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Faas BHW, Astuti G, Melchers WJG, Reuss A, Gilissen C, Macville MVE, Ghesquiere SAI, Houben LMH, Srebniak MI, Geeven G, Rahamat-Langendoen JC, Sistermans EA, Linthorst J. Early detection of active Human CytomegaloVirus (hCMV) infection in pregnant women using data generated for noninvasive fetal aneuploidy testing. EBioMedicine 2024; 100:104983. [PMID: 38365322 PMCID: PMC10878988 DOI: 10.1016/j.ebiom.2024.104983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Prenatal hCMV infections can lead to severe embryopathy and neurological sequelae in neonates. Screening during pregnancy is not recommended by global societies, as there is no effective therapy. Recently, several groups showed that maternal-fetal hCMV transmission can be strongly reduced by administering anti-viral agents early in pregnancy. This calls for a screening method to identify at risk pregnancies at an appropriate gestational age, with the possibility for large-scale enrolment. Non-Invasive Prenatal Testing (NIPT) for fetal aneuploidy screening early in pregnancy is already implemented in many countries and performed on a large-scale basis. We investigated the use of whole genome cell-free DNA (cfDNA) sequencing data, generated for the purpose of NIPT, as (pre-)screening tool to identify women with active hCMV-infections, eligible for therapy. METHODS Coded raw sequencing NIPT data from 204,818 pregnant women from three testing laboratories were analyzed for the presence of hCMV-cfDNA. Samples were stratified by cfDNA-hCMV load. For validation and interpretation, diagnostic hCMV-qPCR and serology testing were performed on a subset of cfDNA-hCMV-positive (n = 112) and -negative (n = 127) samples. FINDINGS In 1930 samples (0.94%) hCMV fragments were detected. Validation by hCMV-qPCR showed that samples with high cfDNA-hCMV load tested positive and cfDNA-hCMV-negative samples tested negative. In 32/112 cfDNA-hCMV-positive samples (28.6%) the serological profile suggested a recent primary infection: this was more likely in samples with high cfDNA-hCMV load (78.6%) than in samples with low cfDNA-hCMV load (11.0%). In none of the cfDNA-hCMV-negative samples serology was indicative of a recent primary infection. INTERPRETATION Our study shows that large-scale (pre-)screening for both genetic fetal aberrations and active maternal hCMV infections during pregnancy can be combined in one cfDNA sequencing test, performed on a single blood sample, drawn in the first trimester of pregnancy. FUNDING This work was partly funded by the Prenatal Screening Foundation Nijmegen, the Netherlands.
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Affiliation(s)
- Brigitte H W Faas
- Department of Human Genetics, Radboud University Medical Center Nijmegen, the Netherlands.
| | - Galuh Astuti
- Department of Human Genetics, Radboud University Medical Center Nijmegen, the Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center Nijmegen, the Netherlands
| | - Annette Reuss
- Department of Obstetrics and Gynecology, Radboud University Medical Center Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center Nijmegen, the Netherlands
| | - Merryn V E Macville
- Department of Clinical Genetics, GROW School of Oncology and Reproduction, Maastricht University Medical Center+, the Netherlands
| | - Stijn A I Ghesquiere
- Department of Clinical Genetics, GROW School of Oncology and Reproduction, Maastricht University Medical Center+, the Netherlands
| | - Leonieke M H Houben
- Department of Clinical Genetics, GROW School of Oncology and Reproduction, Maastricht University Medical Center+, the Netherlands
| | | | - Geert Geeven
- Department of Clinical Genetics, Erasmus Medical Center Rotterdam, the Netherlands
| | | | - Erik A Sistermans
- Department of Human Genetics, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, the Netherlands
| | - Jasper Linthorst
- Department of Human Genetics, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, the Netherlands
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Verweij PE, Song Y, Buil JB, Zhang J, Melchers WJG. Antifungal Resistance in Pulmonary Aspergillosis. Semin Respir Crit Care Med 2024; 45:32-40. [PMID: 38196063 DOI: 10.1055/s-0043-1776997] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Aspergilli may cause various pulmonary diseases in humans, including allergic bronchopulmonary aspergillosis (ABPA), chronic pulmonary aspergillosis (CPA), and acute invasive pulmonary aspergillosis (IPA). In addition, chronic colonization may occur in cystic fibrosis (CF). Aspergillus fumigatus represents the main pathogen, which may employ different morphotypes, for example, conidia, hyphal growth, and asexual sporulation, in the various Aspergillus diseases. These morphotypes determine the ease by which A. fumigatus can adapt to stress by antifungal drug exposure, usually resulting in one or more resistance mutations. Key factors that enable the emergence of resistance include genetic variation and selection. The ability to create genetic variation depends on the reproduction mode, including, sexual, parasexual, and asexual, and the population size. These reproduction cycles may take place in the host and/or in the environment, usually when specific conditions are present. Environmental resistance is commonly characterized by tandem repeat (TR)-mediated mutations, while in-host resistance selection results in single-resistance mutations. Reported cases from the literature indicate that environmental resistance mutations are almost exclusively present in patients with IA indicating that the risk for in-host resistance selection is very low. In aspergilloma, single-point mutations are the dominant resistance genotype, while in other chronic Aspergillus diseases, for example, ABPA, CPA, and CF, both TR-mediated and single-resistance mutations are reported. Insights into the pathogenesis of resistance selection in various Aspergillus diseases may help to improve diagnostic and therapeutic strategies.
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Affiliation(s)
- Paul E Verweij
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, the Netherlands
- Center for Infectious Disease Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Yinggai Song
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Dermatology and Venerology, Peking University First Hospital, 8 Xishiku Street, Xicheng District, Beijing, China
- National Clinical Research Center For Skin and Immune Diseases, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
| | - Jochem B Buil
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, the Netherlands
| | - Jianhua Zhang
- Center for Infectious Disease Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, the Netherlands
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3
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Hiel SJP, Hendriks ACA, Eijkenboom JJA, Bosch T, Coolen JPM, Melchers WJG, Anröchte P, Camps SMT, Verweij PE, Zhang J, van Dommelen L. Aspergillus Outbreak in an Intensive Care Unit: Source Analysis with Whole Genome Sequencing and Short Tandem Repeats. J Fungi (Basel) 2024; 10:51. [PMID: 38248960 PMCID: PMC10817286 DOI: 10.3390/jof10010051] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/17/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Whole genome sequencing (WGS) is widely used for outbreak analysis of bacteriology and virology but is scarcely used in mycology. Here, we used WGS for genotyping Aspergillus fumigatus isolates from a potential Aspergillus outbreak in an intensive care unit (ICU) during construction work. After detecting the outbreak, fungal cultures were performed on all surveillance and/or patient respiratory samples. Environmental samples were obtained throughout the ICU. WGS was performed on 30 isolates, of which six patient samples and four environmental samples were related to the outbreak, and twenty samples were unrelated, using the Illumina NextSeq 550. A SNP-based phylogenetic tree was created from outbreak samples and unrelated samples. Comparative analysis (WGS and short tandem repeats (STRs), microsatellite loci analysis) showed that none of the strains were related to each other. The lack of genetic similarity suggests the accumulation of Aspergillus spores in the hospital environment, rather than a single source that supported growth and reproduction of Aspergillus fumigatus. This supports the hypothesis that the Aspergillus outbreak was likely caused by release of Aspergillus fumigatus spores during construction work. Indeed, no new Aspergillus cases were observed in the ICU after cessation of construction. This study demonstrates that WGS is a suitable technique for examining inter-strain relatedness of Aspergillus fumigatus in the setting of an outbreak investigation.
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Affiliation(s)
- Stephan J. P. Hiel
- Department of Intensive Care, Máxima Medical Centre, De Run 4600, 5504 DB Veldhoven, The Netherlands
| | - Amber C. A. Hendriks
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Centre, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jos J. A. Eijkenboom
- Department of Intensive Care, Máxima Medical Centre, De Run 4600, 5504 DB Veldhoven, The Netherlands
| | - Thijs Bosch
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud University Medical Centre, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Paul Anröchte
- Department of Infection Prevention and Control, Máxima Medical Centre, De Run 4600, 5504 DB Veldhoven, The Netherlands
| | - Simone M. T. Camps
- Department of Infection Prevention and Control, Máxima Medical Centre, De Run 4600, 5504 DB Veldhoven, The Netherlands
| | - Paul E. Verweij
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Centre, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jianhua Zhang
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Laura van Dommelen
- Stichting PAMM, Laboratory of Medical Microbiology, De Run 6250, 5504 DL Veldhoven, The Netherlands
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Molina MA, Melchers WJG, Núñez-Samudio V, Landires I. The emerging role of Lactobacillus acidophilus in the cervicovaginal microenvironment. Lancet Microbe 2024; 5:e6-e7. [PMID: 37863085 DOI: 10.1016/s2666-5247(23)00315-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/22/2023]
Affiliation(s)
- Mariano A Molina
- Department of Pathology, VU University Medical Center, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, Netherlands; Imaging and Biomarkers, Cancer Centre Amsterdam, Amsterdam, Netherlands; Instituto de Ciencias Médicas, Las Tablas, Panama.
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Virginia Núñez-Samudio
- Instituto de Ciencias Médicas, Las Tablas, Panama; Sistema Nacional de Investigación, Secretaría Nacional de Ciencia, Tecnología e Innovación, Panama City, Panama
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Tops SCM, Schapendonk CEP, Coolen JPM, Tenover FC, Tickler IA, Melchers WJG, Wertheim HFL. The diagnostic accuracy of the GeneXpert ESBL- ampC prototype assay for rapid PCR-based detection of extended-spectrum beta-lactamase genes directly from urine. Microbiol Spectr 2023; 11:e0311623. [PMID: 37962375 PMCID: PMC10715157 DOI: 10.1128/spectrum.03116-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Early identification of complicated urinary tract infections caused by ESBL-producing Enterobacterales has the potential to limit the use of carbapenems to those patients without alternative antibiotic options and avoid the empirical use of carbapenems in patients without ESBL-producing bacteria. The purpose for such a test will differ by setting and ESBL prevalence rates. Countries with low ESBL rates and cephalosporins as empiric treatment (e.g., The Netherlands) will need a rule-in test to decide to use carbapenems, while countries with high ESBL rates and empiric carbapenem treatment will need a rule-out test for ESBLs to de-escalate therapy early. Anyway, such as a test would-at least theoretically-improve patient care and reduce selective pressure for the emergence of carbapenem resistance.
