Kees Maquelin

Erasmus Universiteit Rotterdam, Rotterdam, South Holland, Netherlands

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Publications (31)105.13 Total impact

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    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.
    No preview · Article · Nov 2015 · European Journal of Clinical Microbiology
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    ABSTRACT: Data of Staphylococcus aureus carriage in Indonesian hospitals are scarce. Therefore, the epidemiology of S. aureus among surgery patients in three academic hospitals in Indonesia was studied. In total, 366 of 1,502 (24.4%) patients carried S. aureus. The methicillin-resistant S. aureus (MRSA) carriage rate was 4.3%, whereas 1.5% of the patients carried Panton-Valentine leukocidin (PVL)-positive methicillin-sensitive S. aureus (MSSA). Semarang and Malang city (odds ratio [OR] 9.4 and OR 9.0), being male (OR 2.4), hospitalization for more than 5 days (OR 11.708), and antibiotic therapy during hospitalization (OR 2.6) were independent determinants for MRSA carriage, whereas prior hospitalization (OR 2.5) was the only one risk factor for PVL-positive MSSA carriage. Typing of MRSA strains by Raman spectroscopy showed three large clusters assigned type 21, 24, and 38, all corresponding to ST239-MRSA-SCCmec type III. In conclusion, MRSA and PVL-positive MSSA are present among patients in surgical wards in Indonesian academic hospitals.
    No preview · Article · Feb 2014 · The American journal of tropical medicine and hygiene
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    ABSTRACT: Raman spectroscopy was used to discriminate between Legionella strains and between E. coli and coliform strains. The relationship between triplicate Raman spectra derived from Legionella bacteria was compared with that derived from a blind set of samples and amplified fragment length polymorphism (AFLP) data from the same strains. Triplicate Raman spectra of E. coli and coliform bacteria were compared with their 16S phylogeny. In all cases Raman spectra were reproducible and could be distinguished from spectra of other organisms down to the strain level. All samples in a blind fourth set were identified correctly. Raman spectra of organisms of the same coliform species clustered according to 16S rRNA gene phylogeny, except for Enterobacter spp. At higher taxonomic levels the relationship between species was less comparable. For Legionella strains the Raman spectra grouped according to AFLP groups, based on the dataset used in this study. Raman spectroscopy could correctly distinguish E. coli from other coliform bacteria and L. pneumophila from non-pneumophila strains. Incubation of Legionella strains in different types of drinking water at different temperatures over a period of one week introduced so little variation in the Raman spectra that only very closely related L. pneumophila strains could not be distinguished from each other. Temperature, ageing and water type did not influence the identification potency of Raman spectroscopy in all cases. Given the accuracy, speed and simplicity of the Raman spectroscopy technique this method seems a welcome addition to the current tools for identification of waterborne bacteria.
    No preview · Article · May 2013 · Analytical methods
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    ABSTRACT: The anterior nares is the site of choice for the Veterans Administration methicillin-resistant Staphylococcus aureus (MRSA) surveillance program; however, correlation between nares colonization and concomitant wound infections has not been well established. The purpose of this study was threefold: to determine the relatedness of MRSA isolates from 40 paired wound and nares specimens by four different strain typing methods, to determine concordance of typing methods, and to establish a baseline of MRSA types at this medical center. Isolates were typed by rep-PCR (DiversiLab System, DL) and SpectraCell Raman analysis (SCRA) (commercially available methods that can be performed within a clinical lab), pulsed-field gel electrophoresis (PFGE) and antibiotic susceptibility profile (AB). Whole genome optical mapping (WGM) (OpGen, Inc.) was performed on selected isolates. All methods agreed that 26 pairs were indistinguishable and four pairs were different. Discrepant results were: SCRA discordant) (4), AB discordant (3), DL and AB discordant (2), and DL and SCRA discordant (1). All WGM agreed with PFGE. After discrepant resolution 80% of the pairs were indistinguishable and 20% were different. 56% of nares results were non-predictive if negative nares and positive wound cultures are included. Methods agreed 85 to 93%; however congruence of isolates to clade was lower. Baseline analysis of types showed 15 pairs were unique to a single patient (30 strains, 38%; 47% of the matching pairs). 25 strains (30%) represented a single clade identical by PFGE, SCRA and DL, decreasing specificity. Typing method and institutional type frequency are important in assessing MRSA strain relatedness.
