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Top J, Verschuuren TD, Viveen MC, Riccio ME, Harbarth S, Kluytmans JAJW, Willems RJL, Paganelli FL. Gut microbiome dynamics in index patients colonized with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales after hospital discharge and their household contacts. Microbiol Spectr 2023; 11:e0127523. [PMID: 37888982 PMCID: PMC10714770 DOI: 10.1128/spectrum.01275-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Colonization with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) often precedes infections and is therefore considered as a great threat for public health. Here, we studied the gut microbiome dynamics in eight index patients colonized with ESBL-PE after hospital discharge and the impact of exposure to this index patient on the gut microbiome dynamics of their household contacts. We showed that the microbiome composition from index patients is different from their household contacts upon hospital discharge and that, in some of the index patients, their microbiome composition over time shifted toward the composition of their household contacts. In contrast, household contacts showed a stable microbiome composition over time irrespective of low-level extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) or extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) gut colonization, suggesting that, in healthy microbiomes, colonization resistance is able to prevent ESBL-PE expansion.
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Affiliation(s)
- Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Marco C. Viveen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - M. Eugenia Riccio
- University of Geneva Hospitals and Faculty of Medicine, Infection Control Program, WHO Collaborating Center, Geneva, Switzerland
| | - Stephan Harbarth
- University of Geneva Hospitals and Faculty of Medicine, Infection Control Program, WHO Collaborating Center, Geneva, Switzerland
| | - Jan A. J. W. Kluytmans
- 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
| | - Fernanda L. Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
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Stege PB, Hordijk J, Sandholt AKS, Zomer AL, Viveen MC, Rogers MRC, Salomons M, Wagenaar JA, Mughini-Gras L, Willems RJL, Paganelli FL. Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition. Microbiol Spectr 2023; 11:e0006323. [PMID: 37404183 PMCID: PMC10434115 DOI: 10.1128/spectrum.00063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The gut microbiome of humans and animals acts as a reservoir of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC). Dogs are known for having a high prevalence of ESBL-EC in their gut microbiota, although their ESBL-EC carrier status often shifts over time. We hypothesized that the gut microbiome composition of dogs is implicated in ESBL-EC colonization status. Therefore, we assessed whether ESBL-EC carriage in dogs is associated with changes in the gut microbiome and resistome. Fecal samples were collected longitudinally from 57 companion dogs in the Netherlands every 2 weeks for a total of 6 weeks (n = 4 samples/dog). Carriage of ESBL-EC was determined through selective culturing and PCR and in line with previous studies, we observed a high prevalence of ESBL-EC carriage in dogs. Using 16s rRNA gene profiling we found significant associations between detected ESBL-EC carriage and an increased abundance of Clostridium sensu stricto 1, Enterococcus, Lactococcus, and the shared genera of Escherichia-Shigella in the dog microbiome. A resistome capture sequencing approach (ResCap) furthermore, revealed associations between detected ESBL-EC carriage and the increased abundance of the antimicrobial resistance genes: cmlA, dfrA, dhfR, floR, and sul3. In summary, our study showed that ESBL-EC carriage is associated with a distinct microbiome and resistome composition. IMPORTANCE The gut microbiome of humans and animals is an important source of multidrug resistant pathogens, including beta-lactamase-producing Escherichia coli (ESBL-EC). In this study, we assessed if the carriage of ESBL-EC in dogs was associated with changes in gut composition of bacteria and antimicrobial resistant genes (ARGs). Therefore, stool samples from 57 dogs were collected every 2 weeks for a total of 6 weeks. Sixty eight percent of the dogs carried ESBL-EC during at least one of the time points analyzed. By investigating the gut microbiome and resistome composition, we observed specific changes at time points when dogs were colonized with ESBL-EC compared to time points whenESBL-EC were not detected. In conclusion, our study highlights the importance to study the microbial diversity in companion animals, as gut colonization of particular antimicrobial resistant bacteria might be an indication of a changed microbial composition that is associated with the selection of particular ARGs.
