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Costa AR, van den Berg DF, Esser JQ, Muralidharan A, van den Bossche H, Bonilla BE, van der Steen BA, Haagsma AC, Fluit AC, Nobrega FL, Haas PJ, Brouns SJJ. Accumulation of defense systems in phage-resistant strains of Pseudomonas aeruginosa. Sci Adv 2024; 10:eadj0341. [PMID: 38394193 PMCID: PMC10889362 DOI: 10.1126/sciadv.adj0341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Prokaryotes encode multiple distinct anti-phage defense systems in their genomes. However, the impact of carrying a multitude of defense systems on phage resistance remains unclear, especially in a clinical context. Using a collection of antibiotic-resistant clinical strains of Pseudomonas aeruginosa and a broad panel of phages, we demonstrate that defense systems contribute substantially to defining phage host range and that overall phage resistance scales with the number of defense systems in the bacterial genome. We show that many individual defense systems target specific phage genera and that defense systems with complementary phage specificities co-occur in P. aeruginosa genomes likely to provide benefits in phage-diverse environments. Overall, we show that phage-resistant phenotypes of P. aeruginosa with at least 19 phage defense systems exist in the populations of clinical, antibiotic-resistant P. aeruginosa strains.
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Affiliation(s)
- Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Daan F. van den Berg
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Jelger Q. Esser
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Aswin Muralidharan
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Halewijn van den Bossche
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Boris Estrada Bonilla
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Baltus A. van der Steen
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Anna C. Haagsma
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Ad C. Fluit
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Franklin L. Nobrega
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Stan J. J. Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
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Martischang R, Seth-Smith H, Verschuuren TD, Héquet D, Gaïa N, François P, Fluit AC, Kluytmans JAJW, Seiffert SN, Tacconelli E, Cherkaoui A, Harbarth S, Egli A, Kohler P. Regional spread of an atypical ESBL-producing Escherichia coli ST131H89 clone among different human and environmental reservoirs in Western Switzerland. Antimicrob Agents Chemother 2024; 68:e0092523. [PMID: 38169291 PMCID: PMC10848748 DOI: 10.1128/aac.00925-23] [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: 07/12/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
We describe the inter-regional spread of a novel ESBL-producing Escherichia coli subclone (ST131H89) in long-term care facility residents, general population, and environmental water sources in Western Switzerland between 2017 and 2020. The study highlights the importance of molecular surveillance for tracking emerging antibiotic-resistant pathogens in healthcare and community settings.
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Affiliation(s)
- Romain Martischang
- Infection Control Programme and WHO Collaborating Centre, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Helena Seth-Smith
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, Applied Microbiology Research, Basel University, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Tess D. Verschuuren
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Delphine Héquet
- Unité Cantonale Hygiène, Prévention et Contrôle de l’infection, Canton de Vaud, Switzerland
| | - Nadia Gaïa
- Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Patrice François
- Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Ad C. Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jan A. J. W. Kluytmans
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Salome N. Seiffert
- Division of Human Microbiology, Centre for Laboratory Medicine, St. Gallen, Switzerland
| | - Evelina Tacconelli
- Department of Diagnostics and Public Health, Infectious Diseases, Verona University, Verona, Italy
- Department of Internal Medicine Infectious Diseases, Tübingen University, Tübingen, Germany
| | | | - Stephan Harbarth
- Infection Control Programme and WHO Collaborating Centre, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, Applied Microbiology Research, Basel University, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Philipp Kohler
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
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3
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Naing SY, Duim B, Broens EM, Schweitzer V, Zomer A, van der Graaf-van Bloois L, van der Meer C, Stellingwerff L, Fluit AC, Wagenaar JA. Molecular Characterization and Clinical Relevance of Taxonomic Reassignment of Staphylococcus schleiferi Subspecies into Two Separate Species, Staphylococcus schleiferi and Staphylococcus coagulans. Microbiol Spectr 2023; 11:e0467022. [PMID: 36853031 PMCID: PMC10101015 DOI: 10.1128/spectrum.04670-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/08/2023] [Indexed: 03/01/2023] Open
Abstract
Staphylococcus schleiferi is an opportunistic pathogen in humans and dogs. Recent taxonomic reassignment of its subspecies (S. schleiferi subsp. schleiferi and S. schleiferi subsp. coagulans) into two separate species (S. schleiferi and S. coagulans) lacks supporting data for diagnostic implications and clinical relevance. We aimed to confirm the reclassification of S. schleiferi by using genomic and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data for a large set of isolates from humans and animals to investigate their molecular epidemiology and clinical relevance. Routine MALDI-TOF analysis and Illumina sequencing were performed on 165 S. schleiferi isolates from the Netherlands. With 33 publicly available genomes, the study included 198 genomes from 149 dogs, 34 humans, and 15 other sources. The Type Strain Genome Server was used to identify species in the genomes, and the MALDI-TOF MS database was extended to improve species differentiation. MALDI-TOF did not discriminate between S. schleiferi and S. coagulans. Genome phylogeny distinguished the two species in two monophyletic clusters. S. schleiferi isolates originated from humans, while S. coagulans isolates were found in animals and three human isolates clustering with the animal isolates. The sialidase B gene (nanB) was a unique marker gene for S. schleiferi, whereas the chrA gene was exclusive for S. coagulans. The mecA gene was exclusively detected in S. coagulans, as were the lnu(A), blaZ, erm(B/C), tet(O/M), and aac(6')-aph(2'') genes. The MALDI-TOF database extension did not improve differentiation between the two species. Even though our whole-genome sequencing-based approach showed clear differentiation between these two species, it remains critical to identify S. schleiferi and S. coagulans correctly in routine diagnostics. IMPORTANCE This study clearly shows that S. schleiferi is a concern in human hospital settings, whereas S. coagulans predominantly causes infections in animals. S. coagulans is more resistant to antibiotics and can sometimes transmit to humans via exposure to infected dogs. Even though genome-based methods can clearly differentiate the two species, current diagnostic methods used routinely in clinical microbiology laboratories cannot distinguish the two bacterial species.
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Affiliation(s)
- Soe Yu Naing
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Birgitta Duim
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Els M. Broens
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Valentijn Schweitzer
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Aldert Zomer
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Linda van der Graaf-van Bloois
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Coby van der Meer
- Certe Medical Microbiology Friesland and Noordoostpolder, Leeuwarden, the Netherlands
| | - Luutsen Stellingwerff
- Certe Medical Microbiology Friesland and Noordoostpolder, Leeuwarden, the Netherlands
| | - Ad C. Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jaap A. Wagenaar
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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Ducarmon QR, van der Bruggen T, Harmanus C, Sanders IMJG, Daenen LGM, Fluit AC, Vossen RHAM, Kloet SL, Kuijper EJ, Smits WK. Clostridioides difficile infection with isolates of cryptic clade C-II: a genomic analysis of polymerase chain reaction ribotype 151. Clin Microbiol Infect 2022; 29:538.e1-538.e6. [PMID: 36509372 DOI: 10.1016/j.cmi.2022.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVES We report a patient case of pseudomembranous colitis associated with a monotoxin-producing Clostridioides difficile belonging to the very rarely diagnosed polymerase chain reaction (PCR) ribotype (RT) 151. To understand why this isolate was not identified using a routine commercial test, we performed a genomic analysis of RT151. METHODS Illumina short-read sequencing was performed on n = 11 RT151s from various geographical regions to study their genomic characteristics and relatedness. Subsequently, we used PacBio circular consensus sequencing to determine the complete genome sequence of isolates belonging to cryptic clades C-I and C-II, which includes the peatient isolate. RESULTS We found that 1) RT151s are polyphyletic with isolates falling into clades 1 and cryptic clades C-I and C-II; 2) RT151 contains both nontoxigenic and toxigenic isolates and 3) RT151 C-II isolates contained monotoxin pathogenicity loci. The isolate from our patient case report contains a novel-pathogenicity loci insertion site, lacked tcdA and had a divergent tcdB sequence that might explain the failure of the diagnostic test. DISCUSSION This study shows that RT151 encompasses both typical and cryptic clades and provides conclusive evidence for C. difficile infection due to clade C-II isolates that was hitherto lacking. Vigilance towards C. difficile infection as a result of cryptic clade isolates is warranted.
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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
| | - Tjomme van der Bruggen
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Céline Harmanus
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ingrid M J G Sanders
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Laura G M Daenen
- Department of Haematology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Rolf H A M Vossen
- Leiden Genome Technology Center, Leiden University Medical Center, Leiden, the Netherlands
| | - Susan L Kloet
- Leiden Genome Technology Center, 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
| | - 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; Centre for Microbial Cell Biology, Leiden, 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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Fluit AC, Bayjanov JR, Benaissa-Trouw BJ, Rogers MRC, Díez-Aguilar M, Cantón R, Tunney MM, Elborn JS, Ekkelenkamp MB. Whole-genome analysis of Haemophilus influenzae strains isolated from persons with cystic fibrosis. J Med Microbiol 2022; 71. [PMID: 36006824 DOI: 10.1099/jmm.0.001570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Haemophilus influenzae is a commensal of the respiratory tract that is frequently present in cystic fibrosis (CF) patients and may cause infection. Antibiotic resistance is well described for CF strains, and virulence factors have been proposed.Hypothesis/Gap. The genetic diversity of H. influenzae strains present in the lungs of persons with CF is largely unknown despite the fact that this organism is considered to be a pathogen in this condition. The aim was to establish the genetic diversity and susceptibility of H. influenzae strains from persons with CF, and to screen the whole genomes of these strains for the presence of antibiotic resistance determinants and proposed virulence factors.Methods. A total of 67 strains, recovered from respiratory samples from persons with CF from the UK (n=1), Poland (n=2), Spain (n=24) and the Netherlands (n=40), were subjected to whole-genome sequencing using Illumina technology and tested for antibiotic susceptibility. Forty-nine of these strains (one per different sequence type) were analysed for encoded virulence factors and resistance determinants.Results. The 67 strains represented 49 different sequence types. Susceptibility testing showed that all strains were susceptible to aztreonam, ciprofloxacin, imipenem and tetracycline. Susceptibility to ampicillin, ampicillin/sulbactam, amoxicillin/clavulanic acid, cefuroxime, cefixime, ceftriaxone, cefepime, meropenem, clarithromycin, co-trimoxazole and levofloxacin ranged from 70.2-98.5%. Only 6/49 strains (12.2%) harboured acquired resistance genes. Mutations associated with a ß-lactamase-negative ampicillin-resistant phenotype were present in four strains (8.2 %). The potential virulence factors, urease, haemoglobin- and haptoglobin-binding protein/carbamate kinase, and OmpP5 (OmpA), were encoded in more than half of the strains. The genes for HMW1, HMW2, H. influenzae adhesin, a IgA-specific serine endopeptidase autotransporter precursor, a TonB-dependent siderophore, an ABC-transporter ATP-binding protein, a methyltransferase, a BolA-family transcriptional regulator, glycosyltransferase Lic2B, a helix-turn-helix protein, an aspartate semialdehyde dehydrogenase and another glycosyltransferase were present in less than half of the strains.Conclusion. The H. influenzae strains showed limited levels of resistance, with the highest being against co-trimoxazole. Sequences encoding a carbamate kinase and a haemoglobin- and haemoglobin-haptoglobin-binding-like protein, a glycosyl transferase and an urease may aid the colonization of the CF lung. The adhesins and other identified putative virulence factors did not seem to be necessary for colonization.
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Affiliation(s)
- Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Jumamurat R Bayjanov
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Barry J Benaissa-Trouw
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Malbert R C Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - María Díez-Aguilar
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Michael M Tunney
- Department of Pulmonology, Queen's University Belfast, Belfast, UK
| | - J Stuart Elborn
- Department of Pulmonology, Queen's University Belfast, Belfast, UK
| | - Miquel B Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
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7
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Fluit AC, Bayjanov JR, Aguilar MD, Cantón R, Elborn S, Tunney MM, Scharringa J, Benaissa-Trouw BJ, Ekkelenkamp MB. Taxonomic position, antibiotic resistance and virulence factor production by Stenotrophomonas isolates from patients with cystic fibrosis and other chronic respiratory infections. BMC Microbiol 2022; 22:129. [PMID: 35549675 PMCID: PMC9097388 DOI: 10.1186/s12866-022-02466-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 02/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The potential pathogenic role of Stenotrophomonas maltophilia in lung disease and in particular in cystic fibrosis is unclear. To develop further understanding of the biology of this taxa, the taxonomic position, antibiotic resistance and virulence factors of S. maltophilia isolates from patients with chronic lung disease were studied. RESULTS A total of 111 isolates recovered between 2003 and 2016 from respiratory samples from patients in five different countries were included. Based on a cut-off of 95%, analysis of average nucleotide identity by BLAST (ANIb) showed that the 111 isolates identified as S. maltophilia by Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) belonged to S. maltophilia (n = 65), S. pavanii (n = 6) and 13 putative novel species (n = 40), which each included 1-5 isolates; these groupings coincided with the results of the 16S rDNA analysis, and the L1 and L2 ß-lactamase Neighbor-Joining phylogeny. Chromosomally encoded aminoglycoside resistance was identified in all S. maltophilia and S. pavani isolates, while acquired antibiotic resistance genes were present in only a few isolates. Nevertheless, phenotypic resistance levels against commonly used antibiotics, determined by standard broth microbroth dilution, were high. Although putative virulence genes were present in all isolates, the percentage of positive isolates varied. The Xps II secretion system responsible for the secretion of the StmPr1-3 proteases was mainly limited to isolates identified as S. maltophilia based on ANIb, but no correlation with phenotypic expression of protease activity was found. The RPF two-component quorum sensing system involved in virulence and antibiotic resistance expression has two main variants with one variant lacking 190 amino acids in the sensing region. CONCLUSIONS The putative novel Stenotrophomonas species recovered from patient samples and identified by MALDI-TOF/MS as S. maltophilia, differed from S. maltophilia in resistance and virulence genes, and therefore possibly in pathogenicity. Revision of the Stenotrophomonas taxonomy is needed in order to reliably identify strains within the genus and elucidate the role of the different species in disease.