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Affiliation(s)
- Sofie C. M. Tops
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Claire E. P. Schapendonk
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Fred C. Tenover
- College of Arts and Sciences, University of Dayton, Dayton, Ohio, USA
| | | | - Willem J. G. Melchers
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heiman F. L. Wertheim
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
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Pouwer AW, Te Grootenhuis NC, Hinten F, de Bock GH, van der Zee AGJ, Melchers WJG, Oonk MHM, de Hullu JA, Hollema H, Bulten J. Prognostic value of HPV-PCR, p16 and p53 immunohistochemical status on local recurrence rate and survival in patients with vulvar squamous cell carcinoma. Virchows Arch 2023:10.1007/s00428-023-03690-8. [PMID: 37938322 DOI: 10.1007/s00428-023-03690-8] [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: 05/05/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
The primary aim of this study was to assess the association between human papilloma virus (HPV) and p53 expression and local recurrence (LR), disease specific survival (DSS), and overall survival (OS) in patients with vulvar squamous cell carcinoma (VSCC). Secondary, the accuracy of p16 immunohistochemistry for HPV status was assessed. The tumor tissue of 255 patients, surgically treated for primary unifocal VSCC between 2000 and 2010, was analyzed. HPV-PCR and P16 and p53 immunohistochemical stainings were performed. All histologic slides were independently reviewed by two expert gyneco-pathologists. Time to first LR, DSS, and OS for the variables p16, p53, and HPV-PCR were compared using univariable and multivariable Cox-regression analyses. In 211/255 (83.5%) patients, HPV-PCR was negative. The local recurrence rate was significantly lower in patients positive with HPV-PCR (10-year LR rate 24.6%) versus negative tumors (47.5%), p = 0.004. After multivariable analyses, this difference remained significant (HR 0.23 (95% CI 0.08-0.62) p = 0.004). There was no difference in LR rate correlated to the p53 expression. DSS and OS did not significantly differ after multivariable analyses for all different subgroups. Sensitivity and specificity of p16 staining for presence of HPV detected by HPV-PCR were 86.4% and 93.8%, respectively. In conclusion, patients with HPV-negative VSCCs have significantly more LR compared to patients with HPV-positive VSCCs, and p16 immunohistochemistry is a reliable surrogate marker for HPV status. No relevant subgroup for LR or survival based on HPV/p53 status could be identified. We advise to perform an HPV-PCR or p16 IHC staining in all patients with VSCC.
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Affiliation(s)
- A W Pouwer
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N C Te Grootenhuis
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - F Hinten
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - G H de Bock
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - A G J van der Zee
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - W J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M H M Oonk
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J A de Hullu
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - H Hollema
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J Bulten
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
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Molina MA, Melchers WJG. Methodological and analytical challenges in microbiome-HPV association studies. J Med Virol 2023; 95:e29260. [PMID: 38009697 DOI: 10.1002/jmv.29260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/29/2023]
Affiliation(s)
- Mariano A Molina
- Department of Pathology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Cancer Centre Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
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Bas S, Sijben J, Bischoff EWMA, Bekkers RLM, de Kok IMCM, Melchers WJG, Siebers AG, van der Waal D, Broeders MJM. Acceptability of risk-based triage in cervical cancer screening: A focus group study. PLoS One 2023; 18:e0289647. [PMID: 37585441 PMCID: PMC10431661 DOI: 10.1371/journal.pone.0289647] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/22/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Compared to the previous cytology-based program, the introduction of primary high-risk human papillomavirus (hrHPV) based screening in 2017 has led to an increased number of referrals. To counter this, triage of hrHPV-positive women in cervical cancer screening can potentially be optimized by taking sociodemographic and lifestyle risk factors for cervical abnormalities into account. Therefore, it is essential to gain knowledge of the views of women (30-60 years) eligible for cervical cancer screening. OBJECTIVE The main goal of this qualitative study was to gain insight in the aspects that influence acceptability of risk-based triage in cervical cancer screening. DESIGN A focus group study in which participants were recruited via four general medical practices, and purposive sampling was used to maximize heterogeneity with regards to age, education level, and cervical cancer screening experiences. APPROACH The focus group discussions were transcribed verbatim and analyzed using reflexive thematic analysis. PARTICIPANTS A total of 28 women (average age: 45.2 years) eligible for cervical cancer screening in The Netherlands participated in seven online focus group discussions. Half of the participants was higher educated, and the participants differed in previous cervical cancer screening participation and screening result. KEY RESULTS In total, 5 main themes and 17 subthemes were identified that determine the acceptability of risk-stratified triage. The main themes are: 1) adequacy of the screening program: an evidence-based program that is able to minimize cancer incidence and reduce unnecessary referrals; 2) personal information (e.g., sensitive topics and stigma); 3) emotional impact: fear and reassurance; 4) communication (e.g., transparency); and 5) autonomy (e.g., prevention). CONCLUSION The current study highlights several challenges regarding the development and implementation of risk-based triage that need attention in order to be accepted by the target group. These challenges include dealing with sensitive topics and a transparent communication strategy.
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Affiliation(s)
- Sharell Bas
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Jasmijn Sijben
- Department of Gastroenterology and Hepatology, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erik W. M. A. Bischoff
- Department of Primary and Community Care, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ruud L. M. Bekkers
- Department of Obstetrics and Gynaecology, Catharina Hospital, Eindhoven, The Netherlands
- Department of Obstetrics and Gynecology, GROW School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Inge M. C. M. de Kok
- Department of Public Health, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Albert G. Siebers
- The Nationwide Network and Registry of Histo-and Cytopathology in the Netherlands (PALGA Foundation), Houten, The Netherlands
| | - Daniëlle van der Waal
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
- Dutch Expert Centre for Screening, Nijmegen, The Netherlands
| | - Mireille J. M. Broeders
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
- Dutch Expert Centre for Screening, Nijmegen, The Netherlands
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Hokken MWJ, Coolen JPM, Steenbreker H, Zoll J, Baltussen TJH, Verweij PE, Melchers WJG. The Transcriptome Response to Azole Compounds in Aspergillus fumigatus Shows Differential Gene Expression across Pathways Essential for Azole Resistance and Cell Survival. J Fungi (Basel) 2023; 9:807. [PMID: 37623579 PMCID: PMC10455693 DOI: 10.3390/jof9080807] [Citation(s) in RCA: 1] [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: 05/31/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
The opportunistic pathogen Aspergillus fumigatus is found on all continents and thrives in soil and agricultural environments. Its ability to readily adapt to novel environments and to produce billions of spores led to the spread of azole-resistant A. fumigatus across the globe, posing a threat to many immunocompromised patients, including critically ill patients with severe influenza or COVID-19. In our study, we sought to compare the adaptational response to azoles from A. fumigatus isolates that differ in azole susceptibility and genetic background. To gain more insight into how short-term adaptation to stressful azole compounds is managed through gene expression, we conducted an RNA-sequencing study on the response of A. fumigatus to itraconazole and the newest clinically approved azole, isavuconazole. We observed many similarities in ergosterol biosynthesis up-regulation across isolates, with the exception of the pan-azole-resistant isolate, which showed very little differential regulation in comparison to other isolates. Additionally, we found differential regulation of membrane efflux transporters, secondary metabolites, iron metabolism, and various stress response and cell signaling mechanisms.
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Affiliation(s)
- Margriet W. J. Hokken
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands (T.J.H.B.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6500 HB Nijmegen, The Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands (T.J.H.B.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6500 HB Nijmegen, The Netherlands
| | - Hilbert Steenbreker
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands (T.J.H.B.)
| | - Jan Zoll
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands (T.J.H.B.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6500 HB Nijmegen, The Netherlands
| | - Tim J. H. Baltussen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands (T.J.H.B.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6500 HB Nijmegen, The Netherlands
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands (T.J.H.B.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6500 HB Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands (T.J.H.B.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6500 HB Nijmegen, The Netherlands
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Moorlag SJCFM, Coolen JPM, van den Bosch B, Jin EHM, Buil JB, Wertheim HFL, Melchers WJG. Targeting the 16S rRNA Gene by Reverse Complement PCR Next-Generation Sequencing: Specific and Sensitive Detection and Identification of Microbes Directly in Clinical Samples. Microbiol Spectr 2023; 11:e0448322. [PMID: 37227289 PMCID: PMC10269728 DOI: 10.1128/spectrum.04483-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
The detection and accurate identification of bacterial species in clinical samples are crucial for diagnosis and appropriate antibiotic treatment. To date, sequencing of the 16S rRNA gene has been widely used as a complementary molecular approach when identification by culture fails. The accuracy and sensitivity of this method are highly affected by the selection of the 16S rRNA gene region targeted. In this study, we assessed the clinical utility of 16S rRNA reverse complement PCR (16S RC-PCR), a novel method based on next-generation sequencing (NGS), for the identification of bacterial species. We investigated the performance of 16S RC-PCR on 11 bacterial isolates, 2 polymicrobial community samples, and 59 clinical samples from patients suspected of having a bacterial infection. The results were compared to culture results, if available, and to the results of Sanger sequencing of the 16S rRNA gene (16S Sanger sequencing). By 16S RC-PCR, all bacterial isolates were accurately identified to the species level. Furthermore, in culture-negative clinical samples, the rate of identification increased from 17.1% (7/41) to 46.3% (19/41) when comparing 16S Sanger sequencing to 16S RC-PCR. We conclude that the use of 16S RC-PCR in the clinical setting leads to an increased sensitivity of detection of bacterial pathogens, resulting in a higher number of diagnosed bacterial infections, and thereby can improve patient care. IMPORTANCE The identification of the causative infectious pathogen in patients suspected of having a bacterial infection is essential for diagnosis and the start of appropriate treatment. Over the past 2 decades, molecular diagnostics have improved the ability to detect and identify bacteria. However, novel techniques that can accurately detect and identify bacteria in clinical samples and that can be implemented in clinical diagnostics are needed. Here, we demonstrate the clinical utility of bacterial identification in clinical samples by a novel method called 16S RC-PCR. Using 16S RC-PCR, we reveal a significant increase in the number of clinical samples in which a potentially clinically relevant pathogen is identified compared to the commonly used 16S Sanger method. Moreover, RC-PCR allows automation and is well suited for implementation in a diagnostic laboratory. In conclusion, the implementation of this method as a diagnostic tool is expected to result in an increased number of diagnosed bacterial infections, and in combination with adequate treatment, this could improve clinical outcomes for patients.
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Affiliation(s)
- Simone J. C. F. M. Moorlag
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Bart van den Bosch
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Elisabeth Hui-Mei Jin
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Jochem B. Buil
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Heiman F. L. Wertheim
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
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11
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Happacher I, Aguiar M, Alilou M, Abt B, Baltussen TJH, Decristoforo C, Melchers WJG, Haas H. The Siderophore Ferricrocin Mediates Iron Acquisition in Aspergillus fumigatus. Microbiol Spectr 2023; 11:e0049623. [PMID: 37199664 PMCID: PMC10269809 DOI: 10.1128/spectrum.00496-23] [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: 02/02/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
The opportunistic fungal pathogen Aspergillus fumigatus utilizes two high-affinity iron uptake mechanisms, termed reductive iron assimilation (RIA) and siderophore-mediated iron acquisition (SIA). The latter has been shown to be crucial for virulence of this fungus and is a target for development of novel strategies for diagnosis and treatment of fungal infections. So far, research on SIA in this mold focused mainly on the hyphal stage, revealing the importance of extracellular fusarinine-type siderophores in iron acquisition as well as of the siderophore ferricrocin in intracellular iron handling. The current study aimed to characterize iron acquisition during germination. High expression of genes involved in biosynthesis and uptake of ferricrocin in conidia and during germination, independent of iron availability, suggested a role of ferricrocin in iron acquisition during germination. In agreement, (i) bioassays indicated secretion of ferricrocin during growth on solid media during both iron sufficiency and limitation, (ii) ferricrocin was identified in the supernatant of conidia germinating in liquid media during both iron sufficiency and limitation, (iii) in contrast to mutants lacking all siderophores, mutants synthesizing ferricrocin but lacking fusarinine-type siderophores were able to grow under iron limitation in the absence of RIA, and (iv) genetic inactivation of the ferricrocin transporter Sit1 decreased germination in the absence of RIA. Taken together, this study revealed that ferricrocin has not only an intracellular role but also functions as an extracellular siderophore to support iron acquisition. The iron availability-independent ferricrocin secretion and uptake during early germination indicate developmental, rather than iron regulation. IMPORTANCE Aspergillus fumigatus is one of the most common airborne fungal pathogens for humans. Low-molecular-mass iron chelators, termed siderophores, have been shown to play a central role in iron homeostasis and, consequently, virulence of this mold. Previous studies demonstrated the crucial role of secreted fusarinine-type siderophores, such as triacetylfusarinine C, in iron acquisition, as well as of the ferrichrome-type siderophore ferricrocin in intracellular iron storage and transport. Here, we demonstrate that ferricrocin is also secreted to mediate iron acquisition during germination together with reductive iron assimilation. During early germination, ferricrocin secretion and uptake were not repressed by iron availability, indicating developmental regulation of this iron acquisition system in this growth phase.