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Affiliation(s)
- Paul B. Stege
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joost Hordijk
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Arnar K. S. Sandholt
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Aldert L. Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from an One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Marco C. Viveen
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Malbert R. C. Rogers
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Moniek Salomons
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from an One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Rob J. L. Willems
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Fernanda L. Paganelli
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
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Boralli CMDS, Paganini JA, Meneses RS, Mata CPSMD, Leite EMM, Schürch AC, Paganelli FL, Willems RJL, Camargo ILBC. Characterization of blaKPC-2 and blaNDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone. Antibiotics (Basel) 2023; 12:antibiotics12050926. [PMID: 37237829 DOI: 10.3390/antibiotics12050926] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
The most common resistance mechanism to carbapenems is the production of carbapenemases. In 2021, the Pan American Health Organization warned of the emergence and increase in new carbapenemase combinations in Enterobacterales in Latin America. In this study, we characterized four Klebsiella pneumoniae isolates harboring blaKPC and blaNDM from an outbreak during the COVID-19 pandemic in a Brazilian hospital. We assessed their plasmids' transference ability, fitness effects, and relative copy number in different hosts. The K. pneumoniae BHKPC93 and BHKPC104 strains were selected for whole genome sequencing (WGS) based on their pulsed-field gel electrophoresis profile. The WGS revealed that both isolates belong to ST11, and 20 resistance genes were identified in each isolate, including blaKPC-2 and blaNDM-1. The blaKPC gene was present on a ~56 Kbp IncN plasmid and the blaNDM-1 gene on a ~102 Kbp IncC plasmid, along with five other resistance genes. Although the blaNDM plasmid contained genes for conjugational transfer, only the blaKPC plasmid conjugated to E. coli J53, without apparent fitness effects. The minimum inhibitory concentrations (MICs) of meropenem/imipenem against BHKPC93 and BHKPC104 were 128/64 and 256/128 mg/L, respectively. Although the meropenem and imipenem MICs against E. coli J53 transconjugants carrying the blaKPC gene were 2 mg/L, this was a substantial increment in the MIC relative to the original J53 strain. The blaKPC plasmid copy number was higher in K. pneumoniae BHKPC93 and BHKPC104 than in E. coli and higher than that of the blaNDM plasmids. In conclusion, two ST11 K. pneumoniae isolates that were part of a hospital outbreak co-harbored blaKPC-2 and blaNDM-1. The blaKPC-harboring IncN plasmid has been circulating in this hospital since at least 2015, and its high copy number might have contributed to the conjugative transfer of this particular plasmid to an E. coli host. The observation that the blaKPC-containing plasmid had a lower copy number in this E. coli strain may explain why this plasmid did not confer phenotypic resistance against meropenem and imipenem.
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Affiliation(s)
- Camila Maria Dos Santos Boralli
- Laboratory of Molecular Epidemiology and Microbiology, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | | | - Rodrigo Silva Meneses
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | | | | | - Anita C Schürch
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Fernanda L Paganelli
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Rob J L Willems
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Ilana Lopes Baratella Cunha Camargo
- Laboratory of Molecular Epidemiology and Microbiology, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
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Claus J, Ten Doesschate T, Gumbs C, van Werkhoven CH, van der Vaart TW, Janssen AB, Smits G, van Binnendijk R, van der Klis F, van Baarle D, Paganelli FL, Leavis H, Verhagen LM, Joosten SA, Bonten MJM, Netea MG, van de Wijgert JHHM. BCG Vaccination of Health Care Workers Does Not Reduce SARS-CoV-2 Infections nor Infection Severity or Duration: a Randomized Placebo-Controlled Trial. mBio 2023; 14:e0035623. [PMID: 36976004 PMCID: PMC10128007 DOI: 10.1128/mbio.00356-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Bacillus Calmette-Guerin (BCG) vaccination has been hypothesized to reduce severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, severity, and/or duration via trained immunity induction. Health care workers (HCWs) in nine Dutch hospitals were randomized to BCG or placebo vaccination (1:1) in March and April 2020 and followed for 1 year. They reported daily symptoms, SARS-CoV-2 test results, and health care-seeking behavior via a smartphone application, and they donated blood for SARS-CoV-2 serology at two time points. A total of 1,511 HCWs were randomized and 1,309 analyzed (665 BCG and 644 placebo). Of the 298 infections detected during the trial, 74 were detected by serology only. The SARS-CoV-2 incidence rates were 0.25 and 0.26 per person-year in the BCG and placebo groups, respectively (incidence rate ratio, 0.95; 95% confidence interval, 0.76 to 1.21; P = 0.732). Only three participants required hospitalization for SARS-CoV-2. The proportions of participants with asymptomatic, mild, or moderate infections and the mean infection durations did not differ between randomization groups. In addition, unadjusted and adjusted logistic regression and Cox proportional hazards models showed no differences between BCG and placebo vaccination for any of these outcomes. The percentage of participants with seroconversion (7.8% versus 2.8%; P = 0.006) and mean SARS-CoV-2 anti-S1 antibody concentration (13.1 versus 4.3 IU/mL; P = 0.023) were higher in the BCG than placebo group at 3 months but not at 6 or 12 months postvaccination. BCG vaccination of HCWs did not reduce SARS-CoV-2 infections nor infection duration or severity (ranging from asymptomatic to moderate). In the first 3 months after vaccination, BCG vaccination may enhance SARS-CoV-2 antibody production during SARS-CoV-2 infection. IMPORTANCE While several BCG trials in adults were conducted during the 2019 coronavirus disease epidemic, our data set is the most comprehensive to date, because we included serologically confirmed infections in addition to self-reported positive SARS-CoV-2 test results. We also collected data on symptoms for every day during the 1-year follow-up period, which enabled us to characterize infections in detail. We found that BCG vaccination did not reduce SARS-CoV-2 infections nor infection duration or severity but may have enhanced SARS-CoV-2 antibody production during SARS-CoV-2 infection in the first 3 months after vaccination. These results are in agreement with other BCG trials that reported negative results (but did not use serological endpoints), except for two trials in Greece and India that reported positive results but had few endpoints and included endpoints that were not laboratory confirmed. The enhanced antibody production is in agreement with prior mechanistic studies but did not translate into protection from SARS-CoV-2 infection.
