2014; 42:e157. [PMID: 25237057 PMCID: PMC4227762 DOI: 10.1093/nar/gku847] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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] [Indexed: 11/23/2022] Open
Abstract
Monoallelic gene expression is typically initiated early in the development of an organism. Dysregulation of monoallelic gene expression has already been linked to several non-Mendelian inherited genetic disorders. In humans, DNA-methylation is deemed to be an important regulator of monoallelic gene expression, but only few examples are known. One important reason is that current, cost-affordable truly genome-wide methods to assess DNA-methylation are based on sequencing post-enrichment. Here, we present a new methodology based on classical population genetic theory, i.e. the Hardy–Weinberg theorem, that combines methylomic data from MethylCap-seq with associated SNP profiles to identify monoallelically methylated loci. Applied on 334 MethylCap-seq samples of very diverse origin, this resulted in the identification of 80 genomic regions featured by monoallelic DNA-methylation. Of these 80 loci, 49 are located in genic regions of which 25 have already been linked to imprinting. Further analysis revealed statistically significant enrichment of these loci in promoter regions, further establishing the relevance and usefulness of the method. Additional validation was done using both 14 whole-genome bisulfite sequencing data sets and 16 mRNA-seq data sets. Importantly, the developed approach can be easily applied to other enrichment-based sequencing technologies, like the ChIP-seq-based identification of monoallelic histone modifications.
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Affiliation(s)
- Sandra Steyaert
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Wim Van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Ayla De Paepe
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Simon Denil
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Klaas Mensaert
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | | | - Wim Vanden Berghe
- PPES, Department of Biomedical Sciences, University of Antwerp, Wilrijk 2610, Belgium
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Tim De Meyer
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
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8
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Mensaert K, Denil S, Trooskens G, Van Criekinge W, Thas O, De Meyer T. Next-generation technologies and data analytical approaches for epigenomics. Environ Mol Mutagen 2014; 55:155-70. [PMID: 24327356 DOI: 10.1002/em.21841] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [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: 08/30/2013] [Revised: 11/27/2013] [Accepted: 11/27/2013] [Indexed: 05/18/2023]
Abstract
Epigenetics refers to the collection of heritable features that modulate the genome-environment interaction without being encoded in the actual DNA sequence. While being mitotically and sometimes even meiotically transmitted, epigenetic traits often demonstrate extensive flexibility. This allows cells to acquire diverse gene expression patterns during differentiation, but also to adapt to a changing environment. However, epigenetic alterations are not always beneficial to the organism, as they are, for example, frequently identified in human diseases such as cancer. Accurate and cost-efficient genome-scale profiling of epigenetic features is thus of major importance to pinpoint these "epimutations," for example, to monitor the epigenetic impact of environmental exposure. Over the last decade, the field of epigenetics has been revolutionized by several innovative "epigenomics" technologies exactly addressing this need. In this review, we discuss and compare widely used next-generation methods to assess DNA methylation and hydroxymethylation, noncoding RNA expression, histone modifications, and nucleosome positioning. Although recent methods are typically based on "second-generation" sequencing, we also pay attention to still commonly used array- and PCR-based methods, and look forward to the additional advantages of single-molecule sequencing. As the current bottleneck in epigenomics research is the analysis rather than generation of data, the basic difficulties and problem-solving strategies regarding data preprocessing and statistical analysis are introduced for the different technologies. Finally, we also consider the complications associated with epigenomic studies of species with yet unsequenced genomes and possible solutions.
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Affiliation(s)
- Klaas Mensaert
- Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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