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Affiliation(s)
- Isidor Happacher
- Institute of Molecular Biology, Biocenter, Medical University Innsbruck, Innsbruck, Austria
| | - Mario Aguiar
- Institute of Molecular Biology, Biocenter, Medical University Innsbruck, Innsbruck, Austria
| | - Mostafa Alilou
- Institute of Pharmacy, Unit of Pharmacognosy, Center for Molecular Biosciences Innsbruck, Austria
| | - Beate Abt
- Institute of Molecular Biology, Biocenter, Medical University Innsbruck, Innsbruck, Austria
| | - Tim J. H. Baltussen
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Clemens Decristoforo
- Department of Nuclear Medicine, Medical University Innsbruck, Innsbruck, Austria
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Hubertus Haas
- Institute of Molecular Biology, Biocenter, Medical University Innsbruck, Innsbruck, Austria
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12
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Buil JB, Huygens S, Dunbar A, Schauwvlieghe A, Reynders M, Langerak D, van Dijk K, Bruns A, Haas PJ, Postma DF, Biemond B, Delma FZ, de Kort E, Melchers WJG, Verweij PE, Rijnders B. Retrospective Multicenter Evaluation of the VirClia Galactomannan Antigen Assay for the Diagnosis of Pulmonary Aspergillosis with Bronchoalveolar Lavage Fluid Samples from Patients with Hematological Disease. J Clin Microbiol 2023; 61:e0004423. [PMID: 37097150 PMCID: PMC10204623 DOI: 10.1128/jcm.00044-23] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/04/2023] [Indexed: 04/26/2023] Open
Abstract
Galactomannan (GM) testing of bronchoalveolar lavage (BAL) fluid samples has become an essential tool to diagnose invasive pulmonary aspergillosis (IPA) and is part of diagnostic guidelines. Enzyme-linked immunosorbent assays (ELISAs) (enzyme immunoassays [EIAs]) are commonly used, but they have a long turnaround time. In this study, we evaluated the performance of an automated chemiluminescence immunoassay (CLIA) with BAL fluid samples. This was a multicenter retrospective study in the Netherlands and Belgium. BAL fluid samples were collected from patients with underlying hematological diseases with a suspected invasive fungal infection. Diagnosis of IPA was based on the 2020 European Organisation for Research and Treatment of Cancer (EORTC)/Mycoses Study Group Education and Research Consortium (MSGERC) consensus definitions. GM results were reported as optical density index (ODI) values. ODI cutoff values for positive results that were evaluated were 0.5, 0.8, and 1.0 for the EIA and 0.16, 0.18, and 0.20 for the CLIA. Probable IPA cases were compared with two control groups, one with no evidence of IPA and another with no IPA or possible IPA. Qualitative agreement was analyzed using Cohen's κ, and quantitative agreement was analyzed by Spearman's correlation. We analyzed 141 BAL fluid samples from 141 patients; 66 patients (47%) had probable IPA, and 56 cases remained probable IPA when the EIA GM result was excluded as a criterion, because they also had positive culture and/or duplicate positive PCR results. Sixty-three patients (45%) had possible IPA and 12 (8%) had no IPA. The sensitivity and specificity of the two tests were quite comparable, and the overall qualitative agreement between EIA and CLIA results was 81 to 89%. The correlation of the actual CLIA and EIA values was strong at 0.72 (95% confidence interval, 0.63 to 0.80). CLIA has similar performance, compared to the gold-standard EIA, with the benefits of faster turnaround because batching is not required. Therefore, CLIA can be used as an alternative GM assay for BAL fluid samples.
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Affiliation(s)
- Jochem B. Buil
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud University Medical Center-Canisius Wilhelmina Hospital, Center of Expertise for Mycology, Nijmegen, The Netherlands
| | - Sammy Huygens
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Albert Dunbar
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Marijke Reynders
- Unit of Molecular Microbiology, Medical Microbiology, Department of Laboratory Medicine, AZ Sint-Jan Brugge AV, Bruges, Belgium
| | - Diana Langerak
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Karin van Dijk
- Department of Medical Microbiology, Amsterdam University Medical Centers, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Anke Bruns
- Department of Internal Medicine, Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Pieter-Jan Haas
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Douwe F. Postma
- Department of Internal Medicine and Infectious Diseases, University Medical Center Groningen, Groningen, The Netherlands
| | - Bart Biemond
- Department of Hematology, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
| | - Fatima Zohra Delma
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elizabeth de Kort
- Radboud University Medical Center-Canisius Wilhelmina Hospital, Center of Expertise for Mycology, Nijmegen, The Netherlands
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud University Medical Center-Canisius Wilhelmina Hospital, Center of Expertise for Mycology, Nijmegen, The Netherlands
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud University Medical Center-Canisius Wilhelmina Hospital, Center of Expertise for Mycology, Nijmegen, The Netherlands
| | - Bart Rijnders
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
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13
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Verhoef L, Bleeker MCG, Polman N, Steenbergen RDM, Ebisch RMF, Melchers WJG, Bekkers RLM, Molijn AC, Quint WG, van Kemenade F, Meijer CJLM, Berkhof J, Heideman DAM. Evaluation of DNA methylation biomarkers ASCL1 and LHX8 on HPV-positive self-collected samples from primary HPV-based screening. Br J Cancer 2023:10.1038/s41416-023-02277-z. [PMID: 37100874 PMCID: PMC10132796 DOI: 10.1038/s41416-023-02277-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Host-cell DNA methylation analysis can be used to triage women with high-risk human papillomavirus (HPV)-positive self-collected cervicovaginal samples, but current data are restricted to under-/never-screened women and referral populations. This study evaluated triage performance in women who were offered primary HPV self-sampling for cervical cancer screening. METHODS Self-collected samples from 593 HPV-positive women who participated in a primary HPV self-sampling trial (IMPROVE study; NTR5078), were tested for the DNA methylation markers ASCL1 and LHX8 using quantitative multiplex methylation-specific PCR (qMSP). The diagnostic performance for CIN3 and cervical cancer (CIN3 + ) was evaluated and compared with that of paired HPV-positive clinician-collected cervical samples. RESULTS Significantly higher methylation levels were found in HPV-positive self-collected samples of women with CIN3 + than control women with no evidence of disease (P values <0.0001). The marker panel ASCL1/LHX8 yielded a sensitivity for CIN3 + detection of 73.3% (63/86; 95% CI 63.9-82.6%), with a corresponding specificity of 61.1% (310/507; 95% CI 56.9-65.4%). The relative sensitivity for detecting CIN3+ was 0.95 (95% CI 0.82-1.10) for self-collection versus clinician-collection, and the relative specificity was 0.82 (95% CI 0.75-0.90). CONCLUSIONS The ASCL1/LHX8 methylation marker panel constitutes a feasible direct triage method for the detection of CIN3 + in HPV-positive women participating in routine screening by self-sampling.
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Affiliation(s)
- Lisanne Verhoef
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Maaike C G Bleeker
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Nicole Polman
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Renée M F Ebisch
- Radboud University Medical Center, Obstetrics and Gynecology, 6525 GA, Nijmegen, the Netherlands
| | - Willem J G Melchers
- Radboud University Medical Center, Medical Microbiology, 6525 GA, Nijmegen, the Netherlands
| | - Ruud L M Bekkers
- GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER, Maastricht, the Netherlands
- Catharina Hospital, 5623 EJ, Eindhoven, the Netherlands
| | - Anco C Molijn
- Eurofins NMDL-LCPL, 2280 CA, Rijswijk, the Netherlands
| | - Wim G Quint
- Eurofins NMDL-LCPL, 2280 CA, Rijswijk, the Netherlands
| | - Folkert van Kemenade
- Erasmus MC University Medical Center, Pathology, 3015 GD, Rotterdam, the Netherlands
| | - Chris J L M Meijer
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Johannes Berkhof
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Epidemiology and Data Science, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Daniëlle A M Heideman
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan 1117, Amsterdam, The Netherlands.
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands.
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14
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Schildkraut JA, Coolen JPM, Severin H, Koenraad E, Aalders N, Melchers WJG, Hoefsloot W, Wertheim HFL, van Ingen J. MGIT Enriched Shotgun Metagenomics for Routine Identification of Nontuberculous Mycobacteria: a Route to Personalized Health Care. J Clin Microbiol 2023; 61:e0131822. [PMID: 36840602 PMCID: PMC10035320 DOI: 10.1128/jcm.01318-22] [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: 02/25/2023] Open
Abstract
Currently, nontuberculous mycobacteria (NTM) are identified using small genomic regions, and species-level identification is often not possible. We introduce a next-generation sequencing (NGS) workflow that identifies mycobacteria to (sub)species level on the basis of the whole genome extracted from enriched shotgun metagenomic data. This technique is used to study the association between genotypes and clinical manifestations to pave the way to more personalized health care. Two sets of clinical isolates (explorative set [n = 212] and validation set [n = 235]) were included. All data were analyzed using a custom pipeline called MyCodentifier. Sequences were matched against a custom hsp65 database (NGS-hsp65) and whole-genome database (NGS-WG) created based on the phylogeny presented by Tortoli et al. (E. Tortoli, T. Fedrizzi, C. J. Meehan, A. Trovato, et al., Infect Genet Evol 56:19-25, 2017, https://doi.org/10.1016/j.meegid.2017.10.013). Lastly, phylogenetic analysis was performed and correlated with clinical manifestation. In the explorative set, we observed 98.6% agreement between the line probe assay and the NGS-hsp65 database. In the validation set, 99.1% agreement between the NGS-WG and NGS-hsp65 databases was seen on the complex level. We identified a cluster of Mycobacterium marinum isolates not represented by the Tortoli et al. phylogeny. Phylogenetic analysis of M. avium complex isolates confirmed misclassification of M. timonense and M. bouchedurhonense and identified subclusters within M. avium although no correlation with clinical manifestation was observed. We performed routine NGS to identify NTM from MGIT enriched shotgun metagenomic data. Phylogenetic analyses identified subtypes of M. avium, but in our set of isolates no correlation with clinical manifestation was found. However, this NGS workflow paves a way for more personalized health care in the future.