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Affiliation(s)
- Juana Claus
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Thijs Ten Doesschate
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Cheyenne Gumbs
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Cornelis H van Werkhoven
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Thomas W van der Vaart
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Axel B Janssen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Gaby Smits
- National Institute of Public Health and the Environment, Bilthoven, Netherlands
| | - Rob van Binnendijk
- National Institute of Public Health and the Environment, Bilthoven, Netherlands
| | - Fiona van der Klis
- National Institute of Public Health and the Environment, Bilthoven, Netherlands
| | - Debbie van Baarle
- National Institute of Public Health and the Environment, Bilthoven, Netherlands
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, Netherlands
| | - Fernanda L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Helen Leavis
- Department of Internal Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Lilly M Verhagen
- Department of Pediatric Infectious Diseases and Immunology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Simone A Joosten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Marc J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Mihai G Netea
- Department of Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Janneke H H M van de Wijgert
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- National Institute of Public Health and the Environment, Bilthoven, Netherlands
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Bui BN, van Hoogenhuijze N, Viveen M, Mol F, Teklenburg G, de Bruin JP, Besselink D, Brentjens LS, Mackens S, Rogers MRC, Steba GS, Broekmans F, Paganelli FL, van de Wijgert JHHM. The endometrial microbiota of women with or without a live birth within 12 months after a first failed IVF/ICSI cycle. Sci Rep 2023; 13:3444. [PMID: 36859567 PMCID: PMC9977966 DOI: 10.1038/s41598-023-30591-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/27/2023] [Indexed: 03/03/2023] Open
Abstract
The endometrial microbiota composition may be associated with implantation success. However, a 'core' composition has not yet been defined. This exploratory study analysed the endometrial microbiota by 16S rRNA sequencing (V1-V2 region) of 141 infertile women whose first IVF/ICSI cycle failed and compared the microbiota profiles of women with and without a live birth within 12 months of follow-up, and by infertility cause and type. Lactobacillus was the most abundant genus in the majority of samples. Women with a live birth compared to those without had significantly higher Lactobacillus crispatus relative abundance (RA) (p = 0.029), and a smaller proportion of them had ≤ 10% L. crispatus RA (42.1% and 70.4%, respectively; p = 0.015). A smaller proportion of women in the male factor infertility group had ≤ 10% L. crispatus RA compared to women in the unexplained and other infertility causes groups combined (p = 0.030). Women with primary infertility compared to secondary infertility had significantly higher L. crispatus RA (p = 0.004); lower proportions of them had ≤ 10% L. crispatus RA (p = 0.009) and > 10% Gardnerella vaginalis RA (p = 0.019). In conclusion, IVF/ICSI success may be associated with L. crispatus RA and secondary infertility with endometrial dysbiosis, more often than primary infertility. These hypotheses should be tested in rigorous well-powered longitudinal studies.
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Affiliation(s)
- Bich Ngoc Bui
- Department of Gynaecology and Reproductive Medicine, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands. .,UMC Utrecht, Huispostnummer F.05.126, Postbus 85500, 3508 GA, Utrecht, The Netherlands.
| | - Nienke van Hoogenhuijze
- grid.7692.a0000000090126352Department of Gynaecology and Reproductive Medicine, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Marco Viveen
- grid.7692.a0000000090126352Department of Medical Microbiology, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Femke Mol
- grid.7177.60000000084992262Center for Reproductive Medicine, Reproduction and Development, Amsterdam University Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Gijs Teklenburg
- grid.452600.50000 0001 0547 5927Isala Fertility Clinic, Isala Hospital, Dokter Van Heesweg 2, 8025 AB Zwolle, The Netherlands
| | - Jan-Peter de Bruin
- grid.413508.b0000 0004 0501 9798Department of Obstetrics and Gynaecology, Jeroen Bosch Hospital, Henri Dunantstraat 1, 5223 GZ ’s-Hertogenbosch, The Netherlands
| | - Dagmar Besselink
- grid.10417.330000 0004 0444 9382Department of Obstetrics and Gynaecology, Radboud University Medical Centre, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Linda Stevens Brentjens
- grid.412966.e0000 0004 0480 1382Department of Obstetrics and Gynaecology, Maastricht University Medical Centre, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands
| | - Shari Mackens
- grid.8767.e0000 0001 2290 8069Brussels IVF, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Malbert R. C. Rogers
- grid.7692.a0000000090126352Department of Medical Microbiology, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Gaby S. Steba
- grid.7692.a0000000090126352Department of Gynaecology and Reproductive Medicine, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Frank Broekmans
- grid.7692.a0000000090126352Department of Gynaecology and Reproductive Medicine, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Fernanda L. Paganelli
- grid.7692.a0000000090126352Department of Medical Microbiology, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Janneke H. H. M. van de Wijgert
- grid.5477.10000000120346234Julius Center for Health Sciences and Primary Care, Utrecht University, Universiteitsweg 100, 3584 CX Utrecht, The Netherlands
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van Kersen W, Bossers A, de Steenhuijsen Piters WAA, de Rooij MMT, Bonten M, Fluit AC, Heederik D, Paganelli FL, Rogers M, Viveen M, Bogaert D, Leavis HL, Smit LAM. Air pollution from livestock farms and the oropharyngeal microbiome of COPD patients and controls. Environ Int 2022; 169:107497. [PMID: 36088872 DOI: 10.1016/j.envint.2022.107497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/22/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Air pollution from livestock farms is known to affect respiratory health of patients with chronic obstructive pulmonary disease (COPD). The mechanisms behind this relationship, however, remain poorly understood. We hypothesise that air pollutants could influence respiratory health through modulation of the airway microbiome. Therefore, we studied associations between air pollution exposure and the oropharyngeal microbiota (OPM) composition of COPD patients and controls in a livestock-dense area. Oropharyngeal swabs were collected from 99 community-based (mostly mild) COPD cases and 184 controls (baseline), and after 6 and 12 weeks. Participants were non-smokers or former smokers. Annual average livestock-related outdoor air pollution at