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van Lingen E, Nooij S, Terveer E, Crossette E, Prince A, Bhattarai S, Watson A, Galazzo G, Menon R, Szabady R, Bucci V, Norman J, van der Woude J, van der Marel S, Verspaget H, van der Meulen-de Jong A, Keller J. Fecal Microbiota Transplantation engraftment after budesonide or placebo in patients with active ulcerative colitis using pre-selected donors: a randomized pilot study. J Crohns Colitis 2024:jjae043. [PMID: 38572716 DOI: 10.1093/ecco-jcc/jjae043] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Indexed: 04/05/2024]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) shows some efficacy in treating patients with ulcerative colitis (UC), although variability has been observed among donors and treatment regimens. We investigated the effect of FMT using rationally selected donors after pretreatment with budesonide or placebo in active UC. METHODS Patients ≥ 18 years old with mild to moderate active UC were randomly assigned to three weeks budesonide (9 mg) or placebo followed by four weekly infusions of a donor feces suspension. Two donors were selected based on microbiota composition, Treg induction and SCFA production in mice. The primary endpoint was engraftment of donor microbiota after FMT. In addition, clinical efficacy was assessed. RESULTS In total, 24 patients were enrolled. Pretreatment with budesonide did not increase donor microbiota engraftment (p=0.56) nor clinical response, and engraftment was not associated with clinical response. At week 14, 10/24 (42%) of patients achieved (partial) remission. Remarkably, patients treated with FMT suspensions from one donor were associated with clinical response (80% of responders, p<0.05) but had lower overall engraftment of donor microbiota. Furthermore, differences in the taxonomic composition of the donors and the engraftment of certain taxa were associated with clinical response. CONCLUSION In this small study, pretreatment with budesonide did not significantly influence engraftment or clinical response after FMT. However, clinical response appeared donor-dependent. Response to FMT may be related to transfer of specific strains instead of overall engraftment, demonstrating the need to characterize mechanisms of actions of strains that maximize therapeutic benefit in ulcerative colitis.
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Affiliation(s)
- Emilie van Lingen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center
| | - Sam Nooij
- Department of Medical Microbiology, Leiden University Medical Center
| | - Elisabeth Terveer
- Department of Medical Microbiology, Leiden University Medical Center
| | | | | | - Shakti Bhattarai
- University of Massachusetts Chan Medical School, Department of Microbiology and Physiological Systems, Worcester, MA 01605 USA
| | | | | | - Rajita Menon
- Vedanta Biosciences, Inc. Cambridge, MA 02139 USA
| | - Rose Szabady
- Vedanta Biosciences, Inc. Cambridge, MA 02139 USA
| | - Vanni Bucci
- University of Massachusetts Chan Medical School, Department of Microbiology and Physiological Systems, Worcester, MA 01605 USA
| | - Jason Norman
- Vedanta Biosciences, Inc. Cambridge, MA 02139 USA
| | | | | | - Hein Verspaget
- Department of Gastroenterology and Hepatology, Leiden University Medical Center
| | | | - Josbert Keller
- Department of Gastroenterology and Hepatology, Leiden University Medical Center
- Department of Gastroenterology and Hepatology, Erasmus Medical Center
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Nooij S, Vendrik KEW, Zwittink RD, Ducarmon QR, Keller JJ, Kuijper EJ, Terveer EM. Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection. Genome Med 2024; 16:37. [PMID: 38419010 PMCID: PMC10902993 DOI: 10.1186/s13073-024-01306-7] [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: 08/23/2023] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Multidrug-resistant (MDR) bacteria are a growing global threat, especially in healthcare facilities. Faecal microbiota transplantation (FMT) is an effective prevention strategy for recurrences of Clostridioides difficile infections and can also be useful for other microbiota-related diseases. METHODS We study the effect of FMT in patients with multiple recurrent C. difficile infections on colonisation with MDR bacteria and antibiotic resistance genes (ARG) on the short (3 weeks) and long term (1-3 years), combining culture methods and faecal metagenomics. RESULTS Based on MDR culture (n = 87 patients), we notice a decrease of 11.5% in the colonisation rate of MDR bacteria after FMT (20/87 before FMT = 23%, 10/87 3 weeks after FMT). Metagenomic sequencing of patient stool samples (n = 63) shows a reduction in relative abundances of ARGs in faeces, while the number of different resistance genes in patients remained higher compared to stools of their corresponding healthy donors (n = 11). Furthermore, plasmid predictions in metagenomic data indicate that patients harboured increased levels of resistance plasmids, which appear unaffected by FMT. In the long term (n = 22 patients), the recipients' resistomes are still donor-like, suggesting the effect of FMT may last for years. CONCLUSIONS Taken together, we hypothesise that FMT restores the gut microbiota to a composition that is closer to the composition of healthy donors, and potential pathogens are either lost or decreased to very low abundances. This process, however, does not end in the days following FMT. It may take months for the gut microbiome to re-establish a balanced state. Even though a reservoir of resistance genes remains, a notable part of which on plasmids, FMT decreases the total load of resistance genes.