    Full-text · Article · Nov 2012 · Journal of clinical microbiology
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    ABSTRACT: Nosocomial outbreaks of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae are an increasing concern in neonatal intensive care units (NICUs). We describe an outbreak of ESBL-producing K. pneumoniae that lasted 5 months and affected 23 neonates in our NICU. Proton pump inhibitor and extended-spectrum cephalosporin exposure were significantly associated with the risk of ESBL-producing K. pneumoniae colonisation and/or infection. Thirty isolates recovered from clinical, screening and environmental samples in the NICU were studied by means of Raman spectroscopy, pulsed-field gel electrophoresis and repetitive extragenic palindromic polymerase chain reaction (rep-PCR). The Raman clustering was in good agreement with the results of the other two molecular methods. Fourteen isolates belonged to the Raman clone 1 and 16 to the Raman clone 3. Molecular analysis showed that all the strains expressed SHV-1 chromosomal resistance, plasmid-encoded TEM-1 and CTX-M-15 β-lactamases. Incompatibility groups of plasmid content identified by PCR-based replicon typing indicated that resistance dissemination was due to the clonal spread of K. pneumoniae and horizontal CTX-M-15 gene transfer between the two clones.
    Full-text · Article · May 2012 · European Journal of Clinical Microbiology
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    ABSTRACT: Enterobacteriaceae are important pathogens of both nosocomial and community-acquired infections. In particular, strains with broad-spectrum beta-lactamases increasingly cause problems in health care settings. Rapid and reliable typing systems are key tools to identify transmission, so that targeted infection control measures can be taken. In this study, we evaluated the performance of Raman spectroscopic analysis (RA) for the typing of multiresistant Escherichia coli and Klebsiella pneumoniae isolates using the SpectraCell RA bacterial strain analyzer (River Diagnostics). Analysis of 96 unrelated isolates revealed that RA generated highly reproducible spectra and exhibited a discriminatory power that is comparable to pulsed-field gel electrophoresis. Furthermore, adequate results were obtained for three collections of clinical isolates. RA was able to discriminate outbreak-related isolates from isolates that were not involved in an outbreak or transmission. Furthermore, it was found that the RA approach recognized clones, irrespective of the extended-spectrum β-lactamase type. It can be concluded that RA is a suitable typing technique for E. coli and K. pneumoniae isolates. Combining high reproducibility, speed, and ease-of-use, this technique may play an important role in monitoring the epidemiology of these important nosocomial species.
    Full-text · Article · Jan 2012 · Journal of clinical microbiology
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    ABSTRACT: Clin Microbiol Infect 2012; 18: 147–152 In order to perform a cost-effective search and destroy policy for methicillin-resistant Staphylococcus aureus (MRSA), a quick and reliable typing method is essential. In an area with a high level of animal-related MRSA ST398, pulsed field gel electrophoresis (PFGE) typing and spa-typing are not sufficient to discriminate between co-incidental findings and true transmission of MRSA. This study is the first to retrospectively show the performance of Raman spectroscopy in 16 well-documented outbreaks. We analysed 525 isolates, 286 MRSA ST398 and 239 from other PFGE clusters with Raman spectroscopy. When epidemiologically linked isolates from the outbreaks were analysed with PFGE as the reference standard, Raman spectroscopy correctly identified 97% of cases that were indistinguishable from the index case. With Raman cluster analysis, the most dominant distinction was between MRSA ST398 and other MRSA of human clonal lineages. Within MRSA ST398, 22 different Raman clusters were identified. Raman typing correctly identified an ST398 (spa type t567) outbreak in a hospital setting. No direct correlation was observed between Raman clusters and spa types. We conclude that Raman spectroscopy is a quick and reliable method of MRSA typing, which can be used in outbreak settings and it is comparable to PFGE, with the added advantage that PFGE non-typeable isolates can also be readily typed using the same sample preparation protocol.
    Full-text · Article · Mar 2011 · Clinical Microbiology and Infection
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    ABSTRACT: Raman spectra of bacteria can be used as highly specific fingerprints, enabling discrimination at strain level. Pseudomonas aeruginosa strains can be strongly pigmented, making it difficult to obtain high quality spectra of such isolates due to high fluorescent spectral backgrounds. Furthermore, the spectra that could be measured with acceptable quality often showed large spectral variations limiting the reproducibility required for strain level discrimination. P. aeruginosa produces a characteristic yellowish green fluorescent pigment, called pyoverdin. Applying a washing procedure to reduce the amount of fluorescent pigment, enabled the highly pigmented isolates to be measured with sufficient spectral quality. Isolation of the pigment/pyoverdin spectral features, together with spectral scaling methods improved reproducibility. It will be important to analyze the range of the spectral variations that can occur and ensure the correction of all of these factors to obtain the highest reproducibility required for strain level typing.