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Affiliation(s)
- Jodie A Schildkraut
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jordy P M Coolen
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Heleen Severin
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ellen Koenraad
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicole Aalders
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Willem J G Melchers
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wouter Hoefsloot
- Radboudumc Center for Infectious Diseases, Department of Pulmonary Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Heiman F L Wertheim
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jakko van Ingen
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
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15
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Brands MT, Swinkels IJ, Aarts AMWM, Verbeek ALM, Merkx MAW, Marres HAM, Kaanders JHAM, Melchers WJG, van Engen-van Grunsven I, Takes RP, Geurts SME. Value of routine follow-up in oropharyngeal squamous cell cancer patients treated with curative intent. Head Neck 2023; 45:586-594. [PMID: 36565244 DOI: 10.1002/hed.27269] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/28/2022] [Accepted: 11/10/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The major goal of routine follow-up in oropharyngeal squamous cell carcinoma (OPSCC) patients is the asymptomatic detection of new disease in order to improve survival. This study evaluated the effect of routine follow-up on overall survival (OS). METHODS A retrospective cohort of 307 consecutive OPSCC patients treated with curative intent between 2006 and 2012 was analyzed. The effectiveness of routine follow-up was studied by comparing treatment-intent and OS in patients with asymptomatically versus symptomatically detected new disease. RESULTS Three- and five-year risks of new disease were 29% (95% CI: 24-34) and 33% (95% CI: 27-39). Of the 81 patients with locoregional recurrence or second primary head and neck cancer, 8 (10%) were detected asymptomatically with no difference in OS with those detected with symptoms. CONCLUSIONS Asymptomatic detection of new disease during routine visits was not associated with improved OS. The focus of follow-up should be on providing psychosocial care and rehabilitation.
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Affiliation(s)
- Maria T Brands
- Netherlands Comprehensive Cancer Organisation, Eindhoven, The Netherlands
| | - Iris J Swinkels
- Department of Primary and Community Care, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anne M W M Aarts
- Radboud Institute for Health Sciences, Department for Health Evidence, Radboud University Medical Centre, Nijmegen, The Netherlands.,Department of Otorhinolaryngology-Head and Neck Surgery, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - André L M Verbeek
- Radboud Institute for Health Sciences, Department for Health Evidence, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Matthias A W Merkx
- Netherlands Comprehensive Cancer Organisation, Eindhoven, The Netherlands.,Department of Oral and Maxillofacial Surgery, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Henri A M Marres
- Department of Otorhinolaryngology-Head and Neck Surgery, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Johannes H A M Kaanders
- Department of Radiation Oncology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Robert P Takes
- Radboud Institute for Health Sciences, Department for Health Evidence, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Sandra M E Geurts
- Radboud Institute for Health Sciences, Department for Health Evidence, Radboud University Medical Centre, Nijmegen, The Netherlands.,Department of Internal Medicine, Division of Medical Oncology, GROW, Maastricht University Medical Center, Maastricht, The Netherlands
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16
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Cogliati M, Arikan-Akdagli S, Barac A, Bostanaru AC, Brito S, Çerikçioğlu N, Efstratiou MA, Ergin Ç, Esposto MC, Frenkel M, Gangneux JP, Gitto A, Gonçalves CI, Guegan H, Gunde-Cimerman N, Güran M, Jonikaitė E, Kataržytė M, Klingspor L, Mares M, Meijer WG, Melchers WJG, Meletiadis J, Nastasa V, Babič MN, Ogunc D, Ozhak B, Prigitano A, Ranque S, Romanò L, Rusu RO, Sabino R, Sampaio A, Silva S, Stephens JH, Tehupeiory-Kooreman M, Velegraki A, Veríssimo C, Segal E, Brandão J. Environmental and bioclimatic factors influencing yeasts and molds distribution along European shores. Sci Total Environ 2023; 859:160132. [PMID: 36400291 DOI: 10.1016/j.scitotenv.2022.160132] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
The present study employed data collected during the Mycosands survey to investigate the environmental factors influencing yeasts and molds distribution along European shores applying a species distribution modelling approach. Occurrence data were compared to climatic datasets (temperature, precipitation, and solar radiation), soil datasets (chemical and physical properties), and water datasets (temperature, salinity, and chlorophyll-a concentration) downloaded from web databases. Analyses were performed by MaxEnt software. Results suggested a different probability of distribution of yeasts and molds along European shores. Yeasts seem to tolerate low temperatures better during winter than molds and this reflects a higher suitability for the Northern European coasts. This difference is more evident considering suitability in waters. Both distributions of molds and yeasts are influenced by basic soil pH, probably because acidic soils are more favorable to bacterial growth. Soils with high nitrogen concentrations are not suitable for fungal growth, which, in contrast, are optimal for plant growth, favored by this environment. Finally, molds show affinity with soil rich in nickel and yeasts with soils rich in cadmium resulting in a distribution mainly at the mouths of European rivers or lagoons, where these metals accumulate in river sediments.
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Affiliation(s)
- M Cogliati
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milano, Italy.
| | - S Arikan-Akdagli
- Mycology Laboratory at Department of Medical Microbiology of Hacettepe University Medical School, Ankara, Turkey
| | - A Barac
- Clinical Centre of Serbia, Clinic for Infectious and Tropical Diseases, Faculty of Medicine, University of Belgrade, Serbia
| | - A C Bostanaru
- Ion Ionescu de la Brad University of Life Sciences, Iasi, Romania
| | - S Brito
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - N Çerikçioğlu
- Mycology Laboratory at Department of Medical Microbiology of Marmara University Medical School, Istanbul, Turkey
| | - M A Efstratiou
- Department of Marine Sciences, University of the Aegean, University Hill, Mytilene, Greece
| | - Ç Ergin
- Department of Medical Microbiology, Medical Faculty, Pamukkale University, Denizli, Turkey
| | - M C Esposto
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milano, Italy
| | - M Frenkel
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - J P Gangneux
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - A Gitto
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, and UCD Conway Institute, University College Dublin, Ireland
| | - C I Gonçalves
- Department of Biology and Environment, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - H Guegan
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - N Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Slovenia
| | - M Güran
- Faculty of Medicine, Eastern Mediterranean University, Famagusta, Northern Cyprus, Mersin, Turkey
| | - E Jonikaitė
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
| | - M Kataržytė
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
| | - L Klingspor
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - M Mares
- Ion Ionescu de la Brad University of Life Sciences, Iasi, Romania
| | - W G Meijer
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, and UCD Conway Institute, University College Dublin, Ireland
| | - W J G Melchers
- Medical Microbiology, Radboud University Medical Centre (Radboudumc), Nijmegen, the Netherlands
| | - J Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - V Nastasa
- Ion Ionescu de la Brad University of Life Sciences, Iasi, Romania
| | - M Novak Babič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Slovenia
| | - D Ogunc
- Department of Medical Microbiology, Akdeniz University Medical School, Antalya, Turkey
| | - B Ozhak
- Department of Medical Microbiology, Akdeniz University Medical School, Antalya, Turkey
| | - A Prigitano
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milano, Italy
| | - S Ranque
- Aix Marseille Univ, IHU-Méditerranée Infection, AP-HM, IRD, SSA, VITROME, Marseille, France
| | - L Romanò
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milano, Italy
| | - R O Rusu
- Ion Ionescu de la Brad University of Life Sciences, Iasi, Romania
| | - R Sabino
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal; Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - A Sampaio
- Department of Biology and Environment, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), UTAD, Vila Real, Portugal
| | - S Silva
- Department of Epidemiology, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - J H Stephens
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, and UCD Conway Institute, University College Dublin, Ireland
| | - M Tehupeiory-Kooreman
- Medical Microbiology, Radboud University Medical Centre (Radboudumc), Nijmegen, the Netherlands
| | - A Velegraki
- Mycology Research Laboratory and UOA/HCPF Culture Collection, Microbiology Department, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Mycology Laboratory, BIOMEDICINE S.A., Athens, Greece
| | - C Veríssimo
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - E Segal
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - J Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; Centre for Environmental and Marine Studies (CESAM) - Department of Animal Biology, University of Lisbon, Lisbon, Portugal
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17
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Aitken CA, Inturrisi F, Kaljouw S, Nieboer D, Siebers AG, Melchers WJG, van den Brule AJC, Molijn A, Hinrichs JWJ, Niesters HGM, van Kemenade FJ, Berkhof J, de Kok IMCM. Sociodemographic Characteristics and Screening Outcomes of Women Preferring Self-Sampling in the Dutch Cervical Cancer Screening Programme: A Population-Based Study. Cancer Epidemiol Biomarkers Prev 2023; 32:183-192. [PMID: 36099416 PMCID: PMC9900317 DOI: 10.1158/1055-9965.epi-22-0712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/21/2022] [Accepted: 09/06/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In the Netherlands, lower high-risk human papillomavirus (hrHPV) positivity but higher cervical intraepithelial neoplasia (CIN) 2+ detection were found in self-collected compared with clinician-collected samples. To investigate the possible reason for these differences, we compared sociodemographic and screening characteristics of women and related these to screening outcomes. METHODS We extracted data from PALGA on all primary hrHPV screens and associated follow-up tests for 857,866 screened women, invited in 2017 and 2018. We linked these data with sociodemographic data from Statistics Netherlands. Logistic regression was performed for hrHPV positivity and CIN 2+/3+ detection. RESULTS Out of the 857,866 women, 6.8% chose to use a self-sampling device. A higher proportion of self-sampling users was ages 30 to 35 years, was not previously screened, was living in a one-person household, or was the breadwinner in the household. After adjustment for these factors self-sampling had lower hrHPV positivity (aOR, 0.65; 95% CI, 0.63-0.68)) as compared with clinician-collected sampling, as well as lower odds of CIN 2+ (aOR, 0.76; 95% CI, 0.70-0.82) and CIN 3+ (aOR, 0.86; 95% CI, 0.78-0.95) detection. CONCLUSIONS It is likely that the observed differences between the two sampling methods are not only related to sociodemographic differences, but related to differences in screening test accuracy and/or background risk. IMPACT Self-sampling can be used for targeting underscreened women, as a more convenient screening tool. Further investigation is required to evaluate how to implement self-sampling, when it is used as a primary instrument in routine screening. See related commentary by Arbyn et al., p. 159.