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Affiliation(s)
- Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands.
| | - Jumamurat R Bayjanov
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
| | - María Díez Aguilar
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain.,Present Address: Servicio de Microbiología, Hospital Universitario La Princesa, Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Stuart Elborn
- Queen's University Belfast, School of Pharmacy, Belfast, UK
| | | | - Jelle Scharringa
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
| | - Barry J Benaissa-Trouw
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
| | - Miquel B Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
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8
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Fluit AC, Bayjanov JR, Aguilar MD, Benaissa-Trouw B, Tunney MM, Westreenen MV, Meis JF, Elborn JS, Cantón R, Ekkelenkamp MB. Taxonomic position, antibiotic resistance and virulence factors of clinical Achromobacter isolates. Front Biosci (Schol Ed) 2022; 14:9. [PMID: 35730434 DOI: 10.31083/j.fbs1402009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 11/06/2022]
Abstract
The role of Achromobacter species in lung disease remains unclear. The aim of this study was to characterize Achromobacter isolated from persons with cystic fibrosis and from other clinical samples. Whole genome sequences from 101 Achromobacter isolates were determined (81 from patients with cystic fibrosis and 20 from other patients) and analysed. Taxonomic analysis showed nine species including two putative novel species. Thirty-five novel sequence types were present. The most active agent was co-trimoxazole followed by imipenem, but Minimal Inhibitory Concentrations (MICs) were high. Acquired antibiotic resistance genes were rare. Their presence did not correlate with minimal inhibitory concentrations suggesting that other mechanisms are involved. Genes for proposed virulence factors were present in only some isolates. Two putative novel species were identified. The putative virulence properties of Achromobacter involved in infections are variable. Despite the high MICs, acquired resistance genes are uncommon.
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Affiliation(s)
- Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
| | - Jumamurat R Bayjanov
- Department of Medical Microbiology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
| | - María Díez Aguilar
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Barry Benaissa-Trouw
- Department of Medical Microbiology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
| | - Michael M Tunney
- School of Pharmacy, Queen's University Belfast, BT9 7BL Belfast, UK
| | - Mireille van Westreenen
- Department of Medical Microbiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), 6532 SZ Nijmegen, The Netherlands.,Centre of Expertise in Mycology Radboudumc/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands.,Department of Medical Microbiology, Radboudumc, 6500 HB Nijmegen, The Netherlands
| | - J Stuart Elborn
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL Belfast, UK
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Miquel B Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
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9
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Ekkelenkamp MB, Díez-Aguilar M, Tunney MM, Elborn JS, Fluit AC, Cantón R. Establishing antimicrobial susceptibility testing methods and clinical breakpoints for inhaled antibiotic therapy. Open Forum Infect Dis 2022; 9:ofac082. [PMID: 35265731 PMCID: PMC8900927 DOI: 10.1093/ofid/ofac082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 11/29/2021] [Accepted: 02/10/2022] [Indexed: 12/05/2022] Open
Abstract
Inhaled antibiotics are a common and valuable therapy for patients suffering from chronic lung infection, with this particularly well demonstrated for patients with cystic fibrosis. However, in vitro tests to predict patient response to inhaled antibiotic therapy are currently lacking. There are indications that antimicrobial susceptibility testing (AST) may have a role in guidance of therapy, but which tests would correlate best still needs to be researched in clinical studies or animal models. Applying the principles of European Committee on Antimicrobial Susceptibility Testing methodology, the analysis of relevant and reliable data correlating different AST tests to patients’ outcomes may yield clinical breakpoints for susceptibility, but these data are currently unavailable. At present, we believe that it is unlikely that standard determination of minimum inhibitory concentration will prove the best predictor.
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Affiliation(s)
- Miquel B Ekkelenkamp
- University Medical Center Utrecht, Department of Medical Microbiology, Utrecht, The Netherlands
| | - María Díez-Aguilar
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Servicio de Microbiología y Parasitología, Hospital Universitario La Princesa, Madrid, Spain
| | - Michael M Tunney
- Queen’s University Belfast, Department of Pulmonology, Belfast, United Kingdom
| | - J Stuart Elborn
- Queen’s University Belfast, Department of Pulmonology, Belfast, United Kingdom
| | - Ad C Fluit
- University Medical Center Utrecht, Department of Medical Microbiology, Utrecht, The Netherlands
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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10
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de Vor L, van Dijk B, van Kessel K, Kavanaugh JS, de Haas C, Aerts PC, Viveen MC, Boel EC, Fluit AC, Kwiecinski JM, Krijger GC, Ramakers RM, Beekman FJ, Dadachova E, Lam MGEH, Vogely HC, van der Wal BCH, van Strijp JAG, Horswill AR, Weinans H, Rooijakkers SHM. Human monoclonal antibodies against Staphylococcus aureus surface antigens recognize in vitro and in vivo biofilm. eLife 2022; 11:e67301. [PMID: 34989676 PMCID: PMC8751199 DOI: 10.7554/elife.67301] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 12/06/2021] [Indexed: 12/22/2022] Open
Abstract
Implant-associated Staphylococcus aureus infections are difficult to treat because of biofilm formation. Bacteria in a biofilm are often insensitive to antibiotics and host immunity. Monoclonal antibodies (mAbs) could provide an alternative approach to improve the diagnosis and potential treatment of biofilm-related infections. Here, we show that mAbs targeting common surface components of S. aureus can recognize clinically relevant biofilm types. The mAbs were also shown to bind a collection of clinical isolates derived from different biofilm-associated infections (endocarditis, prosthetic joint, catheter). We identify two groups of antibodies: one group that uniquely binds S. aureus in biofilm state and one that recognizes S. aureus in both biofilm and planktonic state. Furthermore, we show that a mAb recognizing wall teichoic acid (clone 4497) specifically localizes to a subcutaneously implanted pre-colonized catheter in mice. In conclusion, we demonstrate the capacity of several human mAbs to detect S. aureus biofilms in vitro and in vivo.
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Affiliation(s)
- Lisanne de Vor
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Bruce van Dijk
- Department of Orthopedics, University Medical Centre UtrechtUtrechtNetherlands
| | - Kok van Kessel
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Jeffrey S Kavanaugh
- Department of Immunology and Microbiology, University of Colorado School of MedicineAuroraUnited States
| | - Carla de Haas
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Piet C Aerts
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Marco C Viveen
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Edwin C Boel
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Jakub M Kwiecinski
- Department of Immunology and Microbiology, University of Colorado School of MedicineAuroraUnited States
| | - Gerard C Krijger
- Department of Radiology and Nuclear Medicine, University Medical Centre UtrechtUtrechtNetherlands
| | - Ruud M Ramakers
- MILabs B.VUtrechtNetherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical CenterUtrechtNetherlands
- Department of Radiation Science and Technology, Delft University of TechnologyDelftNetherlands
| | - Freek J Beekman
- MILabs B.VUtrechtNetherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical CenterUtrechtNetherlands
- Department of Radiation Science and Technology, Delft University of TechnologyDelftNetherlands
| | - Ekaterina Dadachova
- College of Pharmacy and Nutrition, University of SaskatchewanSaskatoonCanada
| | - Marnix GEH Lam
- Department of Radiology and Nuclear Medicine, University Medical Centre UtrechtUtrechtNetherlands
| | - H Charles Vogely
- Department of Orthopedics, University Medical Centre UtrechtUtrechtNetherlands
| | - Bart CH van der Wal
- Department of Orthopedics, University Medical Centre UtrechtUtrechtNetherlands
| | - Jos AG van Strijp
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Alexander R Horswill
- Department of Immunology and Microbiology, University of Colorado School of MedicineAuroraUnited States
- Department of Veterans Affairs, Eastern Colorado Health Care SystemDenverUnited States
| | - Harrie Weinans
- Department of Orthopedics, University Medical Centre UtrechtUtrechtNetherlands
- Department of Biomechanical engineering, TU DelftDelftNetherlands
| | - Suzan HM Rooijakkers
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
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11
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Martak D, Guther J, Verschuuren TD, Valot B, Conzelmann N, Bunk S, Riccio ME, Salamanca E, Meunier A, Henriot CP, Brossier CP, Bertrand X, Cooper BS, Harbarth S, Tacconelli E, Fluit AC, Rodriguez-Baño J, Kluytmans JAJW, Peter S, Hocquet D. Populations of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae are different in human-polluted environment and food items: a multicentre European study. Clin Microbiol Infect 2021; 28:447.e7-447.e14. [PMID: 34325070 DOI: 10.1016/j.cmi.2021.07.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 03/23/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 01/22/2023]
Abstract
OBJECTIVES To assess the extent to which food items are a source of extended-spectrum β-lactamase (ESBL) -producing Escherichia coli (ESBL-Ec) and ESBL-producing Klebsiella pneumoniae (ESBL-Kp) for humans in five European cities. METHODS We sampled 122 human polluted (hp)-environments (sewers and polluted rivers, as a proxy of human contamination) and 714 food items in Besançon (France), Geneva (Switzerland), Sevilla (Spain), Tübingen (Germany) and Utrecht (The Netherlands). A total of 254 ESBL-Ec and 39 ESBL-Kp isolates were cultured. All genomes were fully sequenced to compare their sequence types (ST) and core genomes, along with the distribution of blaESBL genes and their genetic supports (i.e. chromosome or plasmid). RESULTS Sequence data revealed that ESBL-Ec and ESBL-Kp isolates from hp-environments were genetically different from those contaminating food items. ESBL-Ec ST131 was widespread in the hp-environment (21.5% of the isolates) but absent from the food items tested. ESBL-Ec ST10 was in similar proportions in hp-environments and food items (15 and 10 isolates, respectively) but mostly carried reservoir-specific blaESBL. blaCTX-M-1 and blaSHV-12 predominated in food-related E. coli isolates (32% and 34% of the isolates, respectively), whereas blaCTX-M-15 and blaCTX-M-27 predominated in isolates from hp-environments (52% and 15% of the isolates, respectively). CONCLUSIONS We found a very limited connection between ESBL-Ec and ESBL-Kp populations retrieved in food items and from hp-environments and blaESBL. This suggests that human-to-human contamination, rather than the food chain, is possibly the most frequent route of ESBL-Ec and ESBL-Kp transmission in high-income countries.
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Affiliation(s)
- Daniel Martak
- Infection Control Unit, University Hospital of Besancon, Besancon, France; UMR 6249, Laboratoire Chrono-environnement, CNRS-Université de Bourgogne Franche-Comté, Besançon, France.
| | - Julia Guther
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Tess D Verschuuren
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Benoit Valot
- UMR 6249, Laboratoire Chrono-environnement, CNRS-Université de Bourgogne Franche-Comté, Besançon, France
| | - Nadine Conzelmann
- Division of Infectious Diseases, Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Stefanie Bunk
- Division of Infectious Diseases, Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - M Eugenia Riccio
- Infection Control Program, Geneva University Hospital and Faculty of Medicine, Geneva, Switzerland
| | - Elena Salamanca
- Department of Infectious Diseases and Clinical Microbiology, University Hospital Virgen Macarena and Department of Medicine, University of Sevilla / Biomedicines Institute of Sevilla (IBiS), Sevilla, Spain
| | - Alexandre Meunier
- Infection Control Unit, University Hospital of Besancon, Besancon, France
| | - Charles P Henriot
- UMR 6249, Laboratoire Chrono-environnement, CNRS-Université de Bourgogne Franche-Comté, Besançon, France
| | | | - Xavier Bertrand
- Infection Control Unit, University Hospital of Besancon, Besancon, France; UMR 6249, Laboratoire Chrono-environnement, CNRS-Université de Bourgogne Franche-Comté, Besançon, France
| | - Ben S Cooper
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Stephan Harbarth
- Infection Control Program, Geneva University Hospital and Faculty of Medicine, Geneva, Switzerland
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany; Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Italy
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Jesús Rodriguez-Baño
- Department of Infectious Diseases and Clinical Microbiology, University Hospital Virgen Macarena and Department of Medicine, University of Sevilla / Biomedicines Institute of Sevilla (IBiS), Sevilla, Spain
| | - Jan A J W Kluytmans
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, the Netherlands; Amphia Hospital Breda, Microvida Laboratory for Medical Microbiology, Breda, the Netherlands
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Didier Hocquet
- Infection Control Unit, University Hospital of Besancon, Besancon, France; UMR 6249, Laboratoire Chrono-environnement, CNRS-Université de Bourgogne Franche-Comté, Besançon, France; Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Régional Universitaire, Besançon, France
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12
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Díez-Aguilar M, Ekkelenkamp M, Morosini MI, Huertas N, Del Campo R, Zamora J, Fluit AC, Tunney MM, Obrecht D, Bernardini F, Cantón R. Anti-biofilm activity of murepavadin against cystic fibrosis Pseudomonas aeruginosa isolates. J Antimicrob Chemother 2021; 76:2578-2585. [PMID: 34283223 DOI: 10.1093/jac/dkab222] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/04/2021] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To determine the activity of murepavadin in comparison with tobramycin, colistin and aztreonam, against cystic fibrosis (CF) Pseudomonas aeruginosa isolates growing in biofilms. The biofilm-epidemiological cut-off (ECOFF) values that include intrinsic resistance mechanisms present in biofilms were estimated. METHODS Fifty-three CF P. aeruginosa isolates from respiratory samples were tested using the Calgary (closed system) device, while 4 [2 clinical (one smooth, one mucoid) and 2 reference strains] were tested using the BioFlux, a microfluidic open model of biofilm testing. Biofilm was stained with SYTO9® and propidium iodide. The minimal biofilm inhibitory concentration (MBIC) and the minimal biofilm eradication concentration (MBEC) were determined. The MBIC-ECOFF and the MBEC-ECOFF were calculated. RESULTS Colistin, tobramycin and murepavadin presented similar MBIC50/MBIC90 values (4/32, 8/64 and 2/32, respectively). Murepavadin exhibited the lowest MBEC90 (64 mg/L). Aztreonam MBIC and MBEC values were higher than those of the other antibiotics tested. Tobramycin and murepavadin had the lowest MBEC-ECOFF (64 and 128 mg/L, respectively), while those of aztreonam and colistin exceeded 512 mg/L. Using the BioFlux, for the PAO1, PAO mutS and the smooth clinical strain, a significant difference (P < 0.0125) was observed when comparing the fluorescence of treated and untreated biofilms. For the mucoid strain, only the biofilm treated with aztreonam (MBIC and MBEC) and tobramycin (MBEC) showed differences with respect to the untreated biofilm. CONCLUSIONS Murepavadin demonstrated good activity against P. aeruginosa biofilms both in open and closed systems. The MBIC-ECOFF and the MBEC-ECOFF are proposed as new parameters to estimate the activity of antibiotics on biofilms.