the home address was predicted using dispersion modelling. OPM composition was analysed using 16S rRNA-based sequencing in all baseline samples and 6-week and 12-week repeated samples of 20 randomly selected subjects (n = 323 samples). A random selection of negative control swabs, taken every sampling day, were also included in the downstream analysis. Both farm-emitted endotoxin and PM10 levels were associated with increased OPM richness in COPD patients (p < 0.05) but not in controls. COPD case-control status was not associated with community structure, while correcting for known confounders (multivariate PERMANOVA p > 0.05). However, members of the genus Streptococcus were more abundant in COPD patients (Benjamini-Hochberg adjusted p < 0.01). Moderate correlation was found between ordinations of 20 subjects analysed at 0, 6, and 12 weeks (Procrustes r = 0.52 to 0.66; p < 0.05; Principal coordinate analysis of Bray-Curtis dissimilarity), indicating that the OPM is relatively stable over a 12 week period and that a single sample sufficiently represents the OPM. Air pollution from livestock farms is associated with OPM richness of COPD patients, suggesting that the OPM of COPD patients is susceptible to alterations induced by exposure to air pollutants.
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Affiliation(s)
- Warner van Kersen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Alex Bossers
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Wouter A A de Steenhuijsen Piters
- University Medical Center Utrecht, Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Myrna M T de Rooij
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Marc Bonten
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ad C Fluit
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Dick Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | | | - Malbert Rogers
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marco Viveen
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Debby Bogaert
- University Medical Center Utrecht, Utrecht, the Netherlands; University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Helen L Leavis
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands.
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Pursey E, Dimitriu T, Paganelli FL, Westra ER, van Houte S. CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200464. [PMID: 34839714 PMCID: PMC8628084 DOI: 10.1098/rstb.2020.0464] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 03/30/2021] [Accepted: 07/21/2021] [Indexed: 01/19/2023] Open
Abstract
The acquisition of antibiotic resistance (ABR) genes via horizontal gene transfer (HGT) is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic material, and may therefore limit the acquisition of ABR. CRISPR-Cas adaptive immune systems are one of the most prevalent defences in bacteria, found in roughly half of bacterial genomes, but it has remained unclear if and how much they contribute to restricting the spread of ABR. We analysed approximately 40 000 whole genomes comprising the full RefSeq dataset for 11 species of clinically important genera of human pathogens, including Enterococcus, Staphylococcus, Acinetobacter and Pseudomonas. We modelled the association between CRISPR-Cas and indicators of HGT, and found that pathogens with a CRISPR-Cas system were less likely to carry ABR genes than those lacking this defence system. Analysis of the mobile genetic elements (MGEs) targeted by CRISPR-Cas supports a model where this host defence system blocks important vectors of ABR. These results suggest a potential 'immunocompromised' state for multidrug-resistant strains that may be exploited in tailored interventions that rely on MGEs, such as phages or phagemids, to treat infections caused by bacterial pathogens. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
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Affiliation(s)
- Elizabeth Pursey
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, Cornwall, UK
| | - Tatiana Dimitriu
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, Cornwall, UK
| | - Fernanda L. Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Edze R. Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, Cornwall, UK
| | - Stineke van Houte
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, Cornwall, UK
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Ten Doesschate T, Abbott IJ, Willems RJL, Top J, Rogers MRC, Bonten MM, Paganelli FL. In vivo acquisition of fosfomycin resistance in Escherichia coli by fosA transmission from commensal flora. J Antimicrob Chemother 2020; 74:3630-3632. [PMID: 31511878 PMCID: PMC6857190 DOI: 10.1093/jac/dkz380] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Thijs Ten Doesschate
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Iain J Abbott
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Malbert R C Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Marc M Bonten
- Department of Medical Microbiology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Fernanda L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
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9
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Berbers RM, Mohamed Hoesein FAA, Ellerbroek PM, van Montfrans JM, Dalm VASH, van Hagen PM, Paganelli FL, Viveen MC, Rogers MRC, de Jong PA, Uh HW, Willems RJL, Leavis HL. Low IgA Associated With Oropharyngeal Microbiota Changes and Lung Disease in Primary Antibody Deficiency. Front Immunol 2020; 11:1245. [PMID: 32636843 PMCID: PMC7318304 DOI: 10.3389/fimmu.2020.01245] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/18/2020] [Indexed: 12/14/2022] Open
Abstract
Common Variable Immunodeficiency (CVID) and X-linked agammaglobulinemia (XLA) are primary antibody deficiencies characterized by hypogammaglobulinemia and recurrent infections, which can lead to structural airway disease (AD) and interstitial lung disease (ILD). We investigated associations between serum IgA, oropharyngeal microbiota composition and severity of lung disease in these patients. In this cross-sectional multicentre study we analyzed oropharyngeal microbiota composition of 86 CVID patients, 12 XLA patients and 49 healthy controls (HC) using next-generation sequencing of the 16S rRNA gene. qPCR was used to estimate bacterial load. IgA was measured in serum. High resolution CT scans were scored for severity of AD and ILD. Oropharyngeal bacterial load was increased in CVID patients with low IgA (p = 0.013) and XLA (p = 0.029) compared to HC. IgA status was associated with distinct beta (between-sample) diversity (p = 0.039), enrichment of (Allo)prevotella, and more severe radiographic lung disease (p = 0.003), independently of recent antibiotic use. AD scores were positively associated with Prevotella, Alloprevotella, and Selenomonas, and ILD scores with Streptococcus and negatively with Rothia. In clinically stable patients with CVID and XLA, radiographic lung disease was associated with IgA deficiency and expansion of distinct oropharyngeal bacterial taxa. Our findings highlight IgA as a potential driver of upper respiratory tract microbiota homeostasis.