    No preview · Article · Aug 2010 · Journal of Biophotonics
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    ABSTRACT: Coagulase-negative staphylococci (CNS) are among the most frequently isolated bacterial species in clinical microbiology, and most CNS-related infections are hospital acquired. Distinguishing between these frequently multiple-antibiotic-resistant isolates is important for both treatment and transmission control. In this study we used isolates of methicillin-resistant coagulase-negative staphylococci (MR-CNS) that were selected from a large surveillance study of the direct spread of MR-CNS. This strain collection was used to evaluate (i) Raman spectroscopy as a typing tool for MR-CNS isolates and (ii) diversity between colonies with identical and different morphologies. Reproducibility was high, with 215 of 216 (99.5%) of the replicate samples for 72 isolates ending up in the same cluster. The concordance with pulsed-field gel electrophoresis (PFGE)-based clusters was 94.4%. We also confirm that the skin of patients can be colonized with multiple MR-CNS types at the same time. Morphological differences between colonies from a single patient sample correlated with differences in Raman and PFGE types. Some morphologically indistinguishable colonies revealed different Raman and PFGE types. This indicates that multiple MR-CNS colonies should be examined to obtain a complete insight into the prevalence of different types and to be able to perform an accurate transmission analysis. Here we show that Raman spectroscopy is a reproducible typing system for MR-CNS isolates. It is a tool for screening variability within a collection of isolates. Because of the high throughput, it enables the analysis of multiple colonies per patient, which will enhance the quality of clinical and epidemiological studies.
    Full-text · Article · Mar 2010 · Journal of clinical microbiology
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    ABSTRACT: Raman spectroscopy has previously been demonstrated to be a highly useful methodology for the identification and/or typing of micro-organisms. In this study, we set out to evaluate whether this technology could also be applied as a tool to discriminate between isolates of Mycoplasma pneumoniae, which is generally considered to be a genetically highly uniform species. In this evaluation, a total of 104 strains of M. pneumoniae were analysed, including two reference strains (strains M129 and FH), and 102 clinical isolates, which were isolated between 1973 and 2005 and originated from various countries. By Raman spectral analysis (Raman typing) of this strain collection, we were able to reproducibly distinguish six different clusters of strains. An unequivocal correlation between Raman typing and P1 genotyping, which is based on sequence differences in the P1 (or MPN141) gene of M. pneumoniae, was not observed. In the two major Raman clusters that we identified (clusters 3 and 6, which together harboured 81 % of the strains), the different P1 subtypes were similarly distributed, and approximately 76 % isolates were of subtype 1, approximately 20 % of subtype 2 and approximately 5 % of variant 2a. Nevertheless, a relatively high prevalence of P1 subtype 2 strains was found in clusters 2 and 5 (100 %), as well as in cluster 1 (75 %) and cluster 4 (71 %); these clusters, however, harboured a small number of strains. Only two of the strains (2 %) could not be typed correctly. Interestingly, analysis of the Raman spectra revealed the presence of carotenoids in M. pneumoniae. This finding is in line with the identification of M. pneumoniae genes that have similarity with genes involved in a biochemical pathway leading to carotenoid synthesis, i.e. the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway. Therefore, we hypothesize that M. pneumoniae hosts an MEP-like pathway for carotenoid synthesis. We conclude that Raman spectroscopy is a convenient tool for discriminating between M. pneumoniae strains, and that it presents a promising supplement to the current methods for typing of this bacterium.
    No preview · Article · May 2009 · Microbiology
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    ABSTRACT: Hospital-acquired infections (HAI) increase morbidity and mortality and constitute a high financial burden on health care systems. An effective weapon against HAI is early detection of potential outbreaks and sources of contamination. Such monitoring requires microbial typing with sufficient reproducibility and discriminatory power. Here, a microbial-typing method is presented, based on Raman spectroscopy. This technique provides strain-specific optical fingerprints in a few minutes instead of several hours to days, as is the case with genotyping methods. Although the method is generally applicable, we used 118 Staphylococcus aureus isolates to illustrate that the discriminatory power matches that of established genotyping techniques (numerical index of diversity [D]=0.989) and that concordance with the gold standard (pulsed-field gel electrophoresis) is high (95%). The Raman clustering of isolates was reproducible to the strain level for five independent cultures, despite the various culture times from 18 h to 24 h. Furthermore, this technique was able to classify stored (-80 degrees C) and recent isolates of a methicillin-resistant Staphylococcus aureus-colonized individual during surveillance studies and did so days earlier than established genotyping techniques did. Its high throughput and ease of use make it suitable for use in routine diagnostic laboratory settings. This will set the stage for continuous, automated, real-time epidemiological monitoring of bacterial infections in a hospital, which can then be followed by timely corrective action by infection prevention teams.