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Affiliation(s)
- María Díez-Aguilar
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Miquel Ekkelenkamp
- Unidad de Bioestadística Clínica, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain
| | - María-Isabel Morosini
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Natalia Huertas
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Rosa Del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Javier Zamora
- Unidad de Bioestadística Clínica, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain
| | - Ad C Fluit
- University Medical Center Utrecht, Department of Medical Microbiology, Utrecht, The Netherlands
| | - Michael M Tunney
- Queen's University Belfast, School of Pharmacy, Belfast, United Kingdom
| | | | | | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
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13
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van den Bunt G, Fluit AC, Spaninks MP, Timmerman AJ, Geurts Y, Kant A, Scharringa J, Mevius D, Wagenaar JA, Bonten MJM, van Pelt W, Hordijk J. Faecal carriage, risk factors, acquisition and persistence of ESBL-producing Enterobacteriaceae in dogs and cats and co-carriage with humans belonging to the same household. J Antimicrob Chemother 2021; 75:342-350. [PMID: 31711228 PMCID: PMC6966097 DOI: 10.1093/jac/dkz462] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [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: 04/26/2019] [Revised: 09/06/2019] [Accepted: 10/10/2019] [Indexed: 11/21/2022] Open
Abstract
Background ESBL-producing Enterobacteriaceae (ESBL-E) are observed in many reservoirs. Pets might play an important role in the dissemination of ESBL-E to humans since they live closely together. Objectives To identify prevalence, risk factors, molecular characteristics, persistence and acquisition of ESBL-E in dogs and cats, and co-carriage in human–pet pairs belonging to the same household. Methods In a nationwide study, one person per household was randomly invited to complete a questionnaire and to submit a faecal sample. Dog and cat owners were invited to also submit a faecal sample from their pet. Repeated sampling after 1 and 6 months was performed in a subset. ESBL-E were obtained through selective culture and characterized by WGS. Logistic regression analyses and random forest models were performed to identify risk factors. Results The prevalence of ESBL-E carriage in these cohorts was 3.8% (95% CI: 2.7%–5.4%) for human participants (n=550), 10.7% (95% CI: 8.3%–13.7%) for dogs (n=555) and 1.4% (95% CI: 0.5%–3.8%) for cats (n=285). Among animals, blaCTX-M-1 was most abundant, followed by blaCTX-M-15. In dogs, persistence of carriage was 57.1% at 1 month and 42.9% at 6 months. Eating raw meat [OR: 8.8, 95% CI: 4.7–16.4; population attributable risk (PAR): 46.5%, 95% CI: 41.3%–49.3%] and dry food (OR: 0.2, 95% CI: 0.1–0.5; PAR: 56.5%, 95% CI: 33.2%–66.6%) were predictors for ESBL-E carriage in dogs. Human–dog co-carriage was demonstrated in five households. Human–cat co-carriage was not observed. Conclusions ESBL-E prevalence was higher in dogs than in humans and lowest in cats. The main risk factor for ESBL-E carriage was eating raw meat. Co-carriage in dogs and household members was uncommon.
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Affiliation(s)
- G van den Bunt
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - A C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - M P Spaninks
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - A J Timmerman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Y Geurts
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - A Kant
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J Scharringa
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - D Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - M J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - W van Pelt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - J Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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14
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Rentenaar RJ, Bovo-Heijmans B, Diggle J, Fluit AC, Wootton M. False amoxicillin/clavulanic acid susceptibility in Bacteroides fragilis using gradient strip tests. Anaerobe 2021; 69:102358. [PMID: 33741507 DOI: 10.1016/j.anaerobe.2021.102358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Repeatedly, too low MIC results were obtained in Bacteroides fragilis quality assessment strains, using gradient strip tests with a ratio of amoxicillin:clavulanic acid of 2:1. We aimed to find the most accurate available gradient strip tests for susceptibility testing of amoxicillin/clavulanic acid in B. fragilis in comparison with agar dilution with EUCAST methodology and breakpoints. METHODS Twenty-seven clinical B. fragilis isolates were investigated using gold standard EUCAST amoxicillin/clavulanic acid agar dilution (fixed clavulanic acid concentration at 2 mg/L, with increasing amoxicillin concentrations) as well as three commercial gradient strip tests: XL (ratio), AUG (ratio) or AMC (fixed concentration). RESULTS Using agar dilution (fixed concentration), 19 isolates were susceptible, 1 isolate was susceptible increased exposure (I) and 7 isolates were resistant. Categorical agreement of the gradient strip tests with agar dilution (fixed concentration) was 70% for XL (ratio), 71% for AUG (ratio) and 89% for AMC (fixed concentration). Very major error rates in comparison with agar dilution (fixed concentration) were 100%, 0%, and 0%, respectively. CONCLUSIONS EUCAST breakpoint usage in amoxicillin/clavulanic acid susceptibility tests for B. fragilis should be accompanied by EUCAST methodology. When using alternative methods such as gradient strip tests, a higher degree of alignment with EUCAST methodology, such as using fixed clavulanic acid concentrations, improves precision.
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Affiliation(s)
- Rob J Rentenaar
- Department of Medical Microbiology, University Medical Center Utrecht, Internal mail no G.04.614, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands.
| | - Bianca Bovo-Heijmans
- Department of Medical Microbiology, University Medical Center Utrecht, Internal mail no G.04.614, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Joanna Diggle
- Specialist Antimicrobial Chemotherapy Unit, Microbiology Cardiff, Public Health Wales, University Hospital of Wales, Heath Park, CARDIFF CF14 4XW, UK
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Internal mail no G.04.614, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Mandy Wootton
- Specialist Antimicrobial Chemotherapy Unit, Microbiology Cardiff, Public Health Wales, University Hospital of Wales, Heath Park, CARDIFF CF14 4XW, UK
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15
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Verschuuren TD, van Hout D, Arredondo-Alonso S, Fluit AC, Reuland EA, Top J, Schürch AC, Bosch T, Bonten MJM, Kluytmans JAJW, Willems RJL. Comparative genomics of ESBL-producing Escherichia coli (ESBL-Ec) reveals a similar distribution of the 10 most prevalent ESBL-Ec clones and ESBL genes among human community faecal and extra-intestinal infection isolates in the Netherlands (2014-17). J Antimicrob Chemother 2021; 76:901-908. [PMID: 33428729 PMCID: PMC7953314 DOI: 10.1093/jac/dkaa534] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/19/2020] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION The human gut microbiota is an important reservoir of ESBL-producing Escherichia coli (ESBL-Ec). Community surveillance studies of ESBL-Ec to monitor circulating clones and ESBL genes are logistically challenging and costly. OBJECTIVES To evaluate if isolates obtained in routine clinical practice can be used as an alternative to monitor the distribution of clones and ESBL genes circulating in the community. METHODS WGS was performed on 451 Dutch ESBL-Ec isolates (2014-17), including 162 community faeces and 289 urine and blood isolates. We compared proportions of 10 most frequently identified STs, PopPUNK-based sequence clusters (SCs) and ESBL gene subtypes and the degree of similarity using Czekanowski's proportional similarity index (PSI). RESULTS Nine out of 10 most prevalent STs and SCs and 8/10 most prevalent ESBL genes in clinical ESBL-Ec were also the most common types in community faeces. The proportions of ST131 (39% versus 23%) and SC131 (40% versus 25%) were higher in clinical isolates than in community faeces (P < 0.01). Within ST131, H30Rx (C2) subclade was more prevalent among clinical isolates (55% versus 26%, P < 0.01). The proportion of ESBL gene blaCTX-M-1 was lower in clinical isolates (5% versus 18%, P < 0.01). Czekanowski's PSI confirmed that the differences in ESBL-Ec from community faeces and clinical isolates were limited. CONCLUSIONS Distributions of the 10 most prevalent clones and ESBL genes from ESBL-Ec community gut colonization and extra-intestinal infection overlapped in majority, indicating that isolates from routine clinical practice could be used to monitor ESBL-Ec clones and ESBL genes in the community.
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Affiliation(s)
- T D Verschuuren
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - D van Hout
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - S Arredondo-Alonso
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - A C Fluit
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - E A Reuland
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
- Saltro Diagnostic Center for Primary Care, Utrecht, The Netherlands
- The Netherlands Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - J Top
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - A C Schürch
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - T Bosch
- The Netherlands Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - M J M Bonten
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - J A J W Kluytmans
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - R J L Willems
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
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16
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van Hengel IAJ, Tierolf MWAM, Valerio VPM, Minneboo M, Fluit AC, Fratila-Apachitei LE, Apachitei I, Zadpoor AA. Self-defending additively manufactured bone implants bearing silver and copper nanoparticles. J Mater Chem B 2021; 8:1589-1602. [PMID: 31848564 DOI: 10.1039/c9tb02434d] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Effective preventive measures against implant-associated infection (IAI) are desperately needed. Therefore, the development of self-defending implants with intrinsic antibacterial properties has gained significant momentum. Biomaterials biofunctionalized with silver (Ag) have resulted in effective antibacterial biomaterials, yet regularly induce cytotoxicity. In this study, the use of both Ag and copper (Cu) nanoparticles (NPs) on TiO2 surfaces was investigated to generate antibacterial and osteoconductive biomaterials. Hence, additively manufactured Ti-6Al-4V volume-porous implants were biofunctionalized with plasma electrolytic oxidation (PEO) through the incorporation of varying ratios of Ag and/or Cu NPs in the TiO2 layer covering the implant surface. For all experimental groups, the surface morphology, chemical composition, ion release profile, generation of reactive ion species, antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) in vitro and ex vivo, as well as the response of pre-osteoblastic MC3T3-E1 cells in metabolic activity and differentiation assays were determined. PEO biofunctionalization resulted in rough and highly porous surfaces that released Ag and Cu ions for 28 days and generated hydroxyl as well as methyl radicals. A strong synergistic bactericidal behavior between Ag and Cu ions was detected, which allowed to decrease the concentration of Ag ions by 10-fold, while maintaining the same level of antibacterial activity. Antibacterial agar diffusion and quantitative assays indicated strong antibacterial activity in vitro for the implants containing Ag and Ag/Cu, while no antibacterial activity was observed for implants bearing only Cu NPs. Moreover, the biofunctionalized implants with ratios of up to 75% Ag and 25% Cu NP totally eradicated all bacteria in an ex vivo model using murine femora. Meanwhile, the biofunctionalized implants did not show any signs of cytotoxicity, while implants bearing only Cu NPs improved the metabolic activity after 7 and 11 days. The biomaterials developed here, therefore, exploit the synergistic behavior of Ag and Cu to simultaneously offer strong antibacterial behavior while fully mitigating the cytotoxicity of Ag against mammalian cells.
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Affiliation(s)
- I A J van Hengel
- Additive Manufacturing Laboratory, Department of Biomechanical Engineering, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands.
| | - M W A M Tierolf
- Additive Manufacturing Laboratory, Department of Biomechanical Engineering, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands.
| | - V P M Valerio
- Additive Manufacturing Laboratory, Department of Biomechanical Engineering, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands.
| | - M Minneboo
- Additive Manufacturing Laboratory, Department of Biomechanical Engineering, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands.
| | - A C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - L E Fratila-Apachitei
- Additive Manufacturing Laboratory, Department of Biomechanical Engineering, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands.
| | - I Apachitei
- Additive Manufacturing Laboratory, Department of Biomechanical Engineering, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands.
| | - A A Zadpoor
- Additive Manufacturing Laboratory, Department of Biomechanical Engineering, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands.
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17
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Riccio ME, Verschuuren T, Conzelmann N, Martak D, Meunier A, Salamanca E, Delgado M, Guther J, Peter S, Paganini J, Martischang R, Sauser J, de Kraker MEA, Cherkaoui A, Fluit AC, Cooper BS, Hocquet D, Kluytmans JAJW, Tacconelli E, Rodriguez-Baño J, Harbarth S. Household acquisition and transmission of extended-spectrum β-lactamase (ESBL) -producing Enterobacteriaceae after hospital discharge of ESBL-positive index patients. Clin Microbiol Infect 2021; 27:1322-1329. [PMID: 33421572 DOI: 10.1016/j.cmi.2020.12.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/20/2020] [Accepted: 12/19/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVES This study aimed to determine rates and risk factors of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) acquisition and transmission within households after hospital discharge of an ESBL-PE-positive index patient. METHODS Two-year prospective cohort study in five European cities. Patients colonized with ESBL-producing Escherichia coli (ESBL-Ec) or Klebsiella pneumoniae (ESBL-Kp), and their household contacts were followed up for 4 months after hospital discharge of the index case. At each follow up, participants provided a faecal sample and personal information. ESBL-PE whole-genome sequences were compared using pairwise single nucleotide polymorphism-based analysis. RESULTS We enrolled 71 index patients carrying ESBL-Ec (n = 45), ESBL-Kp (n = 20) or both (n = 6), and 102 household contacts. The incidence of any ESBL-PE acquisition among household members initially free of ESBL-PE was 1.9/100 participant-weeks at risk. Nineteen clonally related household transmissions occurred (case to contact: 13; contact to case: 6), with an overall rate of 1.18 transmissions/100 participant-weeks at risk. Most of the acquisition and transmission events occurred within the first 2 months after discharge. The rate of ESBL-Kp household transmission (1.16/100 participant-weeks) was higher than of ESBL-Ec (0.93/100 participant-weeks), whereas more acquisitions were noted for ESBL-Ec (1.06/100 participant-weeks) compared with ESBL-Kp (0.65/100 participant-weeks). Providing assistance for urinary and faecal excretion to the index case by household members increased the risk of ESBL-PE transmission (adjusted prevalence ratio 4.3; 95% CI 1.3-14.1). CONCLUSIONS ESBL-PE cases discharged from the hospital are an important source of ESBL-PE transmission within households. Most acquisition and transmission events occurred during the first 2 months after hospital discharge and were causally related to care activities at home, highlighting the importance of hygiene measures in community settings. CLINICAL STUDY REGISTRATION German Clinical Trials Register, DRKS-ID: DRKS00013250.