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Affiliation(s)
- Sam Nooij
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands.
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands.
| | - Karuna E W Vendrik
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
- Present address: Centre for Infectious Disease Control, Netherlands Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Romy D Zwittink
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
- Present address: Centre for Infectious Disease Control, Netherlands Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Quinten R Ducarmon
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
| | - Josbert J Keller
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands
- Department of Gastroenterology, Haaglanden Medical Center, The Hague, Netherlands
| | - Ed J Kuijper
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
| | - Elisabeth M Terveer
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
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Terlouw D, Boot A, Ducarmon QR, Nooij S, Suerink M, van Leerdam ME, van Egmond D, Tops CM, Zwittink RD, Ruano D, Langers AMJ, Nielsen M, van Wezel T, Morreau H. Enrichment of colibactin-associated mutational signatures in unexplained colorectal polyposis patients. BMC Cancer 2024; 24:104. [PMID: 38238650 PMCID: PMC10797792 DOI: 10.1186/s12885-024-11849-y] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Colibactin, a genotoxin produced by polyketide synthase harboring (pks+) bacteria, induces double-strand breaks and chromosome aberrations. Consequently, enrichment of pks+Escherichia coli in colorectal cancer and polyposis suggests a possible carcinogenic effect in the large intestine. Additionally, specific colibactin-associated mutational signatures; SBS88 and ID18 in the Catalogue of Somatic Mutations in Cancer database, are detected in colorectal carcinomas. Previous research showed that a recurrent APC splice variant perfectly fits SBS88. METHODS In this study, we explore the presence of colibactin-associated signatures and fecal pks in an unexplained polyposis cohort. Somatic targeted Next-Generation Sequencing (NGS) was performed for 379 patients. Additionally, for a subset of 29 patients, metagenomics was performed on feces and mutational signature analyses using Whole-Genome Sequencing (WGS) on Formalin-Fixed Paraffin Embedded (FFPE) colorectal tissue blocks. RESULTS NGS showed somatic APC variants fitting SBS88 or ID18 in at least one colorectal adenoma or carcinoma in 29% of patients. Fecal metagenomic analyses revealed enriched presence of pks genes in patients with somatic variants fitting colibactin-associated signatures compared to patients without variants fitting colibactin-associated signatures. Also, mutational signature analyses showed enrichment of SBS88 and ID18 in patients with variants fitting these signatures in NGS compared to patients without. CONCLUSIONS These findings further support colibactins ability to mutagenize colorectal mucosa and contribute to the development of colorectal adenomas and carcinomas explaining a relevant part of patients with unexplained polyposis.
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Affiliation(s)
- Diantha Terlouw
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud Boot
- Department of Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Quinten R Ducarmon
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sam Nooij
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Monique E van Leerdam
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Demi van Egmond
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| | - Carli M Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Romy D Zwittink
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| | - Alexandra M J Langers
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands.
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Terlouw D, Boot A, Ducarmon QR, Nooij S, Jessurun MA, van Leerdam ME, Tops CM, Langers AMJ, Morreau H, van Wezel T, Nielsen M. Colibactin mutational signatures in NTHL1 tumor syndrome and MUTYH associated polyposis patients. Genes Chromosomes Cancer 2024; 63:e23208. [PMID: 37795928 DOI: 10.1002/gcc.23208] [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: 07/04/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Polyketide synthase (pks) island harboring Escherichia coli are, under the right circumstances, able to produce the genotoxin colibactin. Colibactin is a risk factor for the development of colorectal cancer and associated with mutational signatures SBS88 and ID18. This study explores colibactin-associated mutational signatures in biallelic NTHL1 and MUTYH patients. Targeted Next Generation Sequencing (NGS) was performed on colorectal adenomas and carcinomas of one biallelic NTHL and 12 biallelic MUTYH patients. Additional fecal metagenomics and genome sequencing followed by mutational signature analysis was conducted for the NTHL1 patient. Targeted NGS of the NTHL1 patient showed somatic APC variants fitting SBS88 which was confirmed using WGS. Furthermore, fecal metagenomics revealed pks genes. Also, in 1 out of 11 MUTYH patient a somatic variant was detected fitting SBS88. This report shows that colibactin may influence development of colorectal neoplasms in predisposed patients.