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Affiliation(s)
- Roos-Marijn Berbers
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | | | - Pauline M Ellerbroek
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Joris M van Montfrans
- Department of Paediatric Immunology and Infectious Diseases, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Virgil A S H Dalm
- Division of Clinical Immunology, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (RIDC), Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - P Martin van Hagen
- Division of Clinical Immunology, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (RIDC), Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Fernanda L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Marco C Viveen
- Department of Medical Microbiology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Malbert R C Rogers
- Department of Medical Microbiology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Pim A de Jong
- Department of Radiology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Hae-Won Uh
- Department of Biostatistics and Research Support, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
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10
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Pleguezuelos-Manzano C, Puschhof J, Rosendahl Huber A, van Hoeck A, Wood HM, Nomburg J, Gurjao C, Manders F, Dalmasso G, Stege PB, Paganelli FL, Geurts MH, Beumer J, Mizutani T, Miao Y, van der Linden R, van der Elst S, Garcia KC, Top J, Willems RJL, Giannakis M, Bonnet R, Quirke P, Meyerson M, Cuppen E, van Boxtel R, Clevers H. Mutational signature in colorectal cancer caused by genotoxic pks + E. coli. Nature 2020; 580:269-273. [PMID: 32106218 PMCID: PMC8142898 DOI: 10.1038/s41586-020-2080-8] [Citation(s) in RCA: 522] [Impact Index Per Article: 130.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 02/17/2020] [Indexed: 02/06/2023]
Abstract
Various species of the intestinal microbiota have been associated with the development of colorectal cancer1,2, but it has not been demonstrated that bacteria have a direct role in the occurrence of oncogenic mutations. Escherichia coli can carry the pathogenicity island pks, which encodes a set of enzymes that synthesize colibactin3. This compound is believed to alkylate DNA on adenine residues4,5 and induces double-strand breaks in cultured cells3. Here we expose human intestinal organoids to genotoxic pks+ E. coli by repeated luminal injection over five months. Whole-genome sequencing of clonal organoids before and after this exposure revealed a distinct mutational signature that was absent from organoids injected with isogenic pks-mutant bacteria. The same mutational signature was detected in a subset of 5,876 human cancer genomes from two independent cohorts, predominantly in colorectal cancer. Our study describes a distinct mutational signature in colorectal cancer and implies that the underlying mutational process results directly from past exposure to bacteria carrying the colibactin-producing pks pathogenicity island.
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Affiliation(s)
- Cayetano Pleguezuelos-Manzano
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Jens Puschhof
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Axel Rosendahl Huber
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Arne van Hoeck
- Oncode Institute, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Henry M Wood
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Jason Nomburg
- Graduate Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Carino Gurjao
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Freek Manders
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Guillaume Dalmasso
- University Clermont Auvergne, Inserm U1071, INRA USC2018, M2iSH, Clermont-Ferrand, France
| | - Paul B Stege
- 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
| | - Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Joep Beumer
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
| | - Tomohiro Mizutani
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Yi Miao
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Reinier van der Linden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
| | - Stefan van der Elst
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Janetta Top
- 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
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard Bonnet
- University Clermont Auvergne, Inserm U1071, INRA USC2018, M2iSH, Clermont-Ferrand, France
- Department of Bacteriology, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | - Phil Quirke
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Edwin Cuppen
- Oncode Institute, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
- Hartwig Medical Foundation, Amsterdam, The Netherlands
- CPCT Consortium, Rotterdam, The Netherlands
| | - Ruben van Boxtel
- Oncode Institute, Utrecht, The Netherlands.