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Affiliation(s)
- Maria E Riccio
- Infection Control Programme and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Tess Verschuuren
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Nadine Conzelmann
- Infectious Diseases, Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Daniel Martak
- Infection Control Unit, University Hospital of Besançon, Besançon, France
| | - Alexandre Meunier
- Infection Control Unit, University Hospital of Besançon, Besançon, France
| | - Elena Salamanca
- Infectious Diseases, Microbiology and Preventive Medicine Unit, Virgen Macarena University Hospital, Sevilla, Spain; Department of Medicine, University of Sevilla/Biomedicine Institute of Sevilla, Sevilla, Spain
| | - Mercedes Delgado
- Infectious Diseases, Microbiology and Preventive Medicine Unit, Virgen Macarena University Hospital, Sevilla, Spain; Department of Medicine, University of Sevilla/Biomedicine Institute of Sevilla, Sevilla, Spain
| | - Julia Guther
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Julian Paganini
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Romain Martischang
- Infection Control Programme and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Julien Sauser
- Infection Control Programme and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Marlieke E A de Kraker
- Infection Control Programme and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | | | - Ad C Fluit
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Ben S Cooper
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Didier Hocquet
- Infection Control Unit, University Hospital of Besançon, Besançon, France
| | - Jan A J W Kluytmans
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Evelina Tacconelli
- Infectious Diseases, Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany; Infectious Diseases Division, Department of Diagnostic and Public Health, University Hospital Verona, Verona, Italy
| | - Jesús Rodriguez-Baño
- Infectious Diseases, Microbiology and Preventive Medicine Unit, Virgen Macarena University Hospital, Sevilla, Spain; Department of Medicine, University of Sevilla/Biomedicine Institute of Sevilla, Sevilla, Spain
| | - Stephan Harbarth
- Infection Control Programme and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland.
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18
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van den Bunt G, Fluit AC, Bootsma MCJ, van Duijkeren E, Scharringa J, van Pelt W, Bonten MJM. Dynamics of Intestinal Carriage of Extended-Spectrum Beta-lactamase-Producing Enterobacteriaceae in the Dutch General Population, 2014-2016. Clin Infect Dis 2020; 71:1847-1855. [PMID: 31688916 DOI: 10.1093/cid/ciz1091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 07/31/2019] [Accepted: 11/04/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND In the Netherlands, the prevalence of intestinal extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) carriage in community-dwelling subjects is ~5%. Little is known about the dynamics of ESBL-E carriage. METHODS In a nationwide, population-based study (2014-2016) with 4177 community-dwelling subjects, fecal samples from 656 subjects were collected after 1 (time point [T] = 1) and 6 (T = 2) months. The growth of ESBL-E was quantified and a whole-genome sequence analysis was performed. Subjects were categorized as either an incidental, short-term, or long-term carrier or as a noncarrier. Risk factors were determined by random forest models and logistic regression. The transmissibility and duration of ESBL-E carriage was quantified using a transmission model, which also incorporated previous study data. RESULTS Out of 656 participants, 96 were ESBL-E carriers at T = 0. Of these, 66 (10.1%) subjects were incidental carriers, 22 (3.3%) were short-term carriers, and 38 (5.8%) were long-term carriers; the remaining 530 (80.8%) were noncarriers. The risk factors for long-term carriage were travelling to Asia, swimming in a sea/ocean, and not changing the kitchen towel daily. The log-transformed colony forming units ratio at T = 0 was predictive for ESBL-E carriage at T = 1 (odds ratio [OR], 1.3; 95% confidence interval [CI], 1.2-1.6) and T = 2 (OR, 1.2; 95% CI, 1.1-1.4). Model simulations revealed a median decolonization rate of 2.83/year, an average duration of carriage of 0.35 years, and an acquisition rate of 0.34/year. The trend of the acquisition rate during the study period was close to 0. CONCLUSIONS The risk factors for long-term ESBL-E carriage were travel- and hygiene-related. The dynamics of ESBL-E carriage in the general Dutch population are characterized by balancing decolonization and acquisition rates.
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Affiliation(s)
- Gerrita van den Bunt
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Martin C J Bootsma
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands.,Mathematical Institute, Utrecht University, Utrecht, The Netherlands
| | - Engeline van Duijkeren
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Jelle Scharringa
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wilfrid van Pelt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marc J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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19
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van den Bunt G, van Pelt W, Hidalgo L, Scharringa J, de Greeff SC, Schürch AC, Mughini-Gras L, Bonten MJM, Fluit AC. Prevalence, risk factors and genetic characterisation of extended-spectrum beta-lactamase and carbapenemase-producing Enterobacteriaceae (ESBL-E and CPE): a community-based cross-sectional study, the Netherlands, 2014 to 2016. ACTA ACUST UNITED AC 2020; 24. [PMID: 31615600 PMCID: PMC6794991 DOI: 10.2807/1560-7917.es.2019.24.41.1800594] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [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: 11/24/2022]
Abstract
Background The epidemiology of carriage of extended-spectrum beta-lactamase-producing (ESBL-E) and carbapenemase-producing Enterobacteriaceae (CPE) in the general population is unknown. Aim In this observational study, the prevalence and risk factors for intestinal ESBL-E and CPE carriage in the Dutch general population were determined. ESBL-E were characterised. Methods From 2014 to 2016, ca 2,000 residents were invited monthly to complete a questionnaire and provide a faecal sample, which was tested for ESBL-E. The first 1,758 samples were also tested for CPE. Risk factors for ESBL-E carriage were identified by multivariable logistic regression analysis. ESBL-E isolates underwent whole genome sequencing. Results Of 47,957 individuals invited, 4,177 (8.7%) completed the questionnaire and provided a faecal sample. ESBL-E were detected in 186 (4.5%) individuals, resulting in an adjusted prevalence of 5.0% (95% confidence interval (CI):3.4–6.6%). Risk factors were: born outside the Netherlands (odds ratio (OR): 1.99; 95% CI: 1.16−4.54), eating in restaurants > 20 times/year (OR: 1.70; 95% CI: 1.04−2.76), antibiotic use < 6 months ago (OR: 2.05; 95% CI: 1.05−4.03), swimming in sea/ocean < 12 months ago (OR: 1.63; 95% CI: 1.11−2.39), travelling to Africa (OR: 3.03; 95% CI: 1.23−7.46) or Asia (OR: 2.00; 95% CI: 1.02−3.90) < 12 months ago, and not changing kitchen towels daily (OR: 2.19; 95% CI: 1.24−3.87). The last had the largest population attributable risk (PAR) (47.5%). Eighty-four of 189 (44.4%) ESBL-E isolates carried blaCTX-M-15. Escherichia coli isolates belonged to 70 different sequence types (ST)s, of which ST131 (42/178 isolates; 23.6%) was most prevalent. Associations were observed between IncFIA plasmids and ST131 and blaCTX-M-27, and between IncI1 and ST88 and blaCTX-M-1. No CPE were detected. Conclusions The prevalence of ESBL-E carriage in the Netherlands’ community-dwelling population is 5.0%. Identified risk factors were mostly travelling (particularly to Asia and Africa) and kitchen hygiene. CPE were not detected.
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Affiliation(s)
- Gerrita van den Bunt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
| | - Wilfrid van Pelt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Laura Hidalgo
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
| | - Jelle Scharringa
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
| | - Sabine C de Greeff
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Anita C Schürch
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
| | - Lapo Mughini-Gras
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Marc J M Bonten
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
| | - Ad C Fluit
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
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20
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van der Houwen TB, van Laar JAM, Kappen JH, van Hagen PM, de Zoete MR, van Muijlwijk GH, Berbers RM, Fluit AC, Rogers M, Groot J, Hazelbag CM, Consolandi C, Severgnini M, Peano C, D'Elios MM, Emmi G, Leavis HL. Behçet's Disease Under Microbiotic Surveillance? A Combined Analysis of Two Cohorts of Behçet's Disease Patients. Front Immunol 2020; 11:1192. [PMID: 32595645 PMCID: PMC7303268 DOI: 10.3389/fimmu.2020.01192] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/13/2020] [Indexed: 12/13/2022] Open
Abstract
Background: In Behçet's disease (BD), an auto-inflammatory vasculitis, an unbalanced gut microbiota can contribute to pro-inflammatory reactions. In separate studies, distinct pro- and anti-inflammatory bacteria associated with BD have been identified. Methods: To establish disease-associated determinants, we performed gut microbiome profiling in BD patients from the Netherlands (n = 19) and Italy (n = 13), matched healthy controls (HC) from the Netherlands (n = 17) and Italy (n = 15) and oral microbiome profiling in Dutch BD patients (n = 18) and HC (n = 15) by 16S rRNA gene sequencing. In addition, we used fecal IgA-SEQ analysis to identify specific IgA coated bacterial taxa in Dutch BD patients (n = 13) and HC (n = 8). Results: In BD stool samples alpha-diversity was conserved, whereas beta-diversity analysis showed no clustering based on disease, but a significant segregation by country of origin. Yet, a significant decrease of unclassified Barnesiellaceae and Lachnospira genera was associated with BD patients compared to HC. Subdivided by country, the Italian cohort displays a significant decrease of unclassified Barnesiellaceae and Lachnospira genera, in the Dutch cohort this decrease is only a trend. Increased IgA-coating of Bifidobacterium spp., Dorea spp. and Ruminococcus bromii species was found in stool from BD patients. Moreover, oral Dutch BD microbiome displayed increased abundance of Spirochaetaceae and Dethiosulfovibrionaceae families. Conclusions: BD patients show decreased fecal abundance of Barnesiellaceae and Lachnospira and increased oral abundance of Spirochaetaceae and Dethiosulfovibrionaceae. In addition, increased fecal IgA coating of Bifidobacterium, Ruminococcus bromii and Dorea may reflect retention of anti-inflammatory species and neutralization of pathosymbionts in BD, respectively. Additional studies are warranted to relate intestinal microbes with the significance of ethnicity, diet, medication and response with distinct pro- and inflammatory pathways in BD patients.
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Affiliation(s)
- Tim B van der Houwen
- Section Clinical Immunology, Departments of Internal Medicine and Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jan A M van Laar
- Section Clinical Immunology, Departments of Internal Medicine and Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jasper H Kappen
- Allergy and Clinical Immunology, Immunomodulation and Tolerance Group, Inflammation Repair and Development, Imperial College, National Heart and Lung Institute, London, United Kingdom.,Department of Pulmonology, STZ Centre of Excellence for Asthma and COPD, Franciscus Group, Rotterdam, United Kingdom
| | - Petrus M van Hagen
- Section Clinical Immunology, Departments of Internal Medicine and Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marcel R de Zoete
- Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Roos-Marijn Berbers
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ad C Fluit
- Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Malbert Rogers
- Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - James Groot
- Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - C Marijn Hazelbag
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | - Clarissa Consolandi
- National Research Council, Institute of Biomedical Technologies, Segrate, Italy
| | - Marco Severgnini
- National Research Council, Institute of Biomedical Technologies, Segrate, Italy
| | - Clelia Peano
- National Research Council, Institute of Genetic and Biomedical Research, UoS Milan, Milan, Italy.,Genomic Unit, Humanitas Clinical and Research Center, Milan, Italy
| | - Mario M D'Elios
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | - Giacomo Emmi
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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21
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Bayjanov JR, Ekkelenkamp MB, Rogers MR, Cantón R, Benaissa-Trouw BJ, Díez-Aguilar M, Tunney M, Fluit AC. Whole-genome analysis of Pandoraea species strains from cystic fibrosis patients. Future Microbiol 2019; 14:1357-1367. [PMID: 31762328 DOI: 10.2217/fmb-2019-0038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Aim: Genetic characterization of Pandoraea strains recovered from cystic fibrosis patients. Materials & methods: The whole-genome sequence of 12 Pandoraea strains was determined using Illumina technology. The position of the strains within the genus Pandoraea was analyzed using selected partial gene sequences, core genome multi-locus sequence typing and average nucleotide identity analysis. Furthermore, the sequences were annotated. Results: The results show that some strains previously identified as Pandoraea pnomenusa, Pandoraea sputorum, Pandoraea oxalativorans and Pandoraea pulmonicola belong to novel species. The strains did not harbor acquired antibiotic resistance genes but encoded an OXA-type ß-lactamase. Conclusion: The taxonomy of the genus Pandoraea needs to be revised.
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Affiliation(s)
- Jumamurat R Bayjanov
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Miquel B Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Malbert Rc Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal & Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Barry J Benaissa-Trouw
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - María Díez-Aguilar
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal & Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Michael Tunney
- Department of Pulmonology, Queen's University Belfast, Northern Ireland, UK
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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22
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Rauwers AW, Troelstra A, Fluit AC, Wissink C, Loeve AJ, Vleggaar FP, Bruno MJ, Vos MC, Bode LG, Monkelbaan JF. Independent root-cause analysis of contributing factors, including dismantling of 2 duodenoscopes, to investigate an outbreak of multidrug-resistant Klebsiella pneumoniae. Gastrointest Endosc 2019; 90:793-804. [PMID: 31102643 DOI: 10.1016/j.gie.2019.05.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 05/05/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Worldwide, an increasing number of duodenoscope-associated outbreaks are reported. The high prevalence rate of contaminated duodenoscopes puts patients undergoing ERCP at risk of exogenous transmission of microorganisms. The contributing factors of the duodenoscope design to contamination are not well understood. This article reports on the investigation after the outbreak of a multidrug-resistant Klebsiella pneumoniae (MRKP) related to 2 Olympus TJF-Q180V duodenoscopes. METHODS We conducted a contact patient screening and microbiologic laboratory database search. Reprocessing procedures were audited, and both duodenoscopes were fully dismantled to evaluate all potential contamination factors. Outcomes were reviewed by an experienced independent expert. RESULTS In total, 102 patients who had undergone an ERCP procedure from January to August 2015 were invited for screening. Cultures were available of 81 patients, yielding 27 MRKP-infected or -colonized patients. Ten patients developed an MRKP-related active infection. The 2 duodenoscopes had attack rates (the number of infected or colonized cases/number of exposed persons) of 35% (17/49) and 29% (7/24), respectively. Identical MRKP isolates were cultured from channel flushes of both duodenoscopes. The review revealed 4 major abnormalities: miscommunication about reprocessing, undetected damaged parts, inadequate repair of duodenoscope damage, and duodenoscope design abnormalities, including the forceps elevator, elevator lever, and instrumentation port sealing. CONCLUSIONS Outbreaks are associated with a combination of factors, including duodenoscope design issues, repair issues, improper cleaning, and systemic monitoring of contamination. To eliminate future duodenoscope-associated infections, a multipronged approach is required, including clear communication by all parties involved, a reliable servicing market, stringent surveillance measures, and eventually new duodenoscope designs and reprocessing procedures with a larger margin of safety.