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Affiliation(s)
- D Terlouw
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - A Boot
- Department of Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Q R Ducarmon
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - S Nooij
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - M A Jessurun
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - M E van Leerdam
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - C M Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - A M J Langers
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - H Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - T van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - M Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Ducarmon QR, Zwittink RD, Willems RPJ, Verhoeven A, Nooij S, van der Klis FRM, Franz E, Kool J, Giera M, Vandenbroucke-Grauls CMJE, Fuentes S, Kuijper EJ. Gut colonisation by extended-spectrum β-lactamase-producing Escherichia coli and its association with the gut microbiome and metabolome in Dutch adults: a matched case-control study. Lancet Microbe 2022; 3:e443-e451. [PMID: 35659906 DOI: 10.1016/s2666-5247(22)00037-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/16/2021] [Accepted: 02/11/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Gut colonisation by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is a risk factor for developing overt infection. The gut microbiome can provide colonisation resistance against enteropathogens, but it remains unclear whether it confers resistance against ESBL-producing E coli. We aimed to identify a potential role of the microbiome in controlling colonisation by this antibiotic-resistant bacterium. METHODS For this matched case-control study, we used faeces from 2751 individuals in a Dutch cross-sectional population study (PIENTER-3) to culture ESBL-producing bacteria. Of these, we selected 49 samples that were positive for an ESBL-producing E coli (ESBL-positive) and negative for several variables known to affect microbiome composition. These samples were matched 1:1 to ESBL-negative samples on the basis of individuals' age, sex, having been abroad or not in the past 6 months, and ethnicity. Shotgun metagenomic sequencing was done and taxonomic species composition and functional annotations (ie, microbial metabolism and carbohydrate-active enzymes) were determined. Targeted quantitative metabolic profiling (proton nuclear magnetic resonance spectroscopy) was done to investigate metabolomic profiles and combinations of univariate (t test and Wilcoxon test), multivariate (principal coordinates analysis, permutational multivariate analysis of variance, and partial least-squares discriminant analysis) and machine-learning approaches (least absolute shrinkage and selection operator and random forests) were used to analyse all the molecular data. FINDINGS No differences in diversity parameters or in relative abundance were observed between ESBL-positive and ESBL-negative groups based on bacterial species-level composition. Machine-learning approaches using microbiota composition did not accurately predict ESBL status (area under the receiver operating characteristic curve [AUROC]=0·41) when using either microbiota composition or any of the functional profiles. The metabolome also did not differ between ESBL groups, as assessed by various methods including random forest (AUROC=0·61). INTERPRETATION By combining multiomics and machine-learning approaches, we conclude that asymptomatic gut carriage of ESBL-producing E coli is not associated with an altered microbiome composition or function. This finding might suggest that microbiome-mediated colonisation resistance against ESBL-producing E coli is not as relevant as it is against other enteropathogens and antibiotic-resistant bacteria. FUNDING None.
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Affiliation(s)
- Quinten R Ducarmon
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, Netherlands; Centre for Microbiome Analyses and Therapeutics, Leiden University Medical Centre, Leiden, Netherlands.