    Full-text · Article · Mar 2009 · Journal of clinical microbiology
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    ABSTRACT: Bacterial typing by Raman spectroscopy is based on small spectral differences that exist between strains, due to differences in their overall molecular composition. These strain-specific spectral differences can be obscured by sources of non-specific signal variance. One such source is the signal contribution of microbial pigments that can vary strongly in intensity. Examples of such pigments are carotenoids in Staphylococcus aureus, and other pigments in Pseudomonas aeruginosa and Mycobacterium lentiflavum. The variance in the intensity of these pigments greatly overshadows strain-specific differences, and therefore lowers spectral reproducibility and causes misclassification of microbial strains. Here a method is presented to determine the spectral signature of pigments of which the relative signal contribution decreases under laser irradiation; so-called photo-bleachable pigments. These signatures are used to eliminate signal variance caused by these pigments by means of the extended multiplicative scatter correction algorithm and spectral interferent subtraction. Application of this method increases the reproducibility of the spectra of microorganisms that contain such pigments to the extent that reproducible identification of samples at strain level is achieved.
    Full-text · Article · Mar 2009 · The Analyst
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    ABSTRACT: A number of rapid identification methods have been developed to improve the accuracy for diagnosis of tuberculosis and to speed up the presumptive identification of Mycobacterium species. Most of these methods have been validated for a limited group of microorganisms only. Here, Raman spectroscopy was compared to 16S rRNA sequencing for the identification of Mycobacterium tuberculosis complex strains and the most frequently found strains of nontuberculous mycobacteria (NTM). A total of 63 strains, belonging to eight distinct species, were analyzed. The sensitivity of Raman spectroscopy for the identification of Mycobacterium species was 95.2%. All M. tuberculosis strains were correctly identified (7 of 7; 100%), as were 54 of 57 NTM strains (94%). The differentiation between M. tuberculosis and NTM was invariably correct for all strains. Moreover, the reproducibility of Raman spectroscopy was evaluated for killed mycobacteria (by heat and formalin) versus viable mycobacteria. The spectra of the heat-inactivated bacteria showed minimal differences compared to the spectra of viable mycobacteria. Therefore, the identification of mycobacteria appears possible without biosafety level 3 precautions. Raman spectroscopy provides a novel answer to the need for rapid species identification of cultured mycobacteria in a clinical diagnostic setting.
    Full-text · Article · Apr 2008 · Journal of clinical microbiology
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    ABSTRACT: This study explored the potential of Raman spectroscopy for the analysis of poly(3-hydroxybutyrate) (PHB) in bacteria. PHB can be formed in large amounts by certain bacteria as a storage material and is of high importance for industrial biodegradable plastic production. Raman spectra were collected from Cupriavidus necator DSM 428 (H16), from its non-PHB-producing mutant strain C. necator DSM 541, and from pure PHB, in order to determine at which Raman shifts a contribution of PHB in bacterial spectra can be expected. The Raman band intensity at ca. 1734 cm(-1) appeared to be suitable for the monitoring of PHB production and consumption. These intensities were linearly related to the PHB concentration (mg L(-1) culture) determined by parallel HPLC analysis. Therefore, Raman spectroscopy is considered as a fast and noninvasive technique for the determination and monitoring of the PHB content in bacteria.
    Full-text · Article · Apr 2008 · Analytical Chemistry
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    ABSTRACT: Amplified fragment length polymorphism genotypes, antibiotic resistance profiles, and toxin profiles of Clostridium difficile strains from Warsaw were determined. The isolates segregate in six major genotypes, coinciding with toxin profiles. Most of the toxin A-negative toxin B-positive toxin CDT-negative strains possess ermB, and several strains were resistant to fluoroquinolones. Resistograms and toxin types of C. difficile strains are epidemicity determinants.
    Full-text · Article · Jun 2007 · Journal of Clinical Microbiology
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    ABSTRACT: A questionnaire-based survey was performed to accumulate data on methodologies used in microbiology laboratories involved in epidemiological typing. Genotyping by PFGE and MLST are currently clearly preferred over phenotyping. The overall wish is to increase the activities by over 20% and additional resources would be used to invest in real-time typing.