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Affiliation(s)
- Arjan W Rauwers
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Annet Troelstra
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Camiel Wissink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Arjo J Loeve
- Department of Biomechanical Engineering, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands; Co van Ledden Hulsebosch Center for Forensic Science and Medicine, Amsterdam, The Netherlands
| | - Frank P Vleggaar
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marco J Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Margreet C Vos
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Lonneke G Bode
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Jan F Monkelbaan
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, The Netherlands
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23
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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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24
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van den Broek T, Janssen NG, Hetem DJ, Bekers W, Kamst M, Fluit AC, van Ingen J, Kusters JG, Rentenaar RJ. INNO-LiPA DNA line probe assay misidentification of M. smegmatis as Mycobacterium fortuitum complex. Diagn Microbiol Infect Dis 2019; 95:114858. [PMID: 31358343 DOI: 10.1016/j.diagmicrobio.2019.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/26/2019] [Accepted: 06/20/2019] [Indexed: 10/26/2022]
Abstract
Seven weeks after being kicked in the face by a cow, a 34-year-old male patient developed a posttraumatic mycobacterial lymphadenitis. A rapidly growing mycobacterial isolate cultured from a surgically drained lymphadenitis pus specimen was identified as Mycobacterium smegmatis by matrix-assisted laser desorption/ionization mass spectrometry and a combination of ITS-, hsp65-, and 16S rRNA-DNA sequence analysis, but as Mycobacterium fortuitum complex using the commercial INNO-LiPA Mycobacteria v2 line probe assay. As it is unclear if the misidentification of this strain is an exception, more research is required.
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Affiliation(s)
- Theo van den Broek
- Department of Medical Microbiology, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands.
| | - Nard G Janssen
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands
| | - David J Hetem
- Department of Medical Microbiology, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands; Department of Medical Microbiology, Haaglanden Medical Center, 2501, CK, The Hague, The Netherlands
| | - Wouter Bekers
- Department of Medical Microbiology, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands
| | - Miranda Kamst
- National Institute for Public Health and the Environment (RIVM), 3720, BA, Bilthoven, The Netherlands
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands
| | - Jakko van Ingen
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, 6500, HB, Nijmegen, The Netherlands
| | - Johannes G Kusters
- Department of Medical Microbiology, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands
| | - Rob J Rentenaar
- Department of Medical Microbiology, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands
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25
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Croes M, Kruyt MC, Boot W, Pouran B, Braham MV, Pakpahan SA, Weinans H, Vogely HC, Fluit AC, Dhert WJ, Alblas J, Öner FC. The role of bacterial stimuli in inflammation-driven bone formation. Eur Cell Mater 2019; 37:402-419. [PMID: 31094449 DOI: 10.22203/ecm.v037a24] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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] [Indexed: 01/31/2023] Open
Abstract
Immune cells and their soluble factors regulate skeletal cells during normal bone regeneration and pathological bone formation. Bacterial infections can trigger immune responses that activate pro-osteogenic pathways, but these are usually overshadowed by osteolysis and concerns of systemic inflammation. The aim of this study was to determine whether the transient local inflammatory reaction to non-viable bacterial immune agonists could lead to favourable new bone formation. In a series of rabbit studies, as proof-of-concept, how tibial intramedullary injection of viable or killed bacterial species affected bone remodelling and new bone formation was determined. Application of killed bacteria led to considerable new bone formation after 4 weeks, without the prolonged systemic inflammation and exaggerated bone lysis seen with active infection. The osteo-immunomodulatory effects of various species of killed bacteria and the dose response relationship were subsequently screened in ectopically-implanted ceramic scaffolds. Histomorphometry after 8 weeks showed that a relatively low dose of killed bacteria enhanced ectopic bone induction. Moreover, lipoteichoic acid - the bacterial cell-wall derived toll-like-receptor (TLR)-2 activator - was identified as an osteo-stimulatory factor. Collectively, the data indicated that bacterial stimuli could be harnessed to stimulate osteogenesis, which occurs through a synergy with osteoinductive signals. This finding holds promise for the use of non-viable bacteria, bacterial antigens, or their simplified analogues as immuno-modulatory bone regenerating tools in bone biomaterials.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - J Alblas
- Department of Orthopaedics University Medical Centre Utrecht, Rm G05.228, P.O. Box 85500, Utrecht 3508 GA, the Netherlands. j.alblas @umcutrecht.nl
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26
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van den Bunt G, Top J, Hordijk J, de Greeff SC, Mughini-Gras L, Corander J, van Pelt W, Bonten MJM, Fluit AC, Willems RJL. Intestinal carriage of ampicillin- and vancomycin-resistant Enterococcus faecium in humans, dogs and cats in the Netherlands. J Antimicrob Chemother 2019; 73:607-614. [PMID: 29294027 DOI: 10.1093/jac/dkx455] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 11/06/2017] [Indexed: 12/24/2022] Open
Abstract
Background The prevalence of ampicillin- and/or vancomycin-resistant Enterococcus faecium (AREf and VREf) has increased in hospitalized patients in the Netherlands. Objectives To quantify the prevalence, risk factors and co-carriage of AREf and VREf in humans, cats and dogs in the Dutch population. Methods From 2014 to 2015, ∼2000 inhabitants of the Netherlands each month were randomly invited to complete a questionnaire and provide a faecal sample. Subjects owning pets were also asked to submit one dog or cat sample. Faecal samples were screened for AREf and VREf. The genetic relatedness of isolates was determined using core genome MLST. Logistic regression analysis was used to determine risk factors. Results Of 25 365 subjects, 4721 (18.6%) completed the questionnaire and 1992 (42.2%) human, 277 dog and 118 cat samples were submitted. AREf was detected in 29 human (1.5%), 71 dog (25.6%) and 6 cat (5.1%) samples. VREf (vanA) was detected in one human and one dog. AREf/VREf co-carriage was not detected in 388 paired samples. The use of antibiotics (OR 4.2, 95% CI 1.7-11.2) and proton pump inhibitors (OR 2.7, 95% CI 1.1-6.3) were risk factors for AREf carriage in humans. In dogs, these were the use of antibiotics (OR 2.3, 95% CI 1.1-4.6) and eating raw meat (OR 3.2, 95% CI 1.4-6.6). Core genome MLST-based phylogenetic linkage indicated clonal relatedness for a minority of human (16.7%) and pet AREf isolates (23.8%) in three clusters. Conclusions Intestinal carriage with AREf or VREf is rare in the Dutch general population. Although AREf carriage is high in dogs, phylogenetic linkage between human and pet AREf isolates was limited.
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Affiliation(s)
- G van den Bunt
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - J Top
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - J Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - S C de Greeff
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - L Mughini-Gras
- Centre for Infectious Disease Control, 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
| | - J Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - W van Pelt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - M J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - A C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - R J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
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27
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Fluit AC, Rentenaar RJ, Ekkelenkamp MB, Severs TT, Mavinkurve-Groothuis AMC, Rogers MRC, Bruin MCA, Wolfs TFW. Fatal Carbapenem Resistance Development in Pseudomonas Aeruginosa Under Meropenem Monotherapy, Caused by Mutations in the OprD Outer Membrane Porin. Pediatr Infect Dis J 2019; 38:398-399. [PMID: 30882731 DOI: 10.1097/inf.0000000000002244] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A 13-year old neutropenic boy succumbed to bacteremia and sepsis with a Pseudomonas aeruginosa strain that rapidly developed resistance to carbapenems during meropenem monotherapy. Whole genome sequencing of the susceptible and resistant blood culture isolates revealed the meropenem-resistant phenotype to be caused by truncation of the OprD gene, which added to a preexisting inactivated mexR gene.
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Affiliation(s)
- Ad C Fluit
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J Rentenaar
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Miquel B Ekkelenkamp
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tim T Severs
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Malbert R C Rogers
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marrie C A Bruin
- Princess Maxima Centre for Pediatric Oncology, Utrecht, The Netherlands
| | - Tom F W Wolfs
- Department of Pediatrics, Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
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28
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Dorado-García A, Smid JH, van Pelt W, Bonten MJM, Fluit AC, van den Bunt G, Wagenaar JA, Hordijk J, Dierikx CM, Veldman KT, de Koeijer A, Dohmen W, Schmitt H, Liakopoulos A, Pacholewicz E, Lam TJGM, Velthuis AG, Heuvelink A, Gonggrijp MA, van Duijkeren E, van Hoek AHAM, de Roda Husman AM, Blaak H, Havelaar AH, Mevius DJ, Heederik DJJ. Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the environment: a pooled analysis. J Antimicrob Chemother 2019; 73:339-347. [PMID: 29165596 DOI: 10.1093/jac/dkx397] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/27/2017] [Indexed: 11/13/2022] Open
Abstract
Background In recent years, ESBL/AmpC-producing Escherichia coli (ESBL/AmpC-EC) have been isolated with increasing frequency from animals, food, environmental sources and humans. With incomplete and scattered evidence, the contribution to the human carriage burden from these reservoirs remains unclear. Objectives To quantify molecular similarities between different reservoirs as a first step towards risk attribution. Methods Pooled data on ESBL/AmpC-EC isolates were recovered from 35 studies in the Netherlands comprising >27 000 samples, mostly obtained between 2005 and 2015. Frequency distributions of ESBL/AmpC genes from 5808 isolates and replicons of ESBL/AmpC-carrying plasmids from 812 isolates were compared across 22 reservoirs through proportional similarity indices (PSIs) and principal component analyses (PCAs). Results Predominant ESBL/AmpC genes were identified in each reservoir. PCAs and PSIs revealed close human-animal ESBL/AmpC gene similarity between human farming communities and their animals (broilers and pigs) (PSIs from 0.8 to 0.9). Isolates from people in the general population had higher similarities to those from human clinical settings, surface and sewage water and wild birds (0.7-0.8), while similarities to livestock or food reservoirs were lower (0.3-0.6). Based on rarefaction curves, people in the general population had more diversity in ESBL/AmpC genes and plasmid replicon types than those in other reservoirs. Conclusions Our 'One Health' approach provides an integrated evaluation of the molecular relatedness of ESBL/AmpC-EC from numerous sources. The analysis showed distinguishable ESBL/AmpC-EC transmission cycles in different hosts and failed to demonstrate a close epidemiological linkage of ESBL/AmpC genes and plasmid replicon types between livestock farms and people in the general population.
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Affiliation(s)
- Alejandro Dorado-García
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80175, 3508 TD Utrecht, The Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, PO Box 80165, 3508 TD Utrecht, The Netherlands
| | - Joost H Smid
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80175, 3508 TD Utrecht, The Netherlands
| | - Wilfrid van Pelt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - Marc J M Bonten
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, The Netherlands.,Department of Medical Microbiology, University Medical Centre Utrecht, PO Box 85500, 3508 GA Utrecht, The Netherlands
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Centre Utrecht, PO Box 85500, 3508 GA Utrecht, The Netherlands
| | - Gerrita van den Bunt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, The Netherlands.,Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, PO Box 85500, 3508 GA Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, PO Box 80165, 3508 TD Utrecht, The Netherlands
| | - Joost Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, PO Box 80165, 3508 TD Utrecht, The Netherlands
| | - Cindy M Dierikx
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - Kees T Veldman
- Wageningen Bioveterinary Research, PO Box 65, 8200 AB Lelystad, The Netherlands
| | - Aline de Koeijer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, The Netherlands.,Wageningen Bioveterinary Research, PO Box 65, 8200 AB Lelystad, The Netherlands
| | - Wietske Dohmen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80175, 3508 TD Utrecht, The Netherlands
| | - Heike Schmitt
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80175, 3508 TD Utrecht, The Netherlands
| | | | - Ewa Pacholewicz
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80175, 3508 TD Utrecht, The Netherlands
| | - Theo J G M Lam
- GD Animal Health, PO Box 9, 7400 AA Deventer, The Netherlands
| | - Annet G Velthuis
- Wageningen Bioveterinary Research, PO Box 65, 8200 AB Lelystad, The Netherlands
| | - Annet Heuvelink
- GD Animal Health, PO Box 9, 7400 AA Deventer, The Netherlands
| | | | - Engeline van Duijkeren
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - Angela H A M van Hoek
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - Ana Maria de Roda Husman
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80175, 3508 TD Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - Hetty Blaak
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - Arie H Havelaar
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80175, 3508 TD Utrecht, The Netherlands.,Institute for Sustainable Food Systems, Emerging Pathogens Institute and Animal Sciences Department, University of Florida, PO Box 100009, Gainesville, FL 32610, USA
| | - Dik J Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, PO Box 80165, 3508 TD Utrecht, The Netherlands.,Wageningen Bioveterinary Research, PO Box 65, 8200 AB Lelystad, The Netherlands
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80175, 3508 TD Utrecht, The Netherlands
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29
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Franssens BT, Fluit AC, Rentenaar RJ. Reproducibility between two readout methods of a commercial broth microdilution assay for Pseudomonas aeruginosa isolates from patients with Cystic Fibrosis. Infect Dis (Lond) 2019; 51:50-55. [PMID: 30654670 DOI: 10.1080/23744235.2018.1500705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa isolates from Cystic fibrosis (CF) patients are growing slowly, and frequently rendering automated susceptibility testing unsuitable. Colistin is an important antibiotic for treatment of P. aeruginosa infections. Broth microdilution is the only EUCAST endorsed antimicrobial susceptibility test for colistin. The VIZION™ device aids in reading broth microdilution plates and allows safe data transfer to laboratory information systems. In this study, reproducibility between visual MIC readout and readout, employing the VIZION™ device was assessed in susceptibility testing of colistin and beta-lactam antibiotics in P. aeruginosa isolates from CF patients. METHODS Fifty-six unique P. aeruginosa isolates were derived from respiratory secretions of CF patients. Susceptibility testing was performed using commercially available microdilution plates. MIC readout by VIZION™ was compared to visual readout aided by a mirror (reference test). RESULTS Pseudomonas aeruginosa isolates displayed significantly slower growth rates compared to quality control isolates. Colistin exact MIC agreement between VIZION™ and visual readout after 24 and 48 h incubation, respectively, was 82% and 95%, essential MIC agreement was 98% and 100%, categorical agreement was 98% and 98% and reliability (weighted kappa) was 0.95 (95% CI = 0.91-0.99) and 0.99 (95% CI = 0.97-1.00). For all five antibiotics, the total number of errors (using VIZION™, in comparison with visual readout) decreased from 15 (5%) to 10 (4%) after 24 and 48 h incubation, respectively. CONCLUSIONS VIZION™ readout reproducibly determines MIC values in comparison with visual readout after 24 h of incubation. Reproducibility between the VIZION™ and visual readout increases after prolonged incubation of 48 h.