| | - Romy D Zwittink
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, Netherlands; Centre for Microbiome Analyses and Therapeutics, Leiden University Medical Centre, Leiden, Netherlands
| | - Roel P J Willems
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centres, Amsterdam Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | - Aswin Verhoeven
- Centre for Proteomics and Metabolomics, Leiden University Medical Centre, Leiden, Netherlands
| | - Sam Nooij
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, Netherlands; Centre for Microbiome Analyses and Therapeutics, Leiden University Medical Centre, Leiden, Netherlands
| | - Fiona R M van der Klis
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Jolanda Kool
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Martin Giera
- Centre for Proteomics and Metabolomics, Leiden University Medical Centre, Leiden, Netherlands
| | - Christina M J E Vandenbroucke-Grauls
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centres, Amsterdam Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | - Susana Fuentes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, Netherlands; Centre for Microbiome Analyses and Therapeutics, Leiden University Medical Centre, Leiden, Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
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6
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Nooij S, Terveer EM. Reply. Gastroenterology 2022; 162:994-995. [PMID: 34863789 DOI: 10.1053/j.gastro.2021.11.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 12/02/2022]
Affiliation(s)
- Sam Nooij
- Leiden University Medical Center, Leiden, the Netherlands
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- Leiden University Medical Center, Leiden, the Netherlands
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Nooij S, Ducarmon QR, Laros JFJ, Zwittink RD, Norman JM, Smits WK, Verspaget HW, Keller JJ, Terveer EM, Kuijper EJ. Fecal Microbiota Transplantation Influences Procarcinogenic Escherichia coli in Recipient Recurrent Clostridioides difficile Patients. Gastroenterology 2021; 161:1218-1228.e5. [PMID: 34126062 DOI: 10.1053/j.gastro.2021.06.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/18/2021] [Accepted: 06/03/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Patients with multiple recurrent Clostridioides difficile infection (rCDI) have a disturbed gut microbiota that can be restored by fecal microbiota transplantation (FMT). Despite extensive screening, healthy feces donors may carry bacteria in their intestinal tract that could have long-term health effects, such as potentially procarcinogenic polyketide synthase-positive (pks+) Escherichia coli. Here, we aim to determine whether the pks abundance and persistence of pks+E coli is influenced by pks status of the donor feces. METHODS In a cohort of 49 patients with rCDI treated with FMT and matching donor samples-the largest cohort of its kind, to our knowledge-we retrospectively screened fecal metagenomes for pks+E coli and compared the presence of pks in patients before and after treatment and to their respective donors. RESULTS The pks island was more prevalent (P = .026) and abundant (P < .001) in patients with rCDI (pre-FMT, 27 of 49 [55%]; median, 0.46 reads per kilobase per million [RPKM] pks) than in healthy donors (3 of 8 donors [37.5%], 11 of 38 samples [29%]; median, 0.01 RPKM pks). The pks status of patients post-FMT depended on the pks status of the donor suspension with which the patient was treated (P = .046). Particularly, persistence (8 of 9 cases) or clearance (13 of 18) of pks+E coli in pks+ patients was correlated to pks in the donor (P = .004). CONCLUSIONS We conclude that FMT contributes to pks+E coli persistence or eradication in patients with rCDI but that donor-to-patient transmission of pks+E coli is unlikely.
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Affiliation(s)
- Sam Nooij
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Netherlands Donor Feces Bank, Leiden, the Netherlands; Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands.
| | - Quinten R Ducarmon
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jeroen F J Laros
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands; Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands; National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Romy D Zwittink
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Wiep Klaas Smits
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hein W Verspaget
- Department of Gastroenterology, Leiden University Medical Center, Leiden, the Netherlands; Department of Biobanking, Leiden University Medical Center, Leiden, the Netherlands
| | - Josbert J Keller
- Department of Gastroenterology, Leiden University Medical Center, Leiden, the Netherlands; Department of Gastroenterology, Haaglanden Medical Center, The Hague, the Netherlands
| | - Elisabeth M Terveer
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Netherlands Donor Feces Bank, Leiden, the Netherlands; Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands