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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11
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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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12
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Paganelli FL, Luyer M, Hazelbag CM, Uh HW, Rogers MRC, Adriaans D, Berbers RM, Hendrickx APA, Viveen MC, Groot JA, Bonten MJM, Fluit AC, Willems RJL, Leavis HL. Roux-Y Gastric Bypass and Sleeve Gastrectomy directly change gut microbiota composition independent of surgery type. Sci Rep 2019; 9:10979. [PMID: 31358818 PMCID: PMC6662812 DOI: 10.1038/s41598-019-47332-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 07/08/2019] [Indexed: 02/07/2023] Open
Abstract
Bariatric surgery in morbid obesity, either through sleeve gastrectomy (SG) or Roux-Y gastric bypass (RYGB), leads to sustainable weight loss, improvement of metabolic disorders and changes in intestinal microbiota. Yet, the relationship between changes in gut microbiota, weight loss and surgical procedure remains incompletely understood. We determined temporal changes in microbiota composition in 45 obese patients undergoing crash diet followed by SG (n = 22) or RYGB (n = 23). Intestinal microbiota composition was determined before intervention (baseline, S1), 2 weeks after crash diet (S2), and 1 week (S3), 3 months (S4) and 6 months (S5) after surgery. Relative to S1, the microbial diversity index declined at S2 and S3 (p < 0.05), and gradually returned to baseline levels at S5. Rikenellaceae relative abundance increased and Ruminococcaceae and Streptococcaceae abundance decreased at S2 (p < 0.05). At S3, Bifidobacteriaceae abundance decreased, whereas those of Streptococcaceae and Enterobacteriaceae increased (p < 0.05). Increased weight loss between S3-S5 was not associated with major changes in microbiota composition. No significant differences appeared between both surgical procedures. In conclusion, undergoing a crash diet and bariatric surgery were associated with an immediate but temporary decline in microbial diversity, with immediate and permanent changes in microbiota composition, independent of surgery type.
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Affiliation(s)
- Fernanda L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Misha Luyer
- Department of Surgery, Catharina Hospital Eindhoven, Eindhoven, The Netherlands
| | - C Marijn Hazelbag
- Department of Biostatistics and Research Support, Julius Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Hae-Won Uh
- Department of Biostatistics and Research Support, Julius Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Malbert R C Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Danielle Adriaans
- Department of Surgery, Catharina Hospital Eindhoven, Eindhoven, The Netherlands
| | - Roos-Marijn Berbers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Antoni P A Hendrickx
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marco C Viveen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - James A Groot
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marc J M Bonten
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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13
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Paganelli FL, Ekkelenkamp MB. Is Microbiota Research Advancing Our Understanding of Infection? Clin Infect Dis 2019; 68:1300-1302. [PMID: 30321292 DOI: 10.1093/cid/ciy712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 08/16/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fernanda L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Miquel B Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
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14
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Paganelli FL, van de Kamer T, Brouwer EC, Leavis HL, Woodford N, Bonten MJ, Willems RJ, Hendrickx AP. Lipoteichoic acid synthesis inhibition in combination with antibiotics abrogates growth of multidrug-resistant Enterococcus faecium. Int J Antimicrob Agents 2017; 49:355-363. [DOI: 10.1016/j.ijantimicag.2016.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/28/2016] [Accepted: 12/03/2016] [Indexed: 01/01/2023]
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15
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Arenas J, Paganelli FL, Rodríguez-Castaño P, Cano-Crespo S, van der Ende A, van Putten JPM, Tommassen J. Expression of the Gene for Autotransporter AutB of Neisseria meningitidis Affects Biofilm Formation and Epithelial Transmigration. Front Cell Infect Microbiol 2016; 6:162. [PMID: 27921012 PMCID: PMC5118866 DOI: 10.3389/fcimb.2016.00162] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/07/2016] [Indexed: 11/15/2022] Open
Abstract
Neisseria meningitidis is a Gram-negative bacterium that resides as a commensal in the upper respiratory tract of humans, but occasionally, it invades the host and causes sepsis and/or meningitis. The bacterium can produce eight autotransporters, seven of which have been studied to some detail. The remaining one, AutB, has not been characterized yet. Here, we show that the autB gene is broadly distributed among pathogenic Neisseria spp. The gene is intact in most meningococcal strains. However, its expression is prone to phase variation due to slipped-strand mispairing at AAGC repeats located within the DNA encoding the signal sequence and is switched off in the vast majority of these strains. Moreover, various genetic disruptions prevent autB expression in most of the strains in which the gene is in phase indicating a strong selection against AutB synthesis. We observed that autB is expressed in two of the strains examined and that AutB is secreted and exposed at the cell surface. Functionality assays revealed that AutB synthesis promotes biofilm formation and delays the passage of epithelial cell layers in vitro. We hypothesize that this autotransporter is produced during the colonization process only in specific niches to facilitate microcolony formation, but its synthesis is switched off probably to evade the immune system and facilitate human tissue invasion.