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Affiliation(s)
- Clare A Aitken
- University Medical Center Rotterdam, Erasmus MC, Department of Public Health, Rotterdam, the Netherlands.,Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Federica Inturrisi
- Amsterdam UMC location Vrije Universiteit Amsterdam, Epidemiology and Data Science, Amsterdam, the Netherlands.,Amsterdam Public Health, Methodology, Amsterdam, the Netherlands
| | - Sylvia Kaljouw
- University Medical Center Rotterdam, Erasmus MC, Department of Public Health, Rotterdam, the Netherlands
| | - Daan Nieboer
- University Medical Center Rotterdam, Erasmus MC, Department of Public Health, Rotterdam, the Netherlands
| | - Albert G Siebers
- The Nationwide Network and Registry of Histo-and Cytopathology in the Netherlands (PALGA Foundation), Houten, the Netherlands
| | - Willem J G Melchers
- Radboud University Medical Center, Medical Microbiology, Nijmegen, the Netherlands
| | | | - Anco Molijn
- DDL Diagnostic Laboratory, NMDL-LCPL, Rijswijk, the Netherlands
| | - John W J Hinrichs
- Symbiant Pathology Expert Centre Hoorn, Hoorn, the Netherlands.,Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hubert G M Niesters
- Division of Clinical Virology, Department of Medical Microbiology, The University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Folkert J van Kemenade
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Johannes Berkhof
- Amsterdam UMC location Vrije Universiteit Amsterdam, Epidemiology and Data Science, Amsterdam, the Netherlands.,Amsterdam Public Health, Methodology, Amsterdam, the Netherlands
| | - Inge M C M de Kok
- University Medical Center Rotterdam, Erasmus MC, Department of Public Health, Rotterdam, the Netherlands
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18
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Ebisch RMF, Rijstenberg LL, Soltani GG, van der Horst J, Vedder JEM, Hermsen M, Bosgraaf RP, Massuger LFAG, Meijer CJLM, Heideman DAM, van Kemenade FJ, Melchers WJG, Bekkers RLM, Siebers AG, Bulten J. Adjunctive use of p16 immunohistochemistry for optimizing management of CIN lesions in a high-risk human papillomavirus-positive population. Acta Obstet Gynecol Scand 2022; 101:1328-1336. [PMID: 36177908 PMCID: PMC9812205 DOI: 10.1111/aogs.14459] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/12/2022] [Accepted: 08/25/2022] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Immunostaining with p16INK4a (p16), a tumor-suppressor surrogate protein biomarker for high-risk human papillomavirus (hrHPV) oncogenic activity, may complement standard hematoxylin and eosin (H&E) histology review, and provide more objective criteria to support the cervical intraepithelial neoplasia (CIN) diagnosis. With this study we assessed the impact of p16 immunohistochemistry on CIN grading in an hrHPV-based screening setting. MATERIAL AND METHODS In this post-hoc analysis, 326 histology follow-up samples from a group of hrHPV-positive women were stained with p16 immunohistochemistry. All H&E samples were centrally revised. The pathologists reported their level of confidence in classifying the CIN lesion. RESULTS Combining H&E and p16 staining resulted in a change of diagnosis in 27.3% (n = 89) of cases compared with the revised H&E samples, with a decrease of 34.5% (n = 18) in CIN1 and 22.7% (n = 15) in CIN2 classifications, and an increase of 18.3% (n = 19) in no CIN and 20.7% (n = 19) in CIN3 diagnoses. The level of confidence in CIN grading by the pathologist increased with adjunctive use of p16 immunohistochemistry to standard H&E. CONCLUSIONS This study shows that adjunctive use of p16 immunohistochemistry to H&E morphology reduces the number of CIN1 and CIN2 classifications with a proportional increase in no CIN and CIN3 diagnoses, compared with standard H&E-based CIN diagnosis alone. The pathologists felt more confident in classifying the material with H&E and p16 immunohistochemistry than by using H&E alone, particularly during assessment of small biopsies. Adjunctive use of p16 immunohistochemistry to standard H&E assessment of CIN would be valuable for the diagnostic accuracy, thereby optimizing CIN management and possibly decreasing overtreatment.
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Affiliation(s)
- Renée M. F. Ebisch
- Department of Obstetrics and GynecologyRadboud University Medical CenterNijmegenThe Netherlands,Department of Obstetrics and GynecologyCatharina Hospital EindhovenEindhovenThe Netherlands
| | | | - Gilda Ghazi Soltani
- Department of PathologyRadboud University Medical CenterNijmegenThe Netherlands
| | | | - Judith E. M. Vedder
- Department of PathologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Meyke Hermsen
- Department of PathologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Remko P. Bosgraaf
- Department of Obstetrics and GynecologyCatharina Hospital EindhovenEindhovenThe Netherlands
| | - Leon F. A. G. Massuger
- Department of Obstetrics and GynecologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Chris J. L. M. Meijer
- Amsterdam UMCVrije Universiteit Amsterdam, Pathology, Cancer Center AmsterdamAmsterdamThe Netherlands
| | - Daniëlle A. M. Heideman
- Amsterdam UMCVrije Universiteit Amsterdam, Pathology, Cancer Center AmsterdamAmsterdamThe Netherlands
| | | | - Willem J. G. Melchers
- Department of Medical MicrobiologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Ruud L. M. Bekkers
- Department of Obstetrics and GynecologyCatharina Hospital EindhovenEindhovenThe Netherlands,GROW, School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Albert G. Siebers
- Department of PathologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Johan Bulten
- Department of PathologyRadboud University Medical CenterNijmegenThe Netherlands
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19
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Molina MA, Andralojc KM, Huynen MA, Leenders WPJ, Melchers WJG. In-depth insights into cervicovaginal microbial communities and hrHPV infections using high-resolution microbiome profiling. NPJ Biofilms Microbiomes 2022; 8:75. [PMID: 36171433 PMCID: PMC9519886 DOI: 10.1038/s41522-022-00336-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 03/08/2022] [Accepted: 09/06/2022] [Indexed: 11/09/2022] Open
Abstract
The cervicovaginal microbiome (CVM) correlates with women's cervical health, and variations in its composition are associated with high-risk human papillomavirus (hrHPV) infection outcomes. Cervicovaginal microbes have been grouped into five community state types (CSTs) based on microbial community composition and abundance. However, studying the impact of CSTs in health and disease is challenging because the current sequencing technologies have limited confident discrimination between closely related and yet functionally different bacterial species. Circular probe-based RNA sequencing (ciRNAseq) achieves high-resolution microbiome profiling and therefore provides in-depth and unambiguous knowledge about the composition of the CVM. Based on ciRNAseq profiling of a large cohort of cervical smears (n = 541), we here define subgroups of CSTs I, III, and IV based on intra-CST differences with respect to abundances of Lactobacillus acidophilus (CSTs I-A vs. I-B and CSTs III-A vs. III-B), Lactobacillus iners (CSTs I-A vs. I-B and CSTs III-A vs. III-B), and Megasphaera genomosp type 1 (CSTs IV-A vs. IV-B). Our results further support the existence of subgroups of CST IV-C that are dominant for non-Lactobacillus species and have intermediate microbial diversity. We also show that CST V is associated with uninfected conditions, and CST IV-A associates with hrHPV-induced cervical disease. In conclusion, we characterized new subdivisions of cervicovaginal CSTs, which may further advance our understanding of women's cervical health and hrHPV-related progression to disease.
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Affiliation(s)
- Mariano A Molina
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands.,Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Karolina M Andralojc
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands.,Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA, Nijmegen, The Netherlands
| | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA, Nijmegen, The Netherlands
| | - William P J Leenders
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA, Nijmegen, The Netherlands.,Predica Diagnostics, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands.
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20
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Song Y, Buil JB, Melchers WJG, Zoll J, Verweij PE. P001 Characteristics and dynamics of azole-resistant Aspergillus fumigatus variants emerging over a 28-year period in the Netherlands. Med Mycol 2022. [PMCID: PMC9516348 DOI: 10.1093/mmy/myac072.p001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/25/2022] Open
Abstract
Poster session 1, September 21, 2022, 12:30 PM - 1:30 PM Background Aspergillus fumigatus, a globally distributed opportunistic pathogen, is the main cause of invasive aspergillosis, especially in immunocompromised patients with high mortality. The emergence of azole-resistant A. fumigatus isolates has been a significant concern worldwide and an important clinical problem. Objectives We aim to determine the presence of variants in a large collection of clinical A. fumigatus isolates from the Netherlands, if the number of variants increased over time and if the presence of additional short nucleotide polymorphisms (SNPs) or tandem repeats (TR) variations impacted on the triazole phenotype. Methods The Radboud University Medical Center has collected 11 813 clinical A. fumigatus isolates since 1994. The collection includes isolates cultured from patients admitted to our own center, isolates sent from other hospitals for identification and in vitro susceptibility testing, and isolates sent from five university medical centers and five teaching hospitals that contribute to the national Aspergillus resistance surveillance. The genotypes were detected by Cyp51A Sanger sequencing. All isolates were subjected to in vitro susceptibility testing using the EUCAST microdilution reference method. Minimal inhibitory concentrations (MICs) were determined for itraconazole, voriconazole, posaconazole, in all isolates and for isavuconazole in isolates cultured in 2015 and thereafter. Results In total, 1826 A. fumigatus isolates harbored azole-resistant mutations in the Cyp51A-gene with 92 genotypes. Tandem Repeat-associated resistance genotypes accounted for 55.43% of the variants and were involved in 1728 isolates (94.63%). TR34/L98H and TR46/Y121F/T289A resistance mutations remained dominant, and increasingly additional SNPs in the Cyp51A-gene or changes to the gene promoter were observed. The G448S mutation was relatively common and present in various genetic backgrounds. This SNP was most often found in isolates harboring the TR46 resistance mechanism (8 variants) and was also observed in two variants in the TR34 genetic background. TR34 and TR46 resistance mutations are associated with 1170 (64.07%) isolates that exhibited a pan-azole resistance phenotype, 547 (29.96%) a multi-azole resistance phenotype, and 75 (4.11%) resistance to a single azole. TR34/L98H confers high itraconazole resistance, while T289A confers high voriconazole resistance in the TR46 background. Isolates with a G448S point mutation show high MICs for both voriconazole and itraconazole. The TR34/L98H/T289A/G448S isolate showed low itraconazole MICs but high voriconazole resistance, and mutations in the promoter region, TR34/C-86 G/L98H, and (T-66 G)/TR34/L98H variants, showed increased voriconazole and isavuconazole MIC compared with the parent phenotype. TR46/Y121F/M172I/T289A/G448S variant was observed with an increased itraconazole (GM MIC 16 mg/L, 1→16 mg/l) and decreased voriconazole (GM MIC 18.664 mg/l, 4→16 mg/l) compared with the parent MIC of TR46/Y121F/T289A, while TR92/Y121F/M172I/T289A/G448S and TR46/Y121F/ T289A/G448S variants showed the consistent MIC distribution with parent genotype. The variants with more combination mutations showed pan-azole resistance with increased MIC distribution. Conclusion Our survey showed a significant increase in resistance genotypes in clinical A. fumigatus over a period of 28 years. Azoles resistance phenotypes vary from resistant variants in clinical isolates; it is an implication for clinical A. fumigatus infection treatment options and antifungal stewardship.
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Affiliation(s)
- Yinggai Song
- Radboudumc Center for Infectious Diseases (RCI) , Radboud University Medical Center, Nijmegen , Netherlands
- Peking University First Hospital , Beijing , China
| | - Jochem B Buil
- Radboudumc Center for Infectious Diseases (RCI) , Radboud University Medical Center, Nijmegen , Netherlands
| | | | - Jan Zoll
- Radboudumc Center for Infectious Diseases (RCI) , Radboud University Medical Center, Nijmegen , Netherlands
| | - Paul E Verweij
- Radboudumc Center for Infectious Diseases (RCI) , Radboud University Medical Center, Nijmegen , Netherlands
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21
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Wiersma D, Vinke A, Siebers AG, Melchers WJG, Bekkers RLM, Loopik DL. The added value of digital imaging to reflex cytology for triage of high‐risk human papillomavirus positive self‐sampled material in cervical cancer screening: a prospective cohort study. BJOG 2022; 130:184-191. [PMID: 35993438 PMCID: PMC10087746 DOI: 10.1111/1471-0528.17272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 03/29/2022] [Accepted: 04/12/2022] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Cytology performed directly on hrHPV-positive self-samples (reflex cytology) is feasible and for women with abnormal cytology, an additional cytology test at the general practitioner could be omitted. The aim of this study is to assess the added value of digital imaging (ThinPrep® Imaging System) on the clinical utility of reflex cytology by reducing screening error. DESIGN A secondary analysis of a prospective cohort study. SETTING One of five Dutch screening laboratories. POPULATION Women tested hrHPV-positive on self-samples between December 2018 and August 2019. METHODS Self-samples were used for reflex cytology with and without digital imaging. The follow-up data (cytological and histological results within 1 year of follow-up) were obtained through the Dutch Pathology Registry (PALGA). MAIN OUTCOME MEASURES Test performance of the reflex cytology was determined by comparing it with physician-collected follow-up results. RESULTS The sensitivity for detecting abnormal cells by reflex cytology on self-samples increased significantly from 26.3% (42/160; 95% confidence interval [CI] 19.6-33.8) without digital imaging to 35.4% (56/158; 95% CI 28-43.4) with digital imaging (P < 0.05) without compromising specificity. Importantly, 41.7% of women with ≥CIN2 (35/84) and 45.6% with ≥CIN3 (26/57) were detected by reflex cytology with digital imaging on hrHPV-positive self-samples. CONCLUSION Digital imaging is of added value to reflex cytology on hrHPV-positive self-samples with a 9% increase in sensitivity. If reflex cytology on self-samples analysed with digital imaging had been implemented in the screening programme, 35.4% of the hrHPV-positive women with abnormal cytology on additional physician-collected samples could have been referred directly for colposcopy.