| | - Ed J Kuijper
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Netherlands Donor Feces Bank, Leiden, the Netherlands; Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands; National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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Konstantinovski MM, Veldkamp KE, Lavrijsen APM, Bosch T, Kraakman MEM, Nooij S, Claas ECJ, Gooskens J. Hospital transmission of borderline oxacillin-resistant Staphylococcus aureus evaluated by whole-genome sequencing. J Med Microbiol 2021; 70. [PMID: 34269673 PMCID: PMC8493421 DOI: 10.1099/jmm.0.001384] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction Staphylococcus aureus is a major cause of hospital infections worldwide. Awareness towards methicillin-resistant S. aureus (MRSA) infections is high but attention towards borderline oxacillin-resistant S. aureus (BORSA) is limited, possibly due to an underestimated clinical relevance, presumption of low incidence and diagnostic limitations. Gap statement BORSA surveillance has not been routinely implemented, and thus consensus with regard to a definition and infection control measures is lacking. Aim Our goals were to investigate the occurrence, molecular characteristics and clinical manifestations of BORSA infections in the hospital setting. Methodology Following an increased incidence in 2016, BORSA cases in 2014/2016 (in our institution) were more specifically evaluated. Medical records were reviewed to investigate epidemiological links, clinical characteristics and outcomes. Resistance and virulence markers were assessed by whole genome sequencing (WGS). Conventional methods: amplified fragment length polymorphism (AFLP) ; multilocus sequence typing (MLST) and multiple locus variable-number tandem repeat analysis (MLVA) were compared with core genome MLST (cgMLST) and whole-genome single nucleotide polymorphism (wgSNP) analysis to confirm genetic clusters. Results From 2009 to 2013, BORSA comprised 0.1 % of all clinical S. aureus strains. In 2016, the incidence was six-fold higher in comparison to the baseline. Whole-genome SNP and cgMLST confirmed two BORSA clusters among patients with dermatological conditions. Patients with BORSA presented with skin infections, and one case developed a severe invasive infection with a fatal outcome. Infection control measures successfully prevented further transmission in both clusters. WGS findings showed that BORSA strains carried multiple resistance and virulence genes with increased pathogenic potential. Conclusion WGS and cgMLST effectively characterized and confirmed BORSA clusters among at-risk patients with clinical manifestations ranging from mild skin infections to life-threatening bacteraemia. Clinical awareness and active monitoring are therefore warranted for the timely implementation of infection control measures to prevent BORSA transmission in high-risk patients.
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Affiliation(s)
| | - Karin Ellen Veldkamp
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
| | | | - Thijs Bosch
- Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, de Bilt, Netherlands
| | - Margriet E M Kraakman
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
| | - Sam Nooij
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
| | - Eric C J Claas
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
| | - Jairo Gooskens
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
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9
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Boekhoud IM, Sidorov I, Nooij S, Harmanus C, Bos-Sanders IMJG, Viprey V, Spittal W, Clark E, Davies K, Freeman J, Kuijper EJ, Smits WK. Haem is crucial for medium-dependent metronidazole resistance in clinical isolates of Clostridioides difficile. J Antimicrob Chemother 2021; 76:1731-1740. [PMID: 33876817 PMCID: PMC8212768 DOI: 10.1093/jac/dkab097] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/02/2021] [Indexed: 01/05/2023] Open
Abstract
Background Until recently, metronidazole was the first-line treatment for Clostridioides difficile infection and it is still commonly used. Though resistance has been reported due to the plasmid pCD-METRO, this does not explain all cases. Objectives To identify factors that contribute to plasmid-independent metronidazole resistance of C. difficile. Methods Here, we investigate resistance to metronidazole in a collection of clinical isolates of C. difficile using a combination of antimicrobial susceptibility testing on different solid agar media and WGS of selected isolates. Results We find that nearly all isolates demonstrate a haem-dependent increase in the MIC of metronidazole, which in some cases leads to isolates qualifying as resistant (MIC >2 mg/L). Moreover, we find an SNP in the haem-responsive gene hsmA, which defines a metronidazole-resistant lineage of PCR ribotype 010/MLST ST15 isolates that also includes pCD-METRO-containing strains. Conclusions Our data demonstrate that haem is crucial for medium-dependent metronidazole resistance in C. difficile.