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Affiliation(s)
- Jesús Arenas
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University Utrecht, Netherlands
| | - Fernanda L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands
| | - Patricia Rodríguez-Castaño
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University Utrecht, Netherlands
| | - Sara Cano-Crespo
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University Utrecht, Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology, Academic Medical Center Amsterdam, Netherlands
| | - Jos P M van Putten
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University Utrecht, Netherlands
| | - Jan Tommassen
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht University Utrecht, Netherlands
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16
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Amin Yavari S, Loozen L, Paganelli FL, Bakhshandeh S, Lietaert K, Groot JA, Fluit AC, Boel CHE, Alblas J, Vogely HC, Weinans H, Zadpoor AA. Antibacterial Behavior of Additively Manufactured Porous Titanium with Nanotubular Surfaces Releasing Silver Ions. ACS Appl Mater Interfaces 2016; 8:17080-17089. [PMID: 27300485 DOI: 10.1021/acsami.6b03152] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Additive manufacturing (3D printing) has enabled fabrication of geometrically complex and fully interconnected porous biomaterials with huge surface areas that could be used for biofunctionalization to achieve multifunctional biomaterials. Covering the huge surface area of such porous titanium with nanotubes has been already shown to result in improved bone regeneration performance and implant fixation. In this study, we loaded TiO2 nanotubes with silver antimicrobial agents to equip them with an additional biofunctionality, i.e., antimicrobial behavior. An optimized anodizing protocol was used to create nanotubes on the entire surface area of direct metal printed porous titanium scaffolds. The nanotubes were then loaded by soaking them in three different concentrations (i.e., 0.02, 0.1, and 0.5 M) of AgNO3 solution. The antimicrobial behavior and cell viability of the developed biomaterials were assessed. As far as the early time points (i.e., up to 1 day) are concerned, the biomaterials were found to be extremely effective in preventing biofilm formation and decreasing the number of planktonic bacteria particularly for the middle and high concentrations of silver ions. Interestingly, nanotubes not loaded with antimicrobial agents also showed significantly smaller numbers of adherent bacteria at day 1, which may be attributed to the bactericidal effect of high aspect ratio nanotopographies. The specimens with the highest concentrations of antimicrobial agents adversely affected cell viability at day 1, but this effect is expected to decrease or disappear in the following days as the rate of release of silver ions was observed to markedly decrease within the next few days. The antimicrobial effects of the biomaterials, particularly the ones with the middle and high concentrations of antimicrobial agents, continued until 2 weeks. The potency of the developed biomaterials in decreasing the number of planktonic bacteria and hindering the formation of biofilms make them promising candidates for combating peri-operative implant-associated infections.
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Affiliation(s)
- S Amin Yavari
- Department of Orthopedics, University Medical Centre Utrecht , 3584 CX Utrecht, The Netherlands
- Department of Biomechanical Engineering, Delft University of Technology , 2628 CD Delft, The Netherlands
| | - L Loozen
- Department of Orthopedics, University Medical Centre Utrecht , 3584 CX Utrecht, The Netherlands
| | - F L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht , 3584 CX Utrecht, The Netherlands
| | - S Bakhshandeh
- Department of Biomechanical Engineering, Delft University of Technology , 2628 CD Delft, The Netherlands
| | - K Lietaert
- 3D Systems-LayerWise NV, 3001 Leuven, Belgium
- Department of Materials Engineering, Katholieke Universiteit Leuven , 3000 Leuven, Belgium
| | - J A Groot
- Department of Medical Microbiology, University Medical Center Utrecht , 3584 CX Utrecht, The Netherlands
| | - A C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht , 3584 CX Utrecht, The Netherlands
| | - C H E Boel
- Department of Medical Microbiology, University Medical Center Utrecht , 3584 CX Utrecht, The Netherlands
| | - J Alblas
- Department of Orthopedics, University Medical Centre Utrecht , 3584 CX Utrecht, The Netherlands
| | - H C Vogely
- Department of Orthopedics, University Medical Centre Utrecht , 3584 CX Utrecht, The Netherlands
| | - H Weinans
- Department of Orthopedics, University Medical Centre Utrecht , 3584 CX Utrecht, The Netherlands
- Department of Biomechanical Engineering, Delft University of Technology , 2628 CD Delft, The Netherlands
- Department of Rheumatology, University Medical Centre Utrecht , 3584 CX Utrecht, The Netherlands
| | - A A Zadpoor
- Department of Biomechanical Engineering, Delft University of Technology , 2628 CD Delft, The Netherlands
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17
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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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de Gier MG, Bauke Albada H, Josten M, Willems R, Leavis H, van Mansveld R, Paganelli FL, Dekker B, Lammers JWJ, Sahl HG, Metzler-Nolte N. Synergistic activity of a short lipidated antimicrobial peptide (lipoAMP) and colistin or tobramycin against Pseudomonas aeruginosa from cystic fibrosis patients. Med Chem Commun 2016. [DOI: 10.1039/c5md00373c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synergistic effects between a lipoAMP and colistin against clinical P. aeruginosa strains isolated from cystic fibrosis patients are described.
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Top J, Paganelli FL, Zhang X, van Schaik W, Leavis HL, van Luit-Asbroek M, van der Poll T, Leendertse M, Bonten MJM, Willems RJL. The Enterococcus faecium enterococcal biofilm regulator, EbrB, regulates the esp operon and is implicated in biofilm formation and intestinal colonization. PLoS One 2013; 8:e65224. [PMID: 23741484 PMCID: PMC3669262 DOI: 10.1371/journal.pone.0065224] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/23/2013] [Indexed: 11/18/2022] Open
Abstract
Nowadays, Enterococcus faecium is one of the leading nosocomial pathogens worldwide. Strains causing clinical infections or hospital outbreaks are enriched in the enterococcal surface protein (Esp) encoding ICEEfm1 mobile genetic element. Previous studies showed that Esp is involved in biofilm formation, endocarditis and urinary tract infections. In this study, we characterized the role of the putative AraC type of regulator (locus tag EfmE1162_2351), which we renamed ebrB and which is, based on the currently available whole genome sequences, always located upstream of the esp gene, and studied its role in Esp surface exposure during growth. A markerless deletion mutant of ebrB resulted in reduced esp expression and complete abolishment of Esp surface exposure, while Esp cell-surface exposure was restored when this mutant was complemented with an intact copy of ebrB. This demonstrates a role for EbrB in esp expression. However, during growth, ebrB expression levels did not change over time, while an increase in esp expression at both RNA and protein level was observed during mid-log and late-log phase. These results indicate the existence of a secondary regulation system for esp, which might be an unknown quorum sensing system as the enhanced esp expression seems to be cell density dependent. Furthermore, we determined that esp is part of an operon of at least 3 genes putatively involved in biofilm formation. A semi-static biofilm model revealed reduced biofilm formation for the EbrB deficient mutant, while dynamics of biofilm formation using a flow cell system revealed delayed biofilm formation in the ebrB mutant. In a mouse intestinal colonization model the ebrB mutant was less able to colonize the gut compared to wild-type strain, especially in the small intestine. These data indicate that EbrB positively regulates the esp operon and is implicated in biofilm formation and intestinal colonization.