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Affiliation(s)
- Danique Wiersma
- Department of Obstetrics and Gynaecology Radboud university medical center Nijmegen the Netherlands
| | - Anne Vinke
- Department of Pathology Radboud university medical center PO Nijmegen The Netherlands
| | - Albert G. Siebers
- Department of Pathology Radboud university medical center Nijmegen The Netherlands
- PALGA, the nationwide network and registry of histo‐ and cytopathology SZ Houten the Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology Radboud university medical center Nijmegen The Netherlands
| | - Ruud L. M. Bekkers
- Department of Obstetrics and Gynaecology Catharina Hospital Eindhoven The Netherlands
- GROW, School for Oncology & Developmental Biology Maastricht University Medical Centre Maastricht The Netherlands
| | - Diede L. Loopik
- Department of Obstetrics and Gynaecology Radboud university medical center Nijmegen The Netherlands
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22
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Visser WCH, de Jong H, Steyaert S, Melchers WJG, Mulders PFA, Schalken JA. Clinical use of the mRNA urinary biomarker SelectMDx test for prostate cancer. Prostate Cancer Prostatic Dis 2022; 25:583-589. [PMID: 35810263 PMCID: PMC9385481 DOI: 10.1038/s41391-022-00562-1] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/11/2022] [Accepted: 06/10/2022] [Indexed: 11/29/2022]
Abstract
Background Molecular biomarker tests are developed as diagnostic tools for prostate cancer (PCa) diagnosis. The SelectMDx (MDxHealth, Nijmegen, The Netherlands) test is a urinary-based biomarker test intended to be used to predict presence of high-grade PCa upon biopsy in men with elevated serum prostate-specific antigen (PSA) levels. Previous validation of the SelectMDx test revealed that 53% of the unnecessary biopsies (biopsies indicating no- or GG1 PCa) could be avoided using the SelectMDx test as a decision-tool to select men for prostate biopsy. The objective of this study is to examine the use of the commercially available SelectMDx test under routine, real-life practice. Methods Men that underwent a SelectMDx test between May 2019 and December 2020 and that were originating from countries that perform the SelectMDx test on a regular basis were included in this study, resulting in 5157 cases from 10 European countries. Clinical parameters, urinary RNA scores, and test outcomes were compared between PSA groups, age groups, countries, and the validation cohort (described previously [4]) using the Mann–Whitney U test, Chi-Square test, Benjamini–Hochberg and Kruskal–Wallis tests. Results 40.72% of the cases received a negative SelectMDx result. The test is also used in patients outside the intended-use population (PSA < 3 and >10 ng/mL). Clinical parameters (age, PSA density, DRE outcome) varied between patient population from individual countries and the validation cohort, resulting in differences in the potential number of saved biopsies using the test. Conclusions The potential number of reduced biopsies in clinical use was 40,72% using the SelectMDx test, assuming a negative SelectMDx test resulted in the decision not to biopsy the patient. This is higher compared to the validation cohort, which is explained by differences in patient population.
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Affiliation(s)
- Wieke C H Visser
- Department of Product Development, MDxHealth BV, Nijmegen, The Netherlands
| | - Hans de Jong
- Department of Product Development, MDxHealth BV, Nijmegen, The Netherlands
| | - Sandra Steyaert
- Department of Computational Biology, Statistics and AI, VOF dobbio, Zelzate, Belgium
| | - Willem J G Melchers
- Department of Product Development, MDxHealth BV, Nijmegen, The Netherlands.,Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter F A Mulders
- Department of Urology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jack A Schalken
- Department of Urology, Radboud University Medical Centre, Nijmegen, The Netherlands.
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23
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Andralojc KM, Elmelik D, Rasing M, Pater B, Siebers AG, Bekkers R, Huynen MA, Bulten J, Loopik D, Melchers WJG, Leenders WPJ. Targeted RNA next generation sequencing analysis of cervical smears can predict the presence of hrHPV-induced cervical lesions. BMC Med 2022; 20:206. [PMID: 35676700 PMCID: PMC9178797 DOI: 10.1186/s12916-022-02386-1] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/26/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Because most cervical cancers are caused by high-risk human papillomaviruses (hrHPVs), cervical cancer prevention programs increasingly employ hrHPV testing as a primary test. The high sensitivity of HPV tests is accompanied by low specificity, resulting in high rates of overdiagnosis and overtreatment. Targeted circular probe-based RNA next generation sequencing (ciRNAseq) allows for the quantitative detection of RNAs of interest with high sequencing depth. Here, we examined the potential of ciRNAseq-testing on cervical scrapes to identify hrHPV-positive women at risk of having or developing high-grade cervical intraepithelial neoplasia (CIN). METHODS We performed ciRNAseq on 610 cervical scrapes from the Dutch cervical cancer screening program to detect gene expression from 15 hrHPV genotypes and from 429 human genes. Differentially expressed hrHPV- and host genes in scrapes from women with outcome "no CIN" or "CIN2+" were identified and a model was built to distinguish these groups. RESULTS Apart from increasing percentages of hrHPV oncogene expression from "no CIN" to high-grade cytology/histology, we identified genes involved in cell cycle regulation, tyrosine kinase signaling pathways, immune suppression, and DNA repair being expressed at significantly higher levels in scrapes with high-grade cytology and histology. Machine learning using random forest on all the expression data resulted in a model that detected 'no CIN' versus CIN2+ in an independent data set with sensitivity and specificity of respectively 85 ± 8% and 72 ± 13%. CONCLUSIONS CiRNAseq on exfoliated cells in cervical scrapes measures hrHPV-(onco)gene expression and host gene expression in one single assay and in the process identifies HPV genotype. By combining these data and applying machine learning protocols, the risk of CIN can be calculated. Because ciRNAseq can be performed in high-throughput, making it cost-effective, it can be a promising screening technology to stratify women at risk of CIN2+. Further increasing specificity by model improvement in larger cohorts is warranted.
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Affiliation(s)
- Karolina M Andralojc
- Department of Biochemistry, Radboudumc, Radboud Institute of Molecular Life Sciences, Geert Grooteplein 26, Nijmegen, 6525 GA, The Netherlands.,Department of Medical Microbiology, Radboudumc, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - Duaa Elmelik
- Department of Biochemistry, Radboudumc, Radboud Institute of Molecular Life Sciences, Geert Grooteplein 26, Nijmegen, 6525 GA, The Netherlands
| | - Menno Rasing
- Predica Diagnostics, Toernooiveld 1, Nijmegen, 6525 ED, The Netherlands
| | - Bernard Pater
- Predica Diagnostics, Toernooiveld 1, Nijmegen, 6525 ED, The Netherlands
| | - Albert G Siebers
- Department of Pathology, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.,PALGA, De Bouw 123, Houten, 3991 SZ, The Netherlands
| | - Ruud Bekkers
- Department of Obstetrics and Gynecology, Catharina Hospital Eindhoven, Michelangelolaan 2, Eindhoven, 5623 EJ, The Netherlands.,GROW, School for Oncology and Reproductive Biology, Maastricht University, Maastricht, The Netherlands
| | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute of Molecular Life Sciences, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - Johan Bulten
- Department of Pathology, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Diede Loopik
- Department of Gynecology and Obstetrics, Radboudumc, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboudumc, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - William P J Leenders
- Department of Biochemistry, Radboudumc, Radboud Institute of Molecular Life Sciences, Geert Grooteplein 26, Nijmegen, 6525 GA, The Netherlands. .,Predica Diagnostics, Toernooiveld 1, Nijmegen, 6525 ED, The Netherlands.
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24
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Ashton GD, Sang F, Blythe M, Zadik D, Holmes N, Malla S, Camps SMT, Wright V, Melchers WJG, Verweij PE, Dyer PS. Use of Bulk Segregant Analysis for Determining the Genetic Basis of Azole Resistance in the Opportunistic Pathogen Aspergillus fumigatus. Front Cell Infect Microbiol 2022; 12:841138. [PMID: 35531335 PMCID: PMC9069965 DOI: 10.3389/fcimb.2022.841138] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/03/2022] [Indexed: 12/19/2022] Open
Abstract
A sexual cycle was described in 2009 for the opportunistic fungal pathogen Aspergillus fumigatus, opening up for the first time the possibility of using techniques reliant on sexual crossing for genetic analysis. The present study was undertaken to evaluate whether the technique 'bulk segregant analysis' (BSA), which involves detection of differences between pools of progeny varying in a particular trait, could be applied in conjunction with next-generation sequencing to investigate the underlying basis of monogenic traits in A. fumigatus. Resistance to the azole antifungal itraconazole was chosen as a model, with a dedicated bioinformatic pipeline developed to allow identification of SNPs that differed between the resistant progeny pool and resistant parent compared to the sensitive progeny pool and parent. A clinical isolate exhibiting monogenic resistance to itraconazole of unknown basis was crossed to a sensitive parent and F1 progeny used in BSA. In addition, the use of backcrossing and increasing the number in progeny pools was evaluated as ways to enhance the efficiency of BSA. Use of F1 pools of 40 progeny led to the identification of 123 candidate genes with SNPs distributed over several contigs when aligned to an A1163 reference genome. Successive rounds of backcrossing enhanced the ability to identify specific genes and a genomic region, with BSA of progeny (using 40 per pool) from a third backcross identifying 46 genes with SNPs, and BSA of progeny from a sixth backcross identifying 20 genes with SNPs in a single 292 kb region of the genome. The use of an increased number of 80 progeny per pool also increased the resolution of BSA, with 29 genes demonstrating SNPs between the different sensitive and resistant groupings detected using progeny from just the second backcross with the majority of variants located on the same 292 kb region. Further bioinformatic analysis of the 292 kb region identified the presence of a cyp51A gene variant resulting in a methionine to lysine (M220K) change in the CYP51A protein, which was concluded to be the causal basis of the observed resistance to itraconazole. The future use of BSA in genetic analysis of A. fumigatus is discussed.
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Affiliation(s)
- George D. Ashton
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Fei Sang
- DeepSeq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Martin Blythe
- DeepSeq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Daniel Zadik
- DeepSeq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Nadine Holmes
- DeepSeq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Sunir Malla
- DeepSeq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Simone M. T. Camps
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Victoria Wright
- DeepSeq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Paul S. Dyer
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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25
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van der Valk PGM, Melchers WJG, Verweij PE. [Diagnosis of suspected superficial fungal infections]. Ned Tijdschr Geneeskd 2022; 166:D6290. [PMID: 35499577] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Most medical microbiology laboratories in the Netherlands have switched from direct potassium hydroxide microscopy and culture to polymerase chain reaction (PCR) testing when diagnosing dermato- and onychomycoses and Candida species in human dander, hair and nails. The predictive value of a PCR test is in most cases higher than the predictive value of KOH microscopy and culture in diagnosing or ruling out a fungal infection and should therefore replace traditional diagnostics in routine care. KOH microscopy and culture should be reserved in cases of therapy failure and suspected false negative PCR testing. An application for a PCR should be performed if there is any doubt about the clinical diagnosis. The application must be accompanied by sufficient clinical information from the patient to enable the microbiologist to determine whether the PCR test used is appropriate.