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Affiliation(s)
- Ilse M Boekhoud
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Igor Sidorov
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sam Nooij
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Céline Harmanus
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Virginie Viprey
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - William Spittal
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Emma Clark
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Kerrie Davies
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Jane Freeman
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland.,National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
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10
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Ducarmon QR, Terveer EM, Nooij S, Bloem MN, Vendrik KEW, Caljouw MAA, Sanders IMJG, van Dorp SM, Wong MC, Zwittink RD, Kuijper EJ. Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home. Genome Med 2021; 13:54. [PMID: 33827686 PMCID: PMC8028076 DOI: 10.1186/s13073-021-00869-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 12/17/2020] [Accepted: 03/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background Nursing home residents have increased rates of intestinal colonisation with multidrug-resistant organisms (MDROs). We assessed the colonisation and spread of MDROs among this population, determined clinical risk factors for MDRO colonisation and investigated the role of the gut microbiota in providing colonisation resistance against MDROs. Methods We conducted a prospective cohort study in a Dutch nursing home. Demographical, epidemiological and clinical data were collected at four time points with 2-month intervals (October 2016–April 2017). To obtain longitudinal data, faecal samples from residents were collected for at least two time points. Ultimately, twenty-seven residents were included in the study and 93 faecal samples were analysed, of which 27 (29.0%) were MDRO-positive. Twelve residents (44.4%) were colonised with an MDRO at at least one time point throughout the 6-month study. Results Univariable generalised estimating equation logistic regression indicated that antibiotic use in the previous 2 months and hospital admittance in the previous year were associated with MDRO colonisation. Characterisation of MDRO isolates through whole-genome sequencing revealed Escherichia coli sequence type (ST)131 to be the most prevalent MDRO and ward-specific clusters of E. coli ST131 were identified. Microbiota analysis by 16S rRNA gene amplicon sequencing revealed no differences in alpha or beta diversity between MDRO-positive and negative samples, nor between residents who were ever or never colonised. Three bacterial taxa (Dorea, Atopobiaceae and Lachnospiraceae ND3007 group) were more abundant in residents never colonised with an MDRO throughout the 6-month study. An unexpectedly high abundance of Bifidobacterium was observed in several residents. Further investigation of a subset of samples with metagenomics showed that various Bifidobacterium species were highly abundant, of which B. longum strains remained identical within residents over time, but were different between residents. Conclusions Our study provides new evidence for the role of the gut microbiota in colonisation resistance against MDROs in the elderly living in a nursing home setting. Dorea, Atopobiaceae and Lachnospiraceae ND3007 group may be associated with protection against MDRO colonisation. Furthermore, we report a uniquely high abundance of several Bifidobacterium species in multiple residents and excluded the possibility that this was due to probiotic supplementation. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00869-z.
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Affiliation(s)
- Quinten R Ducarmon
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands. .,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Elisabeth M Terveer
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sam Nooij
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michelle N Bloem
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Karuna E W Vendrik
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Monique A A Caljouw
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Ingrid M J G Sanders
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sofie M van Dorp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Internal Medicine and Geriatrics, Onze Lieve Vrouwe Gasthuis (OLVG Hospital), Amsterdam, The Netherlands
| | - Man C Wong
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Romy D Zwittink
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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11
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Vendrik KEW, Terveer EM, Kuijper EJ, Nooij S, Boeije-Koppenol E, Sanders IMJG, van Lingen E, Verspaget HW, Berssenbrugge EKL, Keller JJ, van Prehn J. Periodic screening of donor faeces with a quarantine period to prevent transmission of multidrug-resistant organisms during faecal microbiota transplantation: a retrospective cohort study. Lancet Infect Dis 2020; 21:711-721. [PMID: 33275940 DOI: 10.1016/s1473-3099(20)30473-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 04/24/2020] [Accepted: 05/27/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND On June 13, 2019, the US Food and Drug Administration issued a warning after transfer of faeces containing an extended-spectrum β-lactamase (ESBL)-producing Escherichia coli by faecal microbiota transplantation led to bacteraemia in two immunocompromised patients. Consequently, we evaluated the effectiveness of the faeces donor-screening protocol of the Netherlands Donor Faeces Bank, which consists of screening of donors for multidrug-resistant organisms every 3 months, combined with additional screening on indication (eg, after travelling abroad) and application of a quarantine period for all faecal suspensions delivered within those 3 months. METHODS We did a retrospective cohort study of data collected between Jan 1, 2015, and Oct 14, 2019, on the multidrug-resistant organism testing results of donor faeces. Additionally, we tested previously quarantined faecal suspensions approved for faecal microbiota transplantation between Dec 12, 2016, and May 1, 2019, for the presence of multidrug-resistant organisms using both aselective and selective broth enrichment media. Whole-genome sequencing with core-genome multilocus sequence typing (cgMLST) was done on all multidrug-resistant isolates. FINDINGS Among initial screenings, six (9%) of 66 tested individuals were positive for multidrug-resistant organisms and 11 (17%) of 66 tested individuals were positive for multidrug-resistant organisms at any timepoint. Multidrug-resistant organisms were detected in four (25%) of 16 active donors, who had a median donation duration of 268 days (IQR 92 to 366). Among all screening results, 14 (74%) of 19 detected multidrug-resistant organisms were ESBL-producing E coli. 170 (49%) of 344 approved faecal suspensions had corresponding research faeces aliquots available and were tested (from 11 active donors with a median of eight [IQR five to 26] suspensions per donor). No multidrug-resistant organisms were detected in the 170 approved faecal suspensions (one-sided 95% CI 0 to 1·7). cgMLST revealed that all multidrug-resistant organisms were genetically different. INTERPRETATION Healthy faeces donors can become colonised with multidrug-resistant organisms during donation activities. Our screening protocol did not result in approval of multidrug-resistant organism-positive faecal suspensions for microbiota transplantation. FUNDING None.