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Affiliation(s)
- Bas T Franssens
- a Department of Medical Microbiology , University Medical Centre Utrecht , Utrecht , The Netherlands
| | - Ad C Fluit
- a Department of Medical Microbiology , University Medical Centre Utrecht , Utrecht , The Netherlands
| | - Rob J Rentenaar
- a Department of Medical Microbiology , University Medical Centre Utrecht , Utrecht , The Netherlands
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30
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Croes M, de Visser H, Meij BP, Lietart K, van der Wal BCH, Vogely HC, Fluit AC, Boel CHE, Alblas J, Weinans H, Amin Yavari S. Data on a rat infection model to assess porous titanium implant coatings. Data Brief 2018; 21:1642-1648. [PMID: 30505893 PMCID: PMC6247446 DOI: 10.1016/j.dib.2018.10.157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 10/03/2018] [Revised: 10/26/2018] [Accepted: 10/30/2018] [Indexed: 10/31/2022] Open
Abstract
A model is needed to study the effectiveness of different anti-bacterial coatings on complex metal implants in a bone environment. This article shares data on the design of porous titanium implants for intramedullary implantation in the proximal rat tibia. The implant length, diameter and porosity were optimized after testing on cadaveric specimens. This article shares data on which parameters are critical to establish a chronic implant infection in Sprague Dawley rats when using the new implant design. To this end, different strains of Staphylococcus aureus and inoculation doses were investigated.
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Affiliation(s)
- M Croes
- Department of Orthopedics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - H de Visser
- Department of Orthopedics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - B P Meij
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - K Lietart
- 3D Systems - LayerWise NV, Leuven, Belgium.,Department of Metallurgy and Materials Engineering, KU Leuven, Leuven, Belgium
| | - B C H van der Wal
- Department of Orthopedics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - H C Vogely
- Department of Orthopedics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - A C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - C H E Boel
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - J Alblas
- Department of Orthopedics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - H Weinans
- Department of Orthopedics, University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Biomechanical Engineering, Delft University of Technology, Delft, the Netherlands.,Department of Rheumatology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - S Amin Yavari
- Department of Orthopedics, University Medical Center Utrecht, Utrecht, the Netherlands
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31
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Akhavan B, Bakhshandeh S, Najafi-Ashtiani H, Fluit AC, Boel E, Vogely C, van der Wal BCH, Zadpoor AA, Weinans H, Hennink WE, Bilek MM, Amin Yavari S. Direct covalent attachment of silver nanoparticles on radical-rich plasma polymer films for antibacterial applications. J Mater Chem B 2018; 6:5845-5853. [PMID: 32254705 DOI: 10.1039/c8tb01363b] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Prevention and treatment of biomaterial-associated infections (BAI) are imperative requirements for the effective and long-lasting function of orthopedic implants. Surface-functionalization of these materials with antibacterial agents, such as antibiotics, nanoparticles and peptides, is a promising approach to combat BAI. The well-known silver nanoparticles (AgNPs) in particular, although benefiting from strong and broad-range antibacterial efficiency, have been frequently associated with mammalian cell toxicity when physically adsorbed on biomaterials. The majority of irreversible immobilization techniques employed to fabricate AgNP-functionalized surfaces are based on wet-chemistry methods. However, these methods are typically substrate-dependent, complex, and time-consuming. Here we present a simple and dry strategy for the development of polymeric coatings used as platforms for the direct, linker-free covalent attachment of AgNPs onto solid surfaces using ion-assisted plasma polymerization. The resulting coating not only exhibits long-term antibiofilm efficiency against adherent Staphylococcus aureus (S. aureus), but also enhances osteoblast adhesion and proliferation. High resolution X-ray photoelectron spectroscopy (XPS), before and after sodium dodecyl sulfate (SDS) washing, confirms covalent bonding. The development of such silver-functionalized surfaces through a simple, plasma-based process holds great promise for the fabrication of implantable devices with improved tissue-implant integration and reduced biomaterial associated infections.
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Affiliation(s)
- Behnam Akhavan
- School of Aerospace, Mechanical and Mechatronic Engineering, University of Sydney, Sydney, NSW 2006, Australia.
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Díez-Aguilar M, Ekkelenkamp M, Morosini MI, Merino I, de Dios Caballero J, Jones M, van Westreenen M, Tunney MM, Cantón R, Fluit AC. Antimicrobial susceptibility of non-fermenting Gram-negative pathogens isolated from cystic fibrosis patients. Int J Antimicrob Agents 2018; 53:84-88. [PMID: 30240837 DOI: 10.1016/j.ijantimicag.2018.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/01/2018] [Accepted: 09/09/2018] [Indexed: 10/28/2022]
Abstract
Non-fermenting Gram-negative bacteria (NFGNB) are increasingly cultured in respiratory samples from cystic fibrosis (CF) patients. This study determined the antimicrobial susceptibility of clinical CF respiratory isolates from distinct geographical regions. A total of 286 isolates (106 Stenotrophomonas maltophilia, 100 Burkholderia spp., 59 Achromobacter spp., 12 Pandoraea spp., 9 Ralstonia spp.) from the Netherlands, Northern Ireland, Spain, USA and Australia were tested. MIC50/90 values and susceptibility categorisation were determined. Trimethoprim/sulfamethoxazole (SXT) was the most active compound for all micro-organisms (MIC50, 0.12-4 mg/L; MIC90, 1-16 mg/L). For S. maltophilia, 47% and 62% of isolates were susceptible to SXT according to CLSI and EUCAST breakpoints, respectively. Ceftazidime presented lower susceptibility (35%; MIC50, 32 mg/L; MIC90, 256 mg/L). MIC90 values for tobramycin and colistin were >128 mg/L and >16 mg/L, respectively. Regarding Burkholderia, 72%, 56% and 44% were susceptible to SXT, ceftazidime and meropenem, respectively. For both ceftazidime and meropenem, MIC50 and MIC90 values were within the intermediate or resistant category. The most active antibiotics for Achromobacter spp. were SXT (MIC50, 0.5 mg/L; MIC90, 8 mg/L) and imipenem (MIC50, 2 mg/L; MIC90, 8 mg/L). SXT, imipenem and ciprofloxacin were active against 12 Pandoraea spp. (MIC50, 0.12-4 mg/L; MIC90, 1-8 mg/L). Ciprofloxacin (MIC50, 4 mg/L) and SXT (MIC50, 1 mg/L) were the only active antibiotics for Ralstonia spp. There were no statistically significant differences in susceptibility rates between countries. NFGNB other than Pseudomonas aeruginosa are potential pathogens in CF. SXT was demonstrated to be the most active compound against these isolates.
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Affiliation(s)
- María Díez-Aguilar
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Miquel Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - María-Isabel Morosini
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Irene Merino
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Juan de Dios Caballero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Mark Jones
- Basilea Pharmaceutica, Basel, Switzerland
| | - Mireille van Westreenen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | | | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain.
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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Dautzenberg MJD, Bayjanov JR, Leverstein-van Hall MA, Muller AE, Gelinck LBS, Jansen CL, Leyten EMS, Ruys T, Scharringa J, van der Starre RE, Fluit AC, Bonten MJM. Dynamics of colistin and tobramycin resistance among Enterobacter cloacae during prolonged use of selective decontamination of the digestive tract. Antimicrob Resist Infect Control 2018; 7:67. [PMID: 29796252 PMCID: PMC5964641 DOI: 10.1186/s13756-018-0356-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 03/18/2018] [Accepted: 05/01/2018] [Indexed: 11/24/2022] Open
Abstract
Background A high prevalence of colistin resistance among E. cloacae isolates in two intensive care units (ICU) (of 16 and 6 beds) using selective digestive decontamination (SDD) since 1990 instigated a retrospective and prospective investigation to quantify the role of clonal transmission. SDD is topical application of colistin and tobramycin and systemic use of cefotaxime during the first days of ICU-admission. Methods Multi-resistant E. cloacae (MREb) was defined as ESBL production and/or tobramycin non-susceptibility and/or colistin non-susceptibility. Incidence of acquisition and prevalence of carriage with MREb was determined from microbiological culture results. Results Colistin-resistant E. cloacae was first detected in November 2009 and carriage was demonstrated in 141 patients until October 2014. Mean incidence of MREb acquisition was 4.61 and 1.86 per 1000 days at risk in ICUs 1 and 2, respectively, and the mean monthly prevalence of MREb in both ICUs was 7.0 and 3.1%, respectively, without a discernible trend in time. Conversion rates from carriage of colistin-susceptible to resistant E. cloacae were 0.20 and 0.13 per 1000 patient days, respectively. Whole genome sequencing of 149 isolates revealed eight clusters, with the number of SNPs of the largest two clusters ranging between 0 and 116 for cluster 1 (n = 49 isolates), and 0 and 27 for cluster 2 (n = 36 isolates), among isolates derived between 2009 and 2014. Conclusions This study demonstrates a stable low-level endemicity of MREb in two Dutch ICUs with prolonged use of SDD, which was characterized by the persistent presence of two clusters, suggesting incidental clonal transmission. Electronic supplementary material The online version of this article (10.1186/s13756-018-0356-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M J D Dautzenberg
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands.,2Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands.,3Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - J R Bayjanov
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - M A Leverstein-van Hall
- Department of Medical Microbiology, Haaglanden Medisch Centrum, The Hague, the Netherlands.,5Department of Medical Microbiology, Alrijne Hospital, Leiden, the Netherlands
| | - A E Muller
- Department of Medical Microbiology, Haaglanden Medisch Centrum, The Hague, the Netherlands
| | - L B S Gelinck
- Department of Internal Medicine, Haaglanden Medisch Centrum, The Hague, the Netherlands
| | - C L Jansen
- Department of Medical Microbiology, Haaglanden Medisch Centrum, The Hague, the Netherlands
| | - E M S Leyten
- Department of Internal Medicine, Haaglanden Medisch Centrum, The Hague, the Netherlands
| | - T Ruys
- Department of Intensive Care Medicine, Haaglanden Medisch Centrum, The Hague, the Netherlands
| | - J Scharringa
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - R E van der Starre
- Department of Medical Microbiology, Haaglanden Medisch Centrum, The Hague, the Netherlands
| | - A C Fluit
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - M J M Bonten
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands.,2Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
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Ekkelenkamp MB, Vervoorn MT, Bayjanov JR, Fluit AC, Benaissa-Trouw BJ, Ramjankhan FZ. Therapy and Outcome of Staphylococcus aureus Infections of Intracorporeal Ventricular Assist Devices. Artif Organs 2018; 42:983-991. [PMID: 29675919 PMCID: PMC6220828 DOI: 10.1111/aor.13159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/05/2018] [Accepted: 03/15/2018] [Indexed: 12/14/2022]
Abstract
Infection of the driveline or pump pocket is a common complication in patients with ventricular assist devices (VADs) and Staphylococcus aureus is the main pathogen causing such infections. Limited evidence is currently available to guide the choice of antibiotic therapy and the duration of treatment in these patients. Patients at the University Medical Center Utrecht who developed a VAD‐related S. aureus infection between 2007 and 2016 were retrospectively assessed. Blood culture isolates were typed by whole genome sequencing to differentiate between relapses and reinfections, and to determine whether antibiotic therapy had led to acquisition of resistance mutations. Twenty‐eight patients had S. aureus VAD infections. Ten of these patients also suffered S. aureus bacteremia. Discontinuation of antibiotic therapy was followed by relapse in 50% of the patients without prior S. aureus bacteremia and in 80% of patients with bacteremia. Oral cephalexin could ultimately suppress the infection for the duration of follow‐up in 8/8 patients without S. aureus bacteremia and in 3/6 patients with S. aureus bacteremia. Clindamycin failed as suppressive therapy in 4/4 patients. Cephalexin appears an adequate choice for antibiotic suppression of VAD infections with methicillin‐susceptible S. aureus. In patients without systemic symptoms, it may be justified to attempt to stop therapy after treatment of the acute infection, but antibiotic suppression until heart transplant seems indicated in patients with S. aureus bacteremia.
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Affiliation(s)
- Miquel B Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mats T Vervoorn
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Cardiothoracic Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jumamurat R Bayjanov
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Barry J Benaissa-Trouw
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Faiz Z Ramjankhan
- Department of Cardiothoracic Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
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Duim B, Verstappen KMHW, Kalupahana RS, Ranathunga L, Fluit AC, Wagenaar JA. Methicillin-resistant Staphylococcus pseudintermedius among dogs in the description of novel SCCmec variants. Vet Microbiol 2017; 213:136-141. [PMID: 29291997 DOI: 10.1016/j.vetmic.2017.11.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 04/21/2017] [Revised: 11/03/2017] [Accepted: 11/17/2017] [Indexed: 01/11/2023]
Abstract
The presence and genetic characteristics of methicillin-resistant Staphylococcus pseudintermedius (MRSP) in Sri Lanka was investigated to add additional insight into global spread, emergence and evolution of MRSP. A total of 234 samples from dogs visiting veterinary clinics were cultured for staphylococci and the genomes of the MRSP isolates were sequenced, to identify resistance genes, the multilocus sequence types (MLST) and spa types. From a questionnaire the history of antimicrobial treatment and patient information was obtained. S. pseudintermedius was isolated from 116/229 samples, eight of these were MRSP. Six MRSP CC45 isolates contained a pseudo-SCC element ΨSCCmec57395. Two isolates belonging to ST429 (CC761) and ST121 (CC121) contained novel variants of the SCCmec Type V(T) element. The elements were designated SCCmecV(T)SL/066, that carried additional transposon-related genes, and SCCmecV(T)SL/154 that carried a type III restriction-modification system, a type 7 ccr gene complex, and a cadA coding sequence. Thirty-seven percent of the dogs received antimicrobial treatment at the time of sampling of which four dogs were MRSP-positive. The proportion of MRSP among S. pseudintermedius is low compared to other countries, despite the fact that in Sri Lanka antimicrobials for treatment of dogs are available over the counter. Important is the finding of novel type V(T) SCCmec elements, which further underlines the high recombination frequency of SCC elements. The ΨSCCmec57395 was found in isolates of CC45, which is the only sequence type of MRSP known to contain this pseudo-cassette.