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26
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Buil JB, Oliver JD, Law D, Baltussen T, Zoll J, Hokken MWJ, Tehupeiory-Kooreman M, Melchers WJG, Birch M, Verweij PE. Resistance profiling of Aspergillus fumigatus to olorofim indicates absence of intrinsic resistance and unveils the molecular mechanisms of acquired olorofim resistance. Emerg Microbes Infect 2022; 11:703-714. [PMID: 35109772 PMCID: PMC8890541 DOI: 10.1080/22221751.2022.2034485] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Olorofim (F901318) is a new antifungal currently under clinical development that shows both in vitro and in vivo activity against a number of filamentous fungi including Aspergillus fumigatus. In this study, we screened A. fumigatus isolates for intrinsic olorofim-resistant A. fumigatus and evaluated the ability of A. fumigatus to acquire an olorofim-resistant phenotype. No intrinsic resistance was found in 975 clinical A. fumigatus isolates. However, we found that isolates with increased olorofim MICs (> 8 mg/L) could be selected using a high number of conidia and olorofim exposure under laboratory conditions. Assessment of the frequency of acquired olorofim resistance development of A. fumigatus was shown to be higher than for voriconazole but lower than for itraconazole. Sequencing the PyrE gene of isogenic isolates with olorofim MICs of >8 mg/L identified various amino acid substitutions with a hotspot at locus G119. Olorofim was shown to have reduced affinity to mutated target protein dihydroorotate dehydrogenase (DHODH) and the effect of these mutations was proven by introducing the mutations directly in A. fumigatus. We then investigated whether G119 mutations were associated with a fitness cost in A. fumigatus. These experiments showed a small but significant reduction in growth rate for strains with a G119V substitution, while strains with a G119C substitution did not exhibit a reduction in growth rate. These in vitro findings were confirmed in an in vivo pathogenicity model.
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Affiliation(s)
- Jochem B Buil
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
| | | | - Derek Law
- F2G Ltd, Lankro Way, Manchester, United Kingdom
| | - Tim Baltussen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan Zoll
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
| | - Margriet W J Hokken
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marlou Tehupeiory-Kooreman
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
| | - Mike Birch
- F2G Ltd, Lankro Way, Manchester, United Kingdom
| | - Paul E Verweij
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
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27
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Wegner F, Roloff T, Huber M, Cordey S, Ramette A, Gerth Y, Bertelli C, Stange M, Seth-Smith HMB, Mari A, Leuzinger K, Cerutti L, Harshman K, Xenarios I, Le Mercier P, Bittel P, Neuenschwander S, Opota O, Fuchs J, Panning M, Michel C, Hallin M, Demuyser T, De Mendonca R, Savelkoul P, Dingemans J, van der Veer B, Boers SA, Claas ECJ, Coolen JPM, Melchers WJG, Gunell M, Kallonen T, Vuorinen T, Hakanen AJ, Bernhoff E, Hetland MAK, Golan Berman H, Adar S, Moran-Gilad J, Wolf DG, Leib SL, Nolte O, Kaiser L, Schmutz S, Kufner V, Zaheri M, Trkola A, Aamot HV, Hirsch HH, Greub G, Egli A. External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories. J Clin Microbiol 2022; 60:e0169821. [PMID: 34757834 PMCID: PMC8769736 DOI: 10.1128/jcm.01698-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/05/2021] [Indexed: 12/01/2022] Open
Abstract
This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD) and the Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out to 15 clinical laboratories that had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centers were compared were the identification of (i) single nucleotide polymorphisms (SNPs) and indels, (ii) Pango lineages, and (iii) clusters between samples. The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to various depths (up to a 100-fold difference across centers). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignments. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. The pilot EQA was overall a success. It was able to show the high quality of participating laboratories and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.
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Affiliation(s)
- Fanny Wegner
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, University Hospital Geneva, Geneva, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Yannick Gerth
- Center for Laboratory Medicine, Saint Gall, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Madlen Stange
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Helena M. B. Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Alfredo Mari
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Karoline Leuzinger
- Clinical Virology, University Hospital Basel, Basel, Switzerland
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | | | | | | | - Pascal Bittel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jonas Fuchs
- Institute of Virology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Institute of Virology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Charlotte Michel
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Brussels, Belgium
| | - Marie Hallin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Paul Savelkoul
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jozef Dingemans
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
| | - Brian van der Veer
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
| | - Stefan A. Boers
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Eric C. J. Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Marianne Gunell
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Teemu Kallonen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Tytti Vuorinen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Antti J. Hakanen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Eva Bernhoff
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | | | - Hadar Golan Berman
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Jacob Moran-Gilad
- School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Dana G. Wolf
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
- Lautenberg Center for General and Tumor Immunology, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Stephen L. Leib
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Oliver Nolte
- Center for Laboratory Medicine, Saint Gall, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, University Hospital Geneva, Geneva, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hege Vangstein Aamot
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Department of Clinical Molecular Biology (EPIGEN), Akershus University Hospital and University of Oslo, Lørenskog, Norway
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Hans H. Hirsch
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Infectious Diseases and Hospital Epidemiology, University of Basel, Basel, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
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28
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Andralojc KM, Molina MA, Qiu M, Spruijtenburg B, Rasing M, Pater B, Huynen MA, Dutilh BE, Ederveen THA, Elmelik D, Siebers AG, Loopik D, Bekkers RLM, Leenders WPJ, Melchers WJG. Novel high-resolution targeted sequencing of the cervicovaginal microbiome. BMC Biol 2021; 19:267. [PMID: 34915863 PMCID: PMC8680041 DOI: 10.1186/s12915-021-01204-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 06/01/2021] [Accepted: 12/02/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The cervicovaginal microbiome (CVM) plays a significant role in women's cervical health and disease. Microbial alterations at the species level and characteristic community state types (CST) have been associated with acquisition and persistence of high-risk human papillomavirus (hrHPV) infections that may result in progression of cervical lesions to malignancy. Current sequencing methods, especially most commonly used multiplex 16S rRNA gene sequencing, struggle to fully clarify these changes because they generally fail to provide sufficient taxonomic resolution to adequately perform species-level associative studies. To improve CVM species designation, we designed a novel sequencing tool targeting microbes at the species taxonomic rank and examined its potential for profiling the CVM. RESULTS We introduce an accessible and practical circular probe-based RNA sequencing (CiRNAseq) technology with the potential to profile and quantify the CVM. In vitro and in silico validations demonstrate that CiRNAseq can distinctively detect species in a mock mixed microbial environment, with the output data reflecting its ability to estimate microbes' abundance. Moreover, compared to 16S rRNA gene sequencing, CiRNAseq provides equivalent results but with improved sequencing sensitivity. Analyses of a cohort of cervical smears from hrHPV-negative women versus hrHPV-positive women with high-grade cervical intraepithelial neoplasia confirmed known differences in CST occurring in the CVM of women with hrHPV-induced lesions. The technique also revealed variations in microbial diversity and abundance in the CVM of hrHPV-positive women when compared to hrHPV-negative women. CONCLUSIONS CiRNAseq is a promising tool for studying the interplay between the CVM and hrHPV in cervical carcinogenesis. This technology could provide a better understanding of cervicovaginal CST and microbial species during health and disease, prompting the discovery of biomarkers, additional to hrHPV, that can help detect high-grade cervical lesions.
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Affiliation(s)
- Karolina M. Andralojc
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Mariano A. Molina
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mengjie Qiu
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Bram Spruijtenburg
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Menno Rasing
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Bernard Pater
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Martijn A. Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Bas E. Dutilh
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Thomas H. A. Ederveen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Duaa Elmelik
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Albert G. Siebers
- Department of Pathology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Diede Loopik
- Department of Obstetrics and Gynecology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Ruud L. M. Bekkers
- Department of Obstetrics and Gynecology, Catharina Hospital, 5602 ZA Eindhoven, The Netherlands
- GROW, School for Oncology & Developmental Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
| | - William P. J. Leenders
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
- Predica Diagnostics, Toernooiveld 1, 6525 GA Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
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29
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Buil JB, Bronckers IMGJ, Driessen RJB, Do Nguyen Dan T, Melchers WJG, Verweij PE. [Terbinafine resistance explains treatment failure in a patient with tinea corporis]. Ned Tijdschr Geneeskd 2021; 165:D5009. [PMID: 35129895] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BACKGROUND Tinea corporis is a superficial fungal infection of the limbs, chest or back caused by dermatophytes. Local antifungal treatment is often sufficient to treat tinea corporis. Systemic treatment may be needed in more severe cases, in immunocompromised patients or when treatment failure is documented. Treatment failure is relative common and frequent causes are low compliance, low systemic antifungal drug concentrations, reduced penetration of topical agents or an immunocompromised status. Recently, antifungal resistance has been documented in dermatophytes. CASE DESCRIPTION We describe a patient with terbinafine treatment failure caused by antifungal drug resistance. CONCLUSION The frequency of terbinafine resistance in the Netherlands is unknown as no surveillance is performed. Recent reports from both India and European countries indicate that antifungal resistance should be considered in patients with terbinafine treatment failure.
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Affiliation(s)
- Jochem B Buil
- Radboudumc, afd. Medische Microbiologie,Nijmegen
- Contact: Jochem B. Buil
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30
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Delma FZ, Al-Hatmi AMS, Brüggemann RJM, Melchers WJG, de Hoog S, Verweij PE, Buil JB. Molecular Mechanisms of 5-Fluorocytosine Resistance in Yeasts and Filamentous Fungi. J Fungi (Basel) 2021; 7:jof7110909. [PMID: 34829198 PMCID: PMC8623157 DOI: 10.3390/jof7110909] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 10/04/2021] [Revised: 10/19/2021] [Accepted: 10/23/2021] [Indexed: 12/30/2022] Open
Abstract
Effective management and treatment of fungal diseases is hampered by poor diagnosis, limited options for antifungal therapy, and the emergence of antifungal drug resistance. An understanding of molecular mechanisms contributing to resistance is essential to optimize the efficacy of currently available antifungals. In this perspective, one of the oldest antifungals, 5-fluorocytosine (5-FC), has been the focus of recent studies applying advanced genomic and transcriptomic techniques to decipher the order of events at the molecular level that lead to resistance. These studies have highlighted the complexity of resistance and provided new insights that are reviewed in the present paper.
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Affiliation(s)
- Fatima Zohra Delma
- Department of Medical Microbiology, Radboud University Medical Centre, 6252 AG Nijmegen, The Netherlands; (F.Z.D.); (W.J.G.M.); (P.E.V.)
| | - Abdullah M. S. Al-Hatmi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman;
- Centre of Expertise in Mycology Radboudumc/CWZ, Radboudumc Center for Infectious Diseases (RCI), 6252 AG Nijmegen, The Netherlands; (R.J.M.B.); (S.d.H.)