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Affiliation(s)
- Karuna E W Vendrik
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Elisabeth M Terveer
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands.
| | - Sam Nooij
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Eline Boeije-Koppenol
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Ingrid M J G Sanders
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Emilie van Lingen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Hein W Verspaget
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands; Department of Biobanking, Leiden University Medical Center, Leiden, Netherlands
| | - Eric K L Berssenbrugge
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Josbert J Keller
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands; Department of Gastroenterology, Haaglanden Medical Center, The Hague, Netherlands
| | - Joffrey van Prehn
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
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12
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Schmitz D, Nooij S, Janssens T, Cremer J, Vennema H, Kroneman A, Koopmans M. A43 Translational research: NGS metagenomics into clinical diagnostics. Virus Evol 2019. [PMCID: PMC6735915 DOI: 10.1093/ve/vez002.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
As research next-generation sequencing (NGS) metagenomic pipelines transition to clinical diagnostics, the user-base changes from bioinformaticians to biologists, medical doctors, and lab-technicians. Besides the obvious need for benchmarking and assessment of diagnostic outcomes of the pipelines and tools, other focus points remain: reproducibility, data immutability, user-friendliness, portability/scalability, privacy, and a clear audit trail. We have a research metagenomics pipeline that takes raw fastq files and produces annotated contigs, but it is too complicated for non-bioinformaticians. Here, we present preliminary findings in adapting this pipeline for clinical diagnostics. We used information available on relevant fora (www.bioinfo-core.org) and experiences and publications from colleague bioinformaticians in other institutes (COMPARE, UBC, and LUMC). From this information, a robust and user-friendly storage and analysis workflow was designed for non-bioinformaticians in a clinical setting. Via Conda [https://conda.io] and Docker containers [http://www.docker.com], we made our disparate pipeline processes self-contained and reproducible. Furthermore, we moved all pipeline settings into a separate JSON file. After every analysis, the pipeline settings and virtual-environment recipes will be archived (immutably) under a persistent unique identifier. This allows long-term precise reproducibility. Likewise, after every run the raw data and final products will be automatically archived, complying with data retention laws/guidelines. All the disparate processes in the pipeline are parallelized and automated via Snakemake1 (i.e. end-users need no coding skills). In addition, interactive web-reports such as MultiQC [http://multiqc.info] and Krona2 are generated automatically. By combining Snakemake, Conda, and containers, our pipeline is highly portable and easily scaled up for outbreak situations, or scaled down to reduce costs. Since patient privacy is a concern, our pipeline automatically removes human genetic data. Moreover, all source code will be stored on an internal Gitlab server, and, combined with the archived data, ensures a clear audit trail. Nevertheless, challenges remain: (1) reproducible reference databases, e.g. being able to revert to an older version to reproduce old analyses. (2) A user-friendly GUI. (3) Connecting the pipeline and NGS data to in-house LIMS. (4) Efficient long-term storage, e.g. lossless compression algorithms. Nevertheless, this work represents a step forward in making user-friendly clinical diagnostic workflows.