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Affiliation(s)
- Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
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Zhang X, Paganelli FL, Bierschenk D, Kuipers A, Bonten MJM, Willems RJL, van Schaik W. Genome-wide identification of ampicillin resistance determinants in Enterococcus faecium. PLoS Genet 2012; 8:e1002804. [PMID: 22761597 PMCID: PMC3386183 DOI: 10.1371/journal.pgen.1002804] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 05/17/2012] [Indexed: 01/03/2023] Open
Abstract
Enterococcus faecium has become a nosocomial pathogen of major importance, causing infections that are difficult to treat owing to its multi-drug resistance. In particular, resistance to the β-lactam antibiotic ampicillin has become ubiquitous among clinical isolates. Mutations in the low-affinity penicillin binding protein PBP5 have previously been shown to be important for ampicillin resistance in E. faecium, but the existence of additional resistance determinants has been suggested. Here, we constructed a high-density transposon mutant library in E. faecium and developed a transposon mutant tracking approach termed Microarray-based Transposon Mapping (M-TraM), leading to the identification of a compendium of E. faecium genes that contribute to ampicillin resistance. These genes are part of the core genome of E. faecium, indicating a high potential for E. faecium to evolve towards β-lactam resistance. To validate the M-TraM results, we adapted a Cre-lox recombination system to construct targeted, markerless mutants in E. faecium. We confirmed the role of four genes in ampicillin resistance by the generation of targeted mutants and further characterized these mutants regarding their resistance to lysozyme. The results revealed that ddcP, a gene predicted to encode a low-molecular-weight penicillin binding protein with D-alanyl-D-alanine carboxypeptidase activity, was essential for high-level ampicillin resistance. Furthermore, deletion of ddcP sensitized E. faecium to lysozyme and abolished membrane-associated D,D-carboxypeptidase activity. This study has led to the development of a broadly applicable platform for functional genomic-based studies in E. faecium, and it provides a new perspective on the genetic basis of ampicillin resistance in this organism. Enterococcus faecium has emerged as an important nosocomial pathogen around the world. Clinical E. faecium isolates are often resistant to multiple antibiotics, thereby complicating therapeutic interventions. However, the molecular mechanisms that contribute to the recent emergence of E. faecium as a nosocomial pathogen of major importance are only poorly understood, which is, at least partially, due to the lack of appropriate genetic tools for the study of this organism. Here, we developed a systematic genome-wide strategy, based on transposon mutagenesis and microarray-based screening, to identify E. faecium genes that contribute to ampicillin resistance. We also adapted the Cre-lox recombination system to construct targeted, markerless mutants in E. faecium. These tools enabled us to perform both high-throughput genome-wide analysis and specific targeted investigations in a clinical E. faecium isolate. We comprehensively identified, confirmed, and characterized a compendium of genes affecting the sensitivity to ampicillin in E. faecium. The identified intrinsic ampicillin resistance determinants are highly conserved among E. faecium, indicating that this organism has a high potential to evolve towards ampicillin resistance. These ampicillin-resistance determinants may serve as targets for the development of novel antimicrobial therapeutics.
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Affiliation(s)
- Xinglin Zhang
- 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
| | - Damien Bierschenk
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Annemarie Kuipers
- 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
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
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Paganelli FL, Willems RJ, Leavis HL. Optimizing future treatment of enterococcal infections: attacking the biofilm? Trends Microbiol 2011; 20:40-9. [PMID: 22169461 DOI: 10.1016/j.tim.2011.11.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/19/2011] [Accepted: 11/02/2011] [Indexed: 11/16/2022]
Abstract
Enterococcus faecalis and Enterococcus faecium are among the leading causative agents of nosocomial infections and are infamous for their resistance to many antibiotics. They cause difficult-to-treat infections, often originating from biofilm-mediated infections associated with implanted medical devices or endocarditis. Biofilms protect bacteria against antibiotics and phagocytosis, and physical removal of devices or infected tissue is often needed but is frequently not possible. Currently there are no clinically available compounds that disassemble biofilms. In this review we discuss all known structural and regulatory genes involved in enterococcal biofilm formation, the compounds directed against biofilm formation that have been studied, and potentially useful targets for future drugs to treat enterococcal biofilm-associated infections.
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Affiliation(s)
- Fernanda L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
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