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Affiliation(s)
- Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - Koen M H W Verstappen
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - Ruwani S Kalupahana
- Department of Veterinary Public Health and Pharmacology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Sri Lanka.
| | - Lakmali Ranathunga
- Department of Veterinary Public Health and Pharmacology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Sri Lanka.
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands.
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands; Wageningen Bioveterinary Research, Lelystad, The Netherlands.
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Verstappen KM, Willems E, Fluit AC, Duim B, Martens M, Wagenaar JA. Staphylococcus aureus Nasal Colonization Differs among Pig Lineages and Is Associated with the Presence of Other Staphylococcal Species. Front Vet Sci 2017; 4:97. [PMID: 28691012 PMCID: PMC5481302 DOI: 10.3389/fvets.2017.00097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 11/11/2016] [Accepted: 06/08/2017] [Indexed: 12/03/2022] Open
Abstract
Staphylococcus aureus is a common colonizer in pigs, with methicillin-resistant S. aureus (MRSA) in particular being a potential health risk to humans. To reduce the exposure to humans, the colonization in pigs should be reduced. The aim of this study was to quantitatively compare the susceptibility of pig lineages for S. aureus colonization, and if the absence of S. aureus could be associated with the presence or absence of other staphylococcal species. Nasal samples (n = 129) were obtained from seven different pig lineages in the Netherlands, France, and Germany. S. aureus and other staphylococci were enumerated from these samples by real-time (RT)-PCR and culture. Associations were explored between the presence of S. aureus and other staphylococci. S. aureus was detected by RT-PCR on all farms and in samples from pigs of all lineages. Twenty-five percent of the pigs from lineage F (from two farms) were colonized with S. aureus, while in all other lineages it was more than 50% (p < 0.01). Moreover, in S. aureus-positive samples from pigs of lineage F smaller amounts of S. aureus were found than in other lineages. Staphylococcus sciuri, Staphylococcus cohnii, and Staphylococcus saprophyticus were usually not found in combination with S. aureus in these samples. In conclusion: (i) pigs from different genetic lineages have different susceptibilities for colonization with S. aureus. These pigs might contain a genetic factor influencing nasal colonization. (ii) Colonization of S. aureus is also associated with the absence of S. sciuri, S. cohnii, or S. saprophyticus. (iii) The farm environment seems to influence the presence of S. aureus in pigs.
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Affiliation(s)
- Koen M Verstappen
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands
| | | | - Ad C Fluit
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Birgitta Duim
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands
| | | | - Jaap A Wagenaar
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands.,Wageningen Bioveterinary Research, Lelystad, Netherlands
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van den Bunt G, Liakopoulos A, Mevius DJ, Geurts Y, Fluit AC, Bonten MJM, Mughini-Gras L, van Pelt W. ESBL/AmpC-producing Enterobacteriaceae in households with children of preschool age: prevalence, risk factors and co-carriage. J Antimicrob Chemother 2016; 72:589-595. [PMID: 27789683 DOI: 10.1093/jac/dkw443] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/13/2016] [Accepted: 09/20/2016] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES ESBL/AmpC-producing Enterobacteriaceae are an emerging public health concern. As households with preschool children may substantially contribute to the community burden of antimicrobial resistance, we determined the prevalence, risk factors and co-carriage of ESBL/AmpC-producing bacteria in preschool children and their parents. METHODS From April 2013 to January 2015, each month 2000 preschool children were randomly selected from Dutch population registries. The parents were invited to complete an epidemiological questionnaire and to obtain and send a faecal sample from the selected child and from one parent. Samples were tested for ESBL/AmpC-producing bacteria. Logistic regression was used to identify risk factors for ESBL/AmpC carriage in children and parents, and findings were internally validated by bootstrapping. RESULTS In total, 1016 families were included and ESBL/AmpC prevalence was 4.0% (95% CI 3.2%-5.0%); 3.5% (95% CI 2.5%-4.8%) in children and 4.5% (95% CI 3.4%-6.0%) in parents. Attending a daycare centre (DCC) was the only significant risk factor for children (OR 2.1, 95% CI 1.0-4.3). For parents, the only significant risk factor was having one or more children attending DCCs (OR 2.2, 95% CI 1.2-4.8). For parents of ESBL/AmpC-positive children the OR for ESBL/AmpC carriage was 19.7 (95% CI 9.2-42.4). Co-carriage of specific ESBL/AmpC genotypes in child and parent occurred more often than expected by chance (14.6% versus 1.1%, P < 0.001). CONCLUSIONS In this study, intestinal carriage with ESBL/AmpCs was detected in ∼4% of households with preschool children. DCC attendance was a risk factor in both children and parents and co-carriage of specific genotypes frequently occurred in child-parent pairs. These findings suggest household transmission or/and family-specific exposure to common sources of ESBL/AmpC-producing bacteria.
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Affiliation(s)
- G van den Bunt
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands .,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - A Liakopoulos
- Department of Bacteriology and Epidemiology, Central Veterinary Institute (CVI) of Wageningen University, Lelystad, The Netherlands
| | - D J Mevius
- Department of Bacteriology and Epidemiology, Central Veterinary Institute (CVI) of Wageningen University, Lelystad, The Netherlands.,Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Y Geurts
- Department of Bacteriology and Epidemiology, Central Veterinary Institute (CVI) of Wageningen University, Lelystad, The Netherlands
| | - A C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - M J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - L Mughini-Gras
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - W van Pelt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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Smith M, Diederen B, Scharringa J, Leversteijn-van Hall M, Fluit AC, Cohen Stuart J. Rapid and accurate detection of carbapenemase genes in Enterobacteriaceae with the Cepheid Xpert Carba-R assay. J Med Microbiol 2016; 65:951-953. [DOI: 10.1099/jmm.0.000310] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Marion Smith
- Department of Medical Microbiology, Medisch Centrum Alkmaar, Juliana Van Stolberglaan 13, 1814 HB Alkmaar, The Netherlands
| | - Bram Diederen
- Department of Medical Microbiology, Medisch Centrum Alkmaar, Juliana Van Stolberglaan 13, 1814 HB Alkmaar, The Netherlands
- Regional Laboratory of Public Health, Haarlem 2035 RC, The Netherlands
| | - Jelle Scharringa
- Department of Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Ad C. Fluit
- Department of Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - James Cohen Stuart
- Regional Laboratory of Public Health, Haarlem 2035 RC, The Netherlands
- Department of Medical Microbiology, Medisch Centrum Alkmaar, Juliana Van Stolberglaan 13, 1814 HB Alkmaar, The Netherlands
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Verstappen KM, Tulinski P, Duim B, Fluit AC, Carney J, van Nes A, Wagenaar JA. The Effectiveness of Bacteriophages against Methicillin-Resistant Staphylococcus aureus ST398 Nasal Colonization in Pigs. PLoS One 2016; 11:e0160242. [PMID: 27487020 PMCID: PMC4972443 DOI: 10.1371/journal.pone.0160242] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/15/2016] [Indexed: 12/02/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an important colonizer in animals and an opportunistic pathogen in humans. In humans, MRSA can cause infections that might be difficult to treat because of antimicrobial resistance. The use of bacteriophages has been suggested as a potential approach for the control of MRSA colonization to minimize the—often occupational—exposure of humans. The aim of this study was to assess the efficacy of bacteriophage treatment on porcine nasal colonization with MRSA in vitro, in vivo, and ex vivo. The effectiveness of a bacteriophage combination of phage K*710 and P68 was assessed in vitro by incubating them with MRSA V0608892/1 (ST398) measuring the OD600 hourly. To study the in vivo effect, bacteriophages were administered in a gel developed for human application, which contain 109 plaque-forming units (pfu)/mL (K and P68 in a 19.25:1 ratio) for 5 days to piglets (N = 8) that were experimentally colonized with the MRSA strain. Eight piglets experimentally colonized were used as a negative control. The MRSA strain was also used to colonize porcine nasal mucosa explants and bacteriophages were applied to assess the ex vivo efficacy of treatment. Bacteriophages were effective in vitro. In vivo, sixteen piglets were colonized with MRSA but the number of CFU recovered after the application of the bacteriophages in 8 piglets was not reduced compared to the control animals (approx. 105 CFU/swab). In the ex vivo model, 108 CFU were used to establish colonization with MRSA; a reduction of colonization was not observed after application of bacteriophages. However, application of mupirocin both in vivo and ex vivo resulted in a near eradication of MRSA. In conclusion: i) The MRSA strain was killed in the presence of the bacteriophages phage K*710 and P68 in vitro. ii) Bacteriophages did not reduce porcine nasal colonization in vivo or ex vivo. Physiological in vivo and ex vivo conditions may explain these observations. Efficacy in the ex vivo model matched that of the in vivo system.
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Affiliation(s)
- Koen M Verstappen
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Pawel Tulinski
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- * E-mail:
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | | | - Arie van Nes
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Central Veterinary Institute of Wageningen UR, Lelystad, the Netherlands
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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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Kusters JG, van Leeuwen WB, Maquelin K, Blok HEM, Willemse HFM, de Graaf-Miltenburg LAM, Fluit AC, Troelstra A. Raman spectroscopy-based identification of nosocomial outbreaks of the clonal bacterium Escherichia coli. Eur J Clin Microbiol Infect Dis 2015; 35:83-7. [PMID: 26563894 PMCID: PMC4710649 DOI: 10.1007/s10096-015-2511-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 07/01/2015] [Accepted: 10/15/2015] [Indexed: 11/21/2022]
Abstract
DNA-based techniques are frequently used to confirm the relatedness of putative outbreak isolates. These techniques often lack the discriminatory power when analyzing closely related microbes such as E. coli. Here the value of Raman spectroscopy as a typing tool for E. coli in a clinical setting was retrospectively evaluated.
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Affiliation(s)
- J G Kusters
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
| | - W B van Leeuwen
- Department of Innovative Molecular Diagnostics, University of Applied Sciences Leiden, Leiden, The Netherlands
| | - K Maquelin
- Center for Optical Diagnostics and Therapy, Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - H E M Blok
- Center for Optical Diagnostics and Therapy, Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - H F M Willemse
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - L A M de Graaf-Miltenburg
- Center for Optical Diagnostics and Therapy, Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A C Fluit
- Center for Optical Diagnostics and Therapy, Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A Troelstra
- Center for Optical Diagnostics and Therapy, Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands
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Vriens MR, Fluit AC, Troelstra A, Verhoef J, van der Werken C. Is Methicillin-Resistant Staphylococcus Aureus More Contagious than Methicillin-Susceptible S. Aureus in a Surgical Intensive Care Unit? Infect Control Hosp Epidemiol 2015; 23:491-4. [PMID: 12269444 DOI: 10.1086/502094] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Background and Objective:In the Netherlands, the prevalence of methicillin resistance among Staphylococcus aureus isolates has been kept to less than 1% by using active screening programs and isolation. At the University Medical Center Utrecht (UMCU), an active screening program for methicillin-resistant S. aureus (MRSA) in the surgical intensive care unit (ICU) was implemented in 1986. Between 1992 and 2001, only 6 patients with MRSA were admitted to the surgical ICU. However, 4 of these 6 strains were able to spread to 23 other patients and 15 healthcare workers (HCWs). We were surprised by the epidemic behavior of these strains and wondered whether this was exceptional for S. aureus or whether methicillin-susceptible S. aureus (MSSA) was also spreading in the ICU.Design:A 2-month, prospective, observational study to investigate the incidence and spread of MSSA in the surgical ICU of UMCU and historical data collected during a 10-year period regarding MRSA.Setting:A 10-bed surgical ICU in a 1,042-bed teaching hospital.Results:Weekly swabs revealed the presence of MSSA in 11 (24%) of 45 patients and 16 (22%) of 72 HCWs. Of all 4,105 patient–HCW contacts, there were only 21 episodes in which both the patient and the HCW were found to carry MSSA. With the use of pulsed-field gel electrophoresis, no identical strains could be identified.Conclusion:In our surgical ICU, MRSA seems to spread more easily than MSSA, probably because of selection under antibiotic pressure or a still unknown intrinsic factor within MRSA.
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Affiliation(s)
- Menno R Vriens
- Department of Surgery, Eijkman Winkler Institute, University Medical Center, Utrecht, The Netherlands
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Fluit AC, Carpaij N, Majoor EAM, Weinstein RA, Aroutcheva A, Rice TW, Bonten MJM, Willems RJL. Comparison of an ST80 MRSA strain from the USA with European ST80 strains. J Antimicrob Chemother 2014; 70:664-9. [PMID: 25395549 DOI: 10.1093/jac/dku459] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVES A number of community-acquired MRSA (CA-MRSA) clonal lineages dominate worldwide. ST80 was dominant in Europe and has increasingly been described from the Middle East. Here we report the whole genome sequence of the first ST80 CA-MRSA from the USA. METHODS CA-MRSA isolate S0924 was obtained from a patient admitted to Cook County Hospital (Chicago, IL, USA) who came from Syria; the isolate belonged to spa type t044 and ST80. The whole genome sequence of S0924 was determined and compared with three previously published whole genome sequences of ST80 CA-MRSA from Europe and a newly sequenced ST80 CA-MRSA from the Netherlands (S1475). RESULTS Based on spa typing, SCCmec type and virulence gene profile, this US ST80 isolate is indistinguishable from the European CA-MRSA ST80 clone. SNP analysis within the conserved core genome showed clear differences between the strains with up to 144 SNPs differing between S0924 and strain S1800, an ST80 MRSA from Greece. The gene content showed 21 regions of difference between the US and European isolates, although these were largely restricted to mobile genetic elements. Phylogenetic reconstruction indicated that the European strains were more closely related to each other than to the US strain. The SNP data suggest that a common ancestor existed around two decades ago, indicating that the US and European ST80 strains are clonally linked. CONCLUSIONS These data combined with the country of origin of the patient suggest that ST80 S0924 was probably relatively recently introduced into the USA from Syria.