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Affiliation(s)
- D Schmitz
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Erasmus Medical Centre (EMC), Rotterdam, the Netherlands
| | - S Nooij
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Erasmus Medical Centre (EMC), Rotterdam, the Netherlands
| | - T Janssens
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - J Cremer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - H Vennema
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - A Kroneman
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - M Koopmans
- Erasmus Medical Centre (EMC), Rotterdam, the Netherlands
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13
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Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara LC, Vanden Eynden E, Vandamme AM, Deforche K, de Oliveira T. Genome Detective: an automated system for virus identification from high-throughput sequencing data. Bioinformatics 2019; 35:871-873. [PMID: 30124794 PMCID: PMC6524403 DOI: 10.1093/bioinformatics/bty695] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/09/2018] [Accepted: 08/14/2018] [Indexed: 12/20/2022] Open
Abstract
SUMMARY Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. The application uses a novel alignment method that constructs genomes by reference-based linking of de novo contigs by combining amino-acids and nucleotide scores. The software was optimized using synthetic datasets to represent the great diversity of virus genomes. The application was then validated with next generation sequencing data of hundreds of viruses. User time is minimal and it is limited to the time required to upload the data. AVAILABILITY AND IMPLEMENTATION Available online: http://www.genomedetective.com/app/typingtool/virus/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Yumna Moosa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sam Nooij
- The Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
- Laboratory of Hematology Genetic and computational Biology, Goncalo Moniz Research Center, Oswaldo Cruz Foundation (LHGB/CPqGM/FIOCRUZ), Bahia, Brazil
| | | | | | | | - Luiz Carlos Alcantara
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
- Laboratory of Hematology Genetic and computational Biology, Goncalo Moniz Research Center, Oswaldo Cruz Foundation (LHGB/CPqGM/FIOCRUZ), Bahia, Brazil
- Laboratório de Flavivírus, IOC, Fundação Oswaldo Cruz
| | - Ewout Vanden Eynden
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | | | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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14
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Nooij S, Schmitz D, Vennema H, Kroneman A, Koopmans MPG. Overview of Virus Metagenomic Classification Methods and Their Biological Applications. Front Microbiol 2018; 9:749. [PMID: 29740407 PMCID: PMC5924777 DOI: 10.3389/fmicb.2018.00749] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/03/2018] [Indexed: 12/20/2022] Open
Abstract
Metagenomics poses opportunities for clinical and public health virology applications by offering a way to assess complete taxonomic composition of a clinical sample in an unbiased way. However, the techniques required are complicated and analysis standards have yet to develop. This, together with the wealth of different tools and workflows that have been proposed, poses a barrier for new users. We evaluated 49 published computational classification workflows for virus metagenomics in a literature review. To this end, we described the methods of existing workflows by breaking them up into five general steps and assessed their ease-of-use and validation experiments. Performance scores of previous benchmarks were summarized and correlations between methods and performance were investigated. We indicate the potential suitability of the different workflows for (1) time-constrained diagnostics, (2) surveillance and outbreak source tracing, (3) detection of remote homologies (discovery), and (4) biodiversity studies. We provide two decision trees for virologists to help select a workflow for medical or biodiversity studies, as well as directions for future developments in clinical viral metagenomics.
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Affiliation(s)
- Sam Nooij
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.,Viroscience Laboratory, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Dennis Schmitz
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.,Viroscience Laboratory, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Harry Vennema
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Annelies Kroneman
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Marion P G Koopmans
- Emerging and Endemic Viruses, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.,Viroscience Laboratory, Erasmus University Medical Centre, Rotterdam, Netherlands
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15
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Nooij S, Schmitz D, Kroneman A, Vennema H, Koopmans M. A64 Overview of virus metagenomics classification tools. Virus Evol 2018. [PMCID: PMC5905449 DOI: 10.1093/ve/vey010.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Sam Nooij
- National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Erasmus University Medical Centre (EMC), Rotterdam, The Netherlands
| | - Dennis Schmitz
- National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Erasmus University Medical Centre (EMC), Rotterdam, The Netherlands
| | - Annelies Kroneman
- National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Harry Vennema
- National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Marion Koopmans
- National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Erasmus University Medical Centre (EMC), Rotterdam, The Netherlands
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16
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Moosa Y, Vilsker M, Vanden Eyden E, Fonseca V, Nooij S, Deforche K, de Oliveira T. A34 Automated profiling of the human virome from raw metagenomic data. Virus Evol 2017; 3:vew036.033. [PMID: 28845264 PMCID: PMC5565974 DOI: 10.1093/ve/vew036.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yumna Moosa
- Nelson R Mandela School of Medicine College of Health Sciences, University of KwaZulu-Natal (UKZN), South Africa
| | | | | | | | - Sam Nooij
- Rijksinstituut voor Volksgezondheid en Milieu (RIVM), The Netherlands
| | | | - Tulio de Oliveira
- Nelson R Mandela School of Medicine College of Health Sciences, University of KwaZulu-Natal (UKZN), South Africa
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17
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Pretto P, Nesti A, Nooij S, Losert M, Bulthoff H. Tilt-rate perception in vehicle simulation: the role of motion, vision and attention. J Vis 2014. [DOI: 10.1167/14.10.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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