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Top J, Hendrickx APA, van Ampting MTJ, van Limpt K, Knol J, van de Kamer D, Braat JC, Viveen M, Rogers MR, Kemperman H, Willems RJL, Paganelli FL. Low-calcium diet in mice leads to reduced gut colonization by Enterococcus faecium. Microbiologyopen 2019; 8:e936. [PMID: 31568701 PMCID: PMC6925158 DOI: 10.1002/mbo3.936] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 07/16/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 12/26/2022] Open
Abstract
The aim of this study was to determine whether dietary intervention influenced luminal Ca2+ levels and Enterococcus faecium gut colonization in mice. For this purpose, mice fed semi‐synthetic food AIN93 were compared to mice fed AIN93‐low calcium (LC). Administration of AIN93‐LC resulted in lower luminal Ca2+ levels independent of the presence of E. faecium. Furthermore, E. faecium gut colonization was reduced in mice fed AIN93‐LC based on culture, and which was in concordance with a reduction of Enterococcaceae in microbiota analysis. In conclusion, diet intervention might be a strategy for controlling gut colonization of E. faecium, an important opportunistic nosocomial pathogen.
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Affiliation(s)
- Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Antoni P A Hendrickx
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands
| | - Denise van de Kamer
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johanna C Braat
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marco Viveen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Malbert R Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hans Kemperman
- Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Fernanda L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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Arredondo-Alonso S, Rogers MRC, Braat JC, Verschuuren TD, Top J, Corander J, Willems RJL, Schürch AC. Corrigendum: mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species. Microb Genom 2019; 5. [PMID: 30714567 PMCID: PMC6412059 DOI: 10.1099/mgen.0.000249] [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: 11/22/2022] Open
Affiliation(s)
- Sergio Arredondo-Alonso
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Malbert R. C. Rogers
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johanna C. Braat
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tess D. Verschuuren
- 2Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Janetta Top
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- 5Infection Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
- 4Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- 3Faculty of Medicine, Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Rob J. L. Willems
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anita C. Schürch
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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Arredondo-Alonso S, Rogers MRC, Braat JC, Verschuuren TD, Top J, Corander J, Willems RJL, Schürch AC. mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species. Microb Genom 2018; 4. [PMID: 30383524 PMCID: PMC6321875 DOI: 10.1099/mgen.0.000224] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [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] [Indexed: 12/13/2022] Open
Abstract
Assembly of bacterial short-read whole-genome sequencing data frequently results in hundreds of contigs for which the origin, plasmid or chromosome, is unclear. Complete genomes resolved by long-read sequencing can be used to generate and label short-read contigs. These were used to train several popular machine learning methods to classify the origin of contigs from Enterococcus faecium, Klebsiella pneumoniae and Escherichia coli using pentamer frequencies. We selected support-vector machine (SVM) models as the best classifier for all three bacterial species (F1-score E. faecium=0.92, F1-score K. pneumoniae=0.90, F1-score E. coli=0.76), which outperformed other existing plasmid prediction tools using a benchmarking set of isolates. We demonstrated the scalability of our models by accurately predicting the plasmidome of a large collection of 1644 E. faecium isolates and illustrate its applicability by predicting the location of antibiotic-resistance genes in all three species. The SVM classifiers are publicly available as an R package and graphical-user interface called 'mlplasmids'. We anticipate that this tool may significantly facilitate research on the dissemination of plasmids encoding antibiotic resistance and/or contributing to host adaptation.