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Affiliation(s)
- Ad C Fluit
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Neeltje Carpaij
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Eline A M Majoor
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Robert A Weinstein
- Department of Infectious Diseases, Rush University Medical Center, Chicago, IL, USA
| | - Alla Aroutcheva
- Department of Infectious Diseases, Rush University Medical Center, Chicago, IL, USA
| | - Thomas W Rice
- Division of Infectious Disease, John H. Stroger Jr. Hospital of Cook County, Chicago, IL, USA
| | - Marc J M Bonten
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
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Tulinski P, Duim B, Wittink FR, Jonker MJ, Breit TM, van Putten JP, Wagenaar JA, Fluit AC. Staphylococcus aureus ST398 gene expression profiling during ex vivo colonization of porcine nasal epithelium. BMC Genomics 2014; 15:915. [PMID: 25331735 PMCID: PMC4210494 DOI: 10.1186/1471-2164-15-915] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/13/2014] [Indexed: 11/10/2022] Open
Abstract
Background Staphylococcus aureus is a common human and animal opportunistic pathogen. In humans nasal carriage of S. aureus is a risk factor for various infections. Methicillin-resistant S. aureus ST398 is highly prevalent in pigs in Europe and North America. The mechanism of successful pig colonization by MRSA ST398 is poorly understood. Previously, we developed a nasal colonization model of porcine nasal mucosa explants to identify molecular traits involved in nasal MRSA colonization of pigs. Results We report the analysis of changes in the transcription of MRSA ST398 strain S0462 during colonization on the explant epithelium. Major regulated genes were encoding metabolic processes and regulation of these genes may represent metabolic adaptation to nasal mucosa explants. Colonization was not accompanied by significant changes in transcripts of the main virulence associated genes or known human colonization factors. Here, we documented regulation of two genes which have potential influence on S. aureus colonization; cysteine extracellular proteinase (scpA) and von Willebrand factor-binding protein (vWbp, encoded on SaPIbov5). Colonization with isogenic-deletion strains (Δvwbp and ΔscpA) did not alter the ex vivo nasal S. aureus colonization compared to wild type. Conclusions Our results suggest that nasal colonization with MRSA ST398 is a complex event that is accompanied with changes in bacterial gene expression regulation and metabolic adaptation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-915) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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Jonker MJ, de Leeuw WC, Marinković M, Wittink FRA, Rauwerda H, Bruning O, Ensink WA, Fluit AC, Boel CH, Jong MD, Breit TM. Absence/presence calling in microarray-based CGH experiments with non-model organisms. Nucleic Acids Res 2014; 42:e94. [PMID: 24771343 PMCID: PMC4066771 DOI: 10.1093/nar/gku343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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] [Indexed: 01/07/2023] Open
Abstract
Structural variations in genomes are commonly studied by (micro)array-based comparative genomic hybridization. The data analysis methods to infer copy number variation in model organisms (human, mouse) are established. In principle, the procedures are based on signal ratios between test and reference samples and the order of the probe targets in the genome. These procedures are less applicable to experiments with non-model organisms, which frequently comprise non-sequenced genomes with an unknown order of probe targets. We therefore present an additional analysis approach, which does not depend on the structural information of a reference genome, and quantifies the presence or absence of a probe target in an unknown genome. The principle is that intensity values of target probes are compared with the intensities of negative-control probes and positive-control probes from a control hybridization, to determine if a probe target is absent or present. In a test, analyzing the genome content of a known bacterial strain: Staphylococcus aureus MRSA252, this approach proved to be successful, demonstrated by receiver operating characteristic area under the curve values larger than 0.9995. We show its usability in various applications, such as comparing genome content and validating next-generation sequencing reads from eukaryotic non-model organisms.
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Affiliation(s)
- Martijs J Jonker
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Wim C de Leeuw
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Marino Marinković
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
| | - Floyd R A Wittink
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands
| | - Han Rauwerda
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Oskar Bruning
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Wim A Ensink
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands
| | - Ad C Fluit
- Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - C H Boel
- Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mark de Jong
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands
| | - Timo M Breit
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
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Dautzenberg MJ, Ossewaarde JM, de Kraker ME, van der Zee A, van Burgh S, de Greeff SC, Bijlmer HA, Grundmann H, Cohen Stuart JW, Fluit AC, Troelstra A, Bonten M. Successful control of a hospital-wide outbreak of OXA-48 producing Enterobacteriaceae in the Netherlands, 2009 to 2011. Euro Surveill 2014; 19. [DOI: 10.2807/1560-7917.es2014.19.9.20723] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Binary file ES_Abstracts_Final_ECDC.txt matches
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Affiliation(s)
- M J Dautzenberg
- Department of Medical Microbiology, Maasstad Ziekenhuis, Rotterdam, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - J M Ossewaarde
- Department of Medical Microbiology, Maasstad Ziekenhuis, Rotterdam, the Netherlands
| | - M E de Kraker
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - A van der Zee
- Department of Medical Microbiology, Maasstad Ziekenhuis, Rotterdam, the Netherlands
| | - S van Burgh
- Department of Medical Microbiology, Maasstad Ziekenhuis, Rotterdam, the Netherlands
| | - S C de Greeff
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - H A Bijlmer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - H Grundmann
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- University Medical Center Groningen, University of Groningen, the Netherlands
| | - J W Cohen Stuart
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - A C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - A Troelstra
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - M Bonten
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
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van der Zee A, Roorda L, Bosman G, Fluit AC, Hermans M, Smits PHM, van der Zanden AGM, Te Witt R, Bruijnesteijn van Coppenraet LES, Cohen Stuart J, Ossewaarde JM. Multi-centre evaluation of real-time multiplex PCR for detection of carbapenemase genes OXA-48, VIM, IMP, NDM and KPC. BMC Infect Dis 2014; 14:27. [PMID: 24422880 PMCID: PMC3897903 DOI: 10.1186/1471-2334-14-27] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [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: 09/03/2013] [Accepted: 12/24/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Resistance to carbapenem antibiotics is emerging worldwide among Enterobacteriaceae. To prevent hospital transmission due to unnoticed carriage of carbapenemase producing micro-organisms in newly admitted patients, or follow-up of patients in an outbreak setting, a molecular screening method was developed for detection of the most prevalent carbapenemase genes; blaOXA-48, blaVIM, blaIMP, blaNDM and blaKPC. METHODS A real-time multiplex PCR assay was evaluated using a collection of 86 Gram negative isolates, including 62 carbapenemase producers. Seven different laboratories carried out this method and used the assay for detection of the carbapenemase genes on a selection of 20 isolates. RESULTS Both sensitivity and specificity of the multiplex PCR assay was 100%, as established by results on the strain collection and the inter-laboratory comparisons. CONCLUSIONS In this study, we present a multiplex real-time PCR that is a robust, reliable and rapid method for the detection of the most prevalent carbapenemases blaOXA-48, blaVIM, blaIMP, blaNDM and blaKPC, and is suitable for screening of broth cultured rectal swabs and for identification of carbapenemase genes in cultures.
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Affiliation(s)
- Anneke van der Zee
- Maasstad Laboratory, Molecular Diagnostics Unit, Maasstad Hospital, Rotterdam, The Netherlands.
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Schijffelen M, Konstantinov SR, Lina G, Spiliopoulou I, van Duijkeren E, Brouwer EC, Fluit AC. Whole genome analysis of epidemiologically closely related Staphylococcus aureus isolates. PLoS One 2013; 8:e78340. [PMID: 24205205 PMCID: PMC3804489 DOI: 10.1371/journal.pone.0078340] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/17/2013] [Indexed: 11/19/2022] Open
Abstract
The change of the bacteria from colonizers to pathogens is accompanied by a drastic change in expression profiles. These changes may be due to environmental signals or to mutational changes. We therefore compared the whole genome sequences of four sets of S. aureus isolates. Three sets were from the same patients. The isolates of each pair (S1800/S1805, S2396/S2395, S2398/S2397, an isolate from colonization and an isolate from infection, respectively) were obtained within <30 days of each other and the isolate from infection caused skin infections. The isolates were then compared for differences in gene content and SNPs. In addition, a set of isolates from a colonized pig and a farmer from the same farm at the same time (S0462 and S0460) were analyzed. The isolates pair S1800/S1805 showed a difference in a prophage, but these are easily lost or acquired. However, S1805 contained an integrative conjugative element not present in S1800. In addition, 92 SNPs were present in a variety of genes and the isolates S1800 and S1805 were not considered a pair. Between S2395/S2396 two SNPs were present: one was in an intergenic region and one was a synonymous mutation in a putative membrane protein. Between S2397/S2398 only one synonymous mutation in a putative lipoprotein was found. The two farm isolates were very similar and showed 12 SNPs in genes that belong to a number of different functional categories. However, we cannot pinpoint any gene that explains the change from carrier status to infection. The data indicate that differences between the isolate from infection and the colonizing isolate for S2395/S2396 and S2397/S2398 exist as well as between isolates from different hosts, but S1800/S1805 are not clonal.
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Affiliation(s)
- Maarten Schijffelen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sergey R. Konstantinov
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gérard Lina
- Laboratoire de Bactériologie - CNR des Staphylocoques, University Claude Bernard, Lyon 1, Lyon, France
| | - Iris Spiliopoulou
- Department of Microbiology, School of Medicine University of Patras, Patras, Greece
| | - Engeline van Duijkeren
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University Utrecht, The Netherlands
- Centre for Infectious Disease Control Netherlands, Institute of Public Health and Environment, Bilthoven, The Netherlands
| | - Ellen C. Brouwer
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ad C. Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
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Voets GM, Fluit AC, Scharringa J, Schapendonk C, van den Munckhof T, Leverstein-van Hall MA, Stuart JC. Identical plasmid AmpC beta-lactamase genes and plasmid types in E. coli isolates from patients and poultry meat in the Netherlands. Int J Food Microbiol 2013; 167:359-62. [PMID: 24184615 DOI: 10.1016/j.ijfoodmicro.2013.10.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [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: 04/23/2013] [Revised: 09/30/2013] [Accepted: 10/02/2013] [Indexed: 01/08/2023]
Abstract
The increasing prevalence of third-generation cephalosporin-resistant Enterobacteriaceae is a worldwide problem. Recent studies showed that poultry meat and humans share identical Extended-Spectrum Beta-Lactamase genes, plasmid types, and Escherichia coli strain types, suggesting that transmission from poultry meat to humans may occur. The aim of this study was to compare plasmid-encoded Ambler class C beta-lactamase (pAmpC) genes, their plasmids, and bacterial strain types between E. coli isolates from retail chicken meat and clinical isolates in the Netherlands. In total, 98 Dutch retail chicken meat samples and 479 third-generation cephalosporin non-susceptible human clinical E. coli isolates from the same period were screened for pAmpC production. Plasmid typing was performed using PCR-based replicon typing (PBRT). E coli strains were compared using Multi-Locus-Sequence-Typing (MLST). In 12 of 98 chicken meat samples (12%), pAmpC producing E. coli were detected (all blaCMY-2). Of the 479 human E. coli, 25 (5.2%) harboured pAmpC genes (blaCMY-2 n = 22, blaACT n = 2, blaMIR n = 1). PBRT showed that 91% of poultry meat isolates harboured blaCMY-2 on an IncK plasmid, and 9% on an IncI1 plasmid. Of the human blaCMY-2 producing isolates, 42% also harboured blaCMY-2 on an IncK plasmid, and 47% on an IncI1 plasmid. Thus, 68% of human pAmpC producing E. coli have the same AmpC gene (blaCMY-2) and plasmid type (IncI1 or IncK) as found in poultry meat. MLST showed one cluster containing one human isolate and three meat isolates, with an IncK plasmid. These findings imply that a foodborne transmission route of blaCMY-2 harbouring plasmids cannot be excluded and that further evaluation is required.
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Affiliation(s)
- Guido M Voets
- Department of Medical Microbiology, University Medical Centre Utrecht, G04.614, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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van Dijk K, Voets GM, Scharringa J, Voskuil S, Fluit AC, Rottier WC, Leverstein-Van Hall MA, Cohen Stuart JWT. A disc diffusion assay for detection of class A, B and OXA-48 carbapenemases in Enterobacteriaceae using phenyl boronic acid, dipicolinic acid and temocillin. Clin Microbiol Infect 2013; 20:345-9. [PMID: 23927659 DOI: 10.1111/1469-0691.12322] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [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: 03/19/2013] [Revised: 06/27/2013] [Accepted: 06/30/2013] [Indexed: 11/29/2022]
Abstract
Class A and B carbapenemases in Enterobacteriaceae may be detected using carbapenemase inhibition tests with boronic acid derivatives (BA) and dipicolinic acid (DPA)/EDTA, respectively. However, for OXA-48 (like) carbapenemases, no specific inhibitor is available. Because OXA-48 confers high-level temocillin resistance, a disc diffusion assay using temocillin as well as BA and DPA inhibition tests was evaluated for detection of class A, B and OXA-48 carbapenemases. The test collection included 128 well-characterized non-repeat Enterobacteriaceae isolates suspected of carbapenemase production; that is, with meropenem MICs ≥ 0.5 mg/L, including 99 carbapenemase producers (36 KPC, one GES, 31 MBL, four KPC plus VIM, 25 OXA-48, two OXA-162), and 29 ESBL and/or AmpC-producing isolates. PCR and sequencing of beta-lactamase genes was used as a reference test. Phenotypic carbapenemase detection was performed with discs (Rosco) containing meropenem (10 μg), temocillin (30 μg), meropenem + phenyl boronic acid (PBA), meropenem + DPA, meropenem + BA + DPA, and meropenem + cloxacillin (CL). Absence of synergy between meropenem and BA and/or DPA and a temocillin zone ≤10 mm was used to identify OXA-48. The sensitivity for identification of class A, B and OXA-48 carbapenemases was 95%, 90% and 100%, with 96-100% specificity. In non-Proteus species, the sensitivity for class B carbapenemase detection was 97%. All isolates without PBA or DPA synergy and a temocillin disc zone ≤10 mm were OXA-48 (like) positive. In conclusion, carbapenemase inhibition tests with PBA and DPA combined with a temocillin disc provide a reliable phenotypic confirmation method for class A, B and OXA-48 carbapenemases in Enterobacteriaceae.
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Affiliation(s)
- K van Dijk
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands; Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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