    No preview · Article · May 2007 · Journal of Microbiological Methods
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    ABSTRACT: An expanding body of literature suggests Raman spectroscopy is a promising tool for skin cancer diagnosis and in-vivo tumor border demarcation. The development of an in-vivo diagnostic tool is, however, hampered by the fact that construction of fiber optic probes suitable for Raman spectroscopy in the so-called fingerprint region is complicated. In contrast, the use of the high wave-number region allows for fiber optic probes with a very simple design. We investigate whether high wave-number Raman spectroscopy (2800 to 3125 cm(-1)) is able to provide sufficient information for noninvasive discrimination between basal cell carcinoma (BCC) and noninvolved skin. Using a simple fiber optic probe, Raman spectra are obtained from 19 BCC biopsy specimens and 9 biopsy specimens of perilesional skin. A linear discriminant analysis (LDA)-based tissue classification model is developed, which discriminates between BCC and noninvolved skin with high accuracy. This is a crucial step in the development of clinical dermatological applications based on fiber optic Raman spectroscopy.
    No preview · Article · May 2007 · Journal of Biomedical Optics
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    ABSTRACT: We have applied Raman spectroscopy to discriminate between nontumor and tumor bladder tissue and to determine the biochemical differences therein. Tissue samples from 15 patients were collected, and frozen sections were made for Raman spectroscopy and histology. Twenty-five pseudocolor Raman maps were created in which each color represents a cluster of spectra measured on tissue areas of similar biochemical composition. For each cluster, the cluster-averaged spectrum (CAS) was calculated and classified as tumor and nontumor in accordance to pathohistology. Unguided hierarchical clustering was applied to display heterogeneity between and within groups of nontumor and tumor CAS. A linear discriminant analysis model was developed to discriminate between CAS from tumor and nontumor. The model was tested by a leave-one-patient-out validation, 84 of the 90 CAS (93%) were correctly classified with 94% sensitivity and 92% specificity. Biochemical differences between tumor and nontumor CAS areas were analyzed by fitting spectra of pure compounds to the CAS. Nontumor CAS showed higher collagen content while tumor CAS were characterized by higher lipid, nucleic acid, protein, and glycogen content. Raman spectroscopy enabled effective discrimination between tumor and nontumor bladder tissue based on characterized biochemical differences, despite heterogeneity expressed in both tumor and nontumor CAS.
    No preview · Article · Dec 2006 · Analytical Chemistry
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    No preview · Chapter · Aug 2006
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    ABSTRACT: From earlier publications, we noticed that Raman spectra could potentially be used for subspecies identification of microorganisms. Here we evaluated the technique for its use as a typing tool of Acinetobacter species, using a collection of well-characterised strains from five hospital outbreaks. The strains were previously analysed using molecular techniques as cell envelope protein profiling and ribotyping. In this study, we have typed the strains by AFLP analysis and Raman spectroscopy. We compared the results using hierarchical cluster analysis, which showed highly similar groupings by both techniques. There seemed to be some misclassification between two sets of outbreak strains in the Raman analysis. We ascribe this to the clonal relationship between the strains of both outbreaks, described earlier. This results from a highly similar biochemical composition of the strains involved, and hence a highly similar Raman spectrum. We conclude that Raman spectroscopy could be an easy-to-use alternative in epidemiological studies of Acinetobacter strains and a promising starting point for the development of epidemiological studies in general.
    No preview · Article · Feb 2006 · Journal of Microbiological Methods

Publication Stats

1k Citations
105.13 Total Impact Points

Institutions

  • 2000-2014
    • Erasmus Universiteit Rotterdam
      • • Department of Dermatology
      • • Department of Medical Microbiology and Infectious Diseases
      Rotterdam, South Holland, Netherlands
  • 2009-2013
    • Erasmus MC
      • • Department of Medical Microbiology and Infectious Diseases
      • • Department of Dermatology
      Rotterdam, South Holland, Netherlands
  • 2012
    • Leiden University Medical Centre
      Leyden, South Holland, Netherlands
  • 2008
    • Vlietland Ziekenhuis
      Schiedam, South Holland, Netherlands
  • 2007
    • Medical University of Warsaw
      • Zakład Mikrobiologii Farmaceutycznej
      Warsaw, Masovian Voivodeship, Poland
  • 2001-2003
    • Robert Koch Institut
      Berlín, Berlin, Germany