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Huijskens E.G.W.,Laboratory of Medical Microbiology and Immunology | Rossen J.W.A.,University of Groningen | Kluytmans J.A.J.W.,Laboratory of Medical Microbiology and Immunology | Kluytmans J.A.J.W.,Laboratory for Microbiology and Infection Control | And 4 more authors.
Influenza and other Respiratory Viruses | Year: 2014

Background: For the detection of respiratory pathogens, the sampling strategy may influence the diagnostic yield. Ideally, samples from the lower respiratory tract are collected, but they are difficult to obtain. Objectives: In this study, we compared the diagnostic yield in sputum and oropharyngeal samples (OPS) for the detection of respiratory pathogens in patients with community-acquired pneumonia (CAP), with the objective to optimize our diagnostic testing algorithm. Methods: Matched sputum samples, OPS, blood cultures, serum, and urine samples were taken from patients (>18 years) with CAP and tested for the presence of possible respiratory pathogens using bacterial cultures, PCR for 17 viruses and five bacteria and urinary antigen testing. Results: When using only conventional methods, that is, blood cultures, sputum culture, urinary antigen tests, a pathogen was detected in 49·6% of patients (n = 57). Adding molecular detection assays increased the yield to 80%. A pathogen was detected in 77 of the 115 patients in OPS or sputum samples by PCR. The sensitivity of the OPS was lower than that of the sputum samples (57% versus 74%). In particular, bacterial pathogens were more often detected in sputum samples. The sensitivity of OPS for the detection of most viruses was higher than in sputum samples (72% versus 66%), except for human rhinovirus and respiratory syncytial virus. Conclusion: Addition of PCR on both OPS and sputum samples significantly increased the diagnostic yield. For molecular detection of bacterial pathogens, a sputum sample is imperative, but for detection of most viral pathogens, an OPS is sufficient. © 2013 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd. Source


Parwati I.,Padjadjaran University | Alisjahbana B.,Padjadjaran University | Apriani L.,Padjadjaran University | Ottenhoff T.H.,Leiden University | And 4 more authors.
Journal of Infectious Diseases | Year: 2010

Animal studies have shown that the globally emerging Beijing genotype strains of Mycobacterium tuberculosis are more virulent than other strains. We examined whether Beijing strains increase treatment failure in a prospective cohort study in Indonesia. Among 818 tuberculosis cases, positive sputum culture results after 6 months of treatment were more common among patients infected with Beijing strains (33.4%) than among those infected with non-Beijing strains (relative risk, 1.94 [95% confidence interval, 1.26-3.00]), even after adjustment for differences in drug resistance. These data suggest that M. tuberculosis Beijing genotype strains have a higher capacity to withstand tuberculosis treatment, even in the absence of drug resistance. © 2010 by the Infectious Diseases Society of America. All rights reserved. Source


Reuland E.A.,VU University Amsterdam | al Naiemi N.,VU University Amsterdam | al Naiemi N.,Laboratory for Medical Microbiology and Public Health | Raadsen S.A.,VU University Amsterdam | And 3 more authors.
European Journal of Clinical Microbiology and Infectious Diseases | Year: 2014

To determine whether extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E) are present in retail raw vegetables in Amsterdam, the Netherlands, we collected 119 samples of 15 different types of vegetables from various sources. After culture, strain identification and susceptibility testing, ESBL-encoding genes were characterised by a microarray. Four of the 15 vegetable types were contaminated with ESBL-E. Seven samples (6 %) yielded ESBL-E. Three blaCTX-M-15, one blaCTX-M-1, two genes of the CTX-M-9 group and one SHV ESBL-encoding gene were found. The ESBL genes were similar to what is found in enterobacterial strains from human origin. Therefore, raw vegetables might be a source of resistance genes for the enterobacterial strains found in humans. © 2014, The Author(s). Source


Al-Hajoj S.A.M.,King Faisal Specialist Hospital And Research Center | Akkerman O.,Spectrum | Parwati I.,Padjadjaran University | Al-Gamdi S.,Molecular Diagnostic Unit | And 5 more authors.
Journal of Clinical Microbiology | Year: 2010

Five Mycobacterium tuberculosis isolates were obtained from three body sites from a Dutch patient. The isolates displayed a single genotype by 24-locus MIRU-VNTR typing (except for a single locus not amplified from one isolate) but were differentiated by small variations in IS6110 fingerprints, spoligotypes, 6 hypervariable MIRU-VNTR loci, and/or DiversiLab profiles, revealing patterns of microevolution in a clonal infection. Copyright © 2010, American Society for Microbiology. All Rights Reserved. Source


De Beer J.L.,National Institute for Public Health and the Environment RIVM | Akkerman O.W.,University of Groningen | Schurch A.C.,National Institute for Public Health and the Environment RIVM | Schurch A.C.,Radboud University Nijmegen | And 8 more authors.
Journal of Clinical Microbiology | Year: 2014

Variable-number tandem-repeat (VNTR) typing with a panel of 24 loci is the current gold standard in the molecular typing of Mycobacterium tuberculosis complex isolates. However, because of technical problems, a part of the loci often cannot be amplified by multiplex PCRs. Therefore, a considerable number of single-locus PCRs have to be performed for the loci with missing results, which impairs the laboratory work flow. Therefore, the original in-house method described by Supply et al. in 2006 was reevaluated. We modified seven primers and the PCR master mixture and obtained a strongly optimized in-house 24-locus VNTR typing method. The percentage of instantly complete 24-locus VNTR patterns detected in the routine flow of typing activities increased to 84.7% from the 72.3% obtained with the typing conducted with the commercially available Genoscreen MIRU-VNTR typing kit. The analytical sensitivity of the optimized in-house method was assessed by serial dilutions of M. tuberculosis in bronchoalveolar lavage fluid. A 1:10 dilution of the different strains tested was the lowest dilution for the detection of a complete 24-locus VNTR pattern. The optimized in-house 24-locus VNTR typing method will reduce the turnaround time of typing significantly and also the financial burden of these activities. © 2014, American Society for Microbiology. All Rights Reserved. Source

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