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Affiliation(s)
- Sergio Arredondo-Alonso
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Malbert R C Rogers
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johanna C Braat
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tess D Verschuuren
- 2Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Janetta Top
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- 3Faculty of Medicine, Department of Biostatistics, University of Oslo, Oslo, Norway.,4Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.,5Infection Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Rob J L Willems
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anita C Schürch
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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Buelow E, Bello González TDJ, Fuentes S, de Steenhuijsen Piters WAA, Lahti L, Bayjanov JR, Majoor EAM, Braat JC, van Mourik MSM, Oostdijk EAN, Willems RJL, Bonten MJM, van Passel MWJ, Smidt H, van Schaik W. Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects. Microbiome 2017; 5:88. [PMID: 28803549 PMCID: PMC5554972 DOI: 10.1186/s40168-017-0309-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [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: 01/04/2017] [Accepted: 07/13/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND The gut microbiota is a reservoir of opportunistic pathogens that can cause life-threatening infections in critically ill patients during their stay in an intensive care unit (ICU). To suppress gut colonization with opportunistic pathogens, a prophylactic antibiotic regimen, termed "selective decontamination of the digestive tract" (SDD), is used in some countries where it improves clinical outcome in ICU patients. Yet, the impact of ICU hospitalization and SDD on the gut microbiota remains largely unknown. Here, we characterize the composition of the gut microbiota and its antimicrobial resistance genes ("the resistome") of ICU patients during SDD and of healthy subjects. RESULTS From ten patients that were acutely admitted to the ICU, 30 fecal samples were collected during ICU stay. Additionally, feces were collected from five of these patients after transfer to a medium-care ward and cessation of SDD. Feces from ten healthy subjects were collected twice, with a 1-year interval. Gut microbiota and resistome composition were determined using 16S rRNA gene phylogenetic profiling and nanolitre-scale quantitative PCRs. The microbiota of the ICU patients differed from the microbiota of healthy subjects and was characterized by lower microbial diversity, decreased levels of Escherichia coli and of anaerobic Gram-positive, butyrate-producing bacteria of the Clostridium clusters IV and XIVa, and an increased abundance of Bacteroidetes and enterococci. Four resistance genes (aac(6')-Ii, ermC, qacA, tetQ), providing resistance to aminoglycosides, macrolides, disinfectants, and tetracyclines, respectively, were significantly more abundant among ICU patients than in healthy subjects, while a chloramphenicol resistance gene (catA) and a tetracycline resistance gene (tetW) were more abundant in healthy subjects. CONCLUSIONS The gut microbiota of SDD-treated ICU patients deviated strongly from the gut microbiota of healthy subjects. The negative effects on the resistome were limited to selection for four resistance genes. While it was not possible to disentangle the effects of SDD from confounding variables in the patient cohort, our data suggest that the risks associated with ICU hospitalization and SDD on selection for antibiotic resistance are limited. However, we found evidence indicating that recolonization of the gut by antibiotic-resistant bacteria may occur upon ICU discharge and cessation of SDD.
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Affiliation(s)
- Elena Buelow
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
- Université Limoges, INSERM, CHU Limoges, UMR 1092, Limoges, France
| | | | - Susana Fuentes
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Center for Immunology of Infectious Diseases and Vaccines, Bilthoven, The Netherlands
| | - Wouter A A de Steenhuijsen Piters
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Pediatric Immunology and Infectious Diseases, The Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leo Lahti
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Jumamurat R Bayjanov
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eline A M Majoor
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johanna C Braat
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maaike S M van Mourik
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Evelien A N Oostdijk
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marc J M Bonten
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mark W J van Passel
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Center of Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom.
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Paganelli FL, Huebner J, Singh KV, Zhang X, van Schaik W, Wobser D, Braat JC, Murray BE, Bonten MJM, Willems RJL, Leavis HL. Genome-wide Screening Identifies Phosphotransferase System Permease BepA to Be Involved in Enterococcus faecium Endocarditis and Biofilm Formation. J Infect Dis 2016; 214:189-95. [PMID: 26984142 DOI: 10.1093/infdis/jiw108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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: 12/10/2015] [Accepted: 03/07/2016] [Indexed: 02/02/2023] Open
Abstract
Enterococcus faecium is a common cause of nosocomial infections, of which infective endocarditis is associated with substantial mortality. In this study, we used a microarray-based transposon mapping (M-TraM) approach to evaluate a rat endocarditis model and identified a gene, originally annotated as "fruA" and renamed "bepA," putatively encoding a carbohydrate phosphotransferase system (PTS) permease (biofilm and endocarditis-associated permease A [BepA]), as important in infective endocarditis. This gene is highly enriched in E. faecium clinical isolates and absent in commensal isolates that are not associated with infection. Confirmation of the phenotype was established in a competition experiment of wild-type and a markerless bepA mutant in a rat endocarditis model. In addition, deletion of bepA impaired biofilm formation in vitro in the presence of 100% human serum and metabolism of β-methyl-D-glucoside. β-glucoside metabolism has been linked to the metabolism of glycosaminoglycans that are exposed on injured heart valves, where bacteria attach and form vegetations. Therefore, we propose that the PTS permease BepA is directly implicated in E. faecium pathogenesis.
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Affiliation(s)
- Fernanda L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Johannes Huebner
- Division of Pediatric Infectious Diseases, Hauner Children's Hospital, Ludwigs-Maximilian Universität München Center for Infectious Disease and Travel Medicine, University Medical Center Freiburg, Germany
| | - Kavindra V Singh
- Department of Internal Medicine, Division of Infectious Diseases Center for the Study of Emerging and Re-emerging Pathogens
| | - Xinglin Zhang
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Dominique Wobser
- Center for Infectious Disease and Travel Medicine, University Medical Center Freiburg, Germany
| | - Johanna C Braat
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Barbara E Murray
- Department of Internal Medicine, Division of Infectious Diseases Center for the Study of Emerging and Re-emerging Pathogens Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston
| | - Marc J M Bonten
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Helen L Leavis
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
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