- Foundation Atlas of Clinical Fungi, 1214 GP Hilversum, The Netherlands
| | - Roger J. M. Brüggemann
- Centre of Expertise in Mycology Radboudumc/CWZ, Radboudumc Center for Infectious Diseases (RCI), 6252 AG Nijmegen, The Netherlands; (R.J.M.B.); (S.d.H.)
- Department of Pharmacy, Radboud University Medical Center, 6252 AG Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, 6252 AG Nijmegen, The Netherlands; (F.Z.D.); (W.J.G.M.); (P.E.V.)
- Centre of Expertise in Mycology Radboudumc/CWZ, Radboudumc Center for Infectious Diseases (RCI), 6252 AG Nijmegen, The Netherlands; (R.J.M.B.); (S.d.H.)
| | - Sybren de Hoog
- Centre of Expertise in Mycology Radboudumc/CWZ, Radboudumc Center for Infectious Diseases (RCI), 6252 AG Nijmegen, The Netherlands; (R.J.M.B.); (S.d.H.)
- Foundation Atlas of Clinical Fungi, 1214 GP Hilversum, The Netherlands
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboud University Medical Centre, 6252 AG Nijmegen, The Netherlands; (F.Z.D.); (W.J.G.M.); (P.E.V.)
- Centre of Expertise in Mycology Radboudumc/CWZ, Radboudumc Center for Infectious Diseases (RCI), 6252 AG Nijmegen, The Netherlands; (R.J.M.B.); (S.d.H.)
| | - Jochem B. Buil
- Department of Medical Microbiology, Radboud University Medical Centre, 6252 AG Nijmegen, The Netherlands; (F.Z.D.); (W.J.G.M.); (P.E.V.)
- Centre of Expertise in Mycology Radboudumc/CWZ, Radboudumc Center for Infectious Diseases (RCI), 6252 AG Nijmegen, The Netherlands; (R.J.M.B.); (S.d.H.)
- Correspondence: ; Tel.: +31-24-361-4356
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31
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Hartog GD, Ederveen THA, Venkatasubramanian PB, Ferwerda G, van den Kieboom CH, van der Gaast-de Jongh CE, Vissers M, Zoll J, Melchers WJG, Huynen MA, Rots N, Rahamat-Langendoen J, de Jonge MI. Chemokine profiling in children and adults with symptomatic and asymptomatic respiratory viral infections. J Infect 2021; 83:709-737. [PMID: 34715239 DOI: 10.1016/j.jinf.2021.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 10/20/2022]
Abstract
Molecular diagnosis; Viral infection; Chemokines; Disease prognosis; CXCL10; CXCL11; CCL3; CCL4; CCL5; Random forest.
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Affiliation(s)
- G Den Hartog
- Centre for Immunology of Infectious Diseases and Vaccination, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, the Netherlands.
| | - T H A Ederveen
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - P B Venkatasubramanian
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - G Ferwerda
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - C H van den Kieboom
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - C E van der Gaast-de Jongh
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - M Vissers
- Centre for Immunology of Infectious Diseases and Vaccination, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, the Netherlands
| | - J Zoll
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands; Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - W J G Melchers
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands; Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - M A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - N Rots
- Centre for Immunology of Infectious Diseases and Vaccination, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, the Netherlands
| | - J Rahamat-Langendoen
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands; Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - M I de Jonge
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
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32
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Coolen JPM, Wolters F, Tostmann A, van Groningen LFJ, Bleeker-Rovers CP, Tan ECTH, van der Geest-Blankert N, Hautvast JLA, Hopman J, Wertheim HFL, Rahamat-Langendoen JC, Storch M, Melchers WJG. SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis. J Clin Virol 2021; 144:104993. [PMID: 34619382 PMCID: PMC8487099 DOI: 10.1016/j.jcv.2021.104993] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/21/2021] [Accepted: 09/29/2021] [Indexed: 12/28/2022]
Abstract
During the course of the SARS-CoV-2 pandemic reports of mutations with effects on spreading and vaccine effectiveness emerged. Large scale mutation analysis using rapid SARS-CoV-2 Whole Genome Sequencing (WGS) is often unavailable but could support public health organizations and hospitals in monitoring transmission and rising levels of mutant strains. Here we report a novel WGS technique for SARS-CoV-2, the EasySeq™ RC-PCR SARS-CoV-2 WGS kit. By applying a reverse complement polymerase chain reaction (RC-PCR), an Illumina library preparation is obtained in a single PCR, thereby saving time, resources and facilitating high-throughput screening. Using this WGS technique, we evaluated SARS-CoV-2 diversity and possible transmission within a group of 173 patients and healthcare workers (HCW) of the Radboud university medical center during 2020. Due to the emergence of variants of concern, we screened SARS-CoV-2 positive samples in 2021 for identification of mutations and lineages. With use of EasySeq™ RC-PCR SARS-CoV-2 WGS kit we were able to obtain reliable results to confirm outbreak clusters and additionally identify new previously unassociated links in a considerably easier workaround compared to current methods. Furthermore, various SARS-CoV-2 variants of interest were detected among samples and validated against an Oxford Nanopore sequencing amplicon strategy which illustrates this technique is suitable for surveillance and monitoring current circulating variants.
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Affiliation(s)
- Jordy P M Coolen
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands.
| | - Femke Wolters
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Alma Tostmann
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | | | - Chantal P Bleeker-Rovers
- Department of Internal Medicine, division of Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Edward C T H Tan
- Department of Emergency Medicine, Radboud university medical center, Nijmegen, The Netherlands; Department of Surgery, Radboud university medical center, Nijmegen, The Netherlands
| | | | | | - Joost Hopman
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Heiman F L Wertheim
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Janette C Rahamat-Langendoen
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Marko Storch
- London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 84 Wood Lane, London, W12 0BZ, United Kingdom of Great Britain and Northern Ireland, United Kingdom
| | - Willem J G Melchers
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
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33
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Verhoef L, Bleeker MCG, Polman N, Steenbergen RDM, Meijer CJLM, Melchers WJG, Bekkers RL, Molijn AC, Quint WG, van Kemenade FJ, Berkhof J, Heideman DAM. Performance of DNA methylation analysis of ASCL1, LHX8, ST6GALNAC5, GHSR, ZIC1 and SST for the triage of HPV-positive women: Results from a Dutch primary HPV-based screening cohort. Int J Cancer 2021; 150:440-449. [PMID: 34558659 PMCID: PMC9293097 DOI: 10.1002/ijc.33820] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 05/18/2021] [Revised: 08/17/2021] [Accepted: 08/31/2021] [Indexed: 01/12/2023]
Abstract
Methylation of host‐cell deoxyribonucleic acid (DNA) has been proposed as a promising biomarker for triage of high‐risk (hr) human papillomavirus (HPV) positive women at screening. Our study aims to validate recently identified host‐cell DNA methylation markers for triage in an hrHPV‐positive cohort derived from primary HPV‐based cervical screening in The Netherlands. Methylation markers ASCL1, LHX8, ST6GALNAC5, GHSR, ZIC1 and SST were evaluated relative to the ACTB reference gene by multiplex quantitative methylation‐specific PCR (qMSP) in clinician‐collected cervical samples (n = 715) from hrHPV‐positive women (age 29‐60 years), who were enrolled in the Dutch IMPROVE screening trial (NTR5078). Primary clinical end‐point was cervical intraepithelial neoplasia grade 3 (CIN3) or cancer (CIN3+). The single‐marker and bi‐marker methylation classifiers developed for CIN3 detection in a previous series of hrHPV‐positive clinician‐collected cervical samples were applied. The diagnostic accuracy was visualised using receiver operating characteristic (ROC) curves and assessed through area under the ROC curve (AUC). The performance of the methylation markers to detect CIN3+ was determined using the predefined threshold calibrated at 70% clinical specificity. Individual methylation makers showed good performance for CIN3+ detection, with highest AUC for ASCL1 (0.844) and LHX8 (0.830). Combined as a bi‐marker panel with predefined threshold, ASCL1/LHX8 yielded a CIN3+ sensitivity of 76.9% (70/91; 95% CI 68.3‐85.6%) at a specificity of 74.5% (465/624; 95% CI 71.1‐77.9%). In conclusion, our study shows that the individual host‐cell DNA methylation classifiers and the bi‐marker panel ASCL1/LHX8 have clinical utility for the detection of CIN3+ in hrHPV‐positive women invited for routine screening.
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Affiliation(s)
- Lisanne Verhoef
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Maaike C G Bleeker
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Nicole Polman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Chris J L M Meijer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Willem J G Melchers
- Radboud University Medical Center, Medical Microbiology, Nijmegen, The Netherlands
| | - Ruud L Bekkers
- GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands.,Department of Obstetrics and Gynaecology, Catharina Hospital, Eindhoven, The Netherlands
| | - Anco C Molijn
- DDL Diagnostic Laboratory, NMDL-LCPL, Rijswijk, The Netherlands
| | - Wim G Quint
- DDL Diagnostic Laboratory, NMDL-LCPL, Rijswijk, The Netherlands
| | | | - Johannes Berkhof
- Amsterdam UMC, Vrije Universiteit Amsterdam, Epidemiology and Data Science, Amsterdam, The Netherlands
| | - Daniëlle A M Heideman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
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34
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Brandão J, Gangneux JP, Arikan-Akdagli S, Barac A, Bostanaru AC, Brito S, Bull M, Çerikçioğlu N, Chapman B, Efstratiou MA, Ergin Ç, Frenkel M, Gitto A, Gonçalves CI, Guégan H, Gunde-Cimerman N, Güran M, Irinyi L, Jonikaitė E, Kataržytė M, Klingspor L, Mares M, Meijer WG, Melchers WJG, Meletiadis J, Meyer W, Nastasa V, Babič MN, Ogunc D, Ozhak B, Prigitano A, Ranque S, Rusu RO, Sabino R, Sampaio A, Silva S, Stephens JH, Tehupeiory-Kooreman M, Tortorano AM, Velegraki A, Veríssimo C, Wunderlich GC, Segal E. Mycosands: Fungal diversity and abundance in beach sand and recreational waters - Relevance to human health. Sci Total Environ 2021; 781:146598. [PMID: 33812107 DOI: 10.1016/j.scitotenv.2021.146598] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
The goal of most studies published on sand contaminants is to gather and discuss knowledge to avoid faecal contamination of water by run-offs and tide-retractions. Other life forms in the sand, however, are seldom studied but always pointed out as relevant. The Mycosands initiative was created to generate data on fungi in beach sands and waters, of both coastal and freshwater inland bathing sites. A team of medical mycologists and water quality specialists explored the sand culturable mycobiota of 91 bathing sites, and water of 67 of these, spanning from the Atlantic to the Eastern Mediterranean coasts, including the Italian lakes and the Adriatic, Baltic, and Black Seas. Sydney (Australia) was also included in the study. Thirteen countries took part in the initiative. The present study considered several fungal parameters (all fungi, several species of the genus Aspergillus and Candida and the genera themselves, plus other yeasts, allergenic fungi, dematiaceous fungi and dermatophytes). The study considered four variables that the team expected would influence the results of the analytical parameters, such as coast or inland location, urban and non-urban sites, period of the year, geographical proximity and type of sediment. The genera most frequently found were Aspergillus spp., Candida spp., Fusarium spp. and Cryptococcus spp. both in sand and in water. A site-blind median was found to be 89 Colony-Forming Units (CFU) of fungi per gram of sand in coastal and inland freshwaters, with variability between 0 and 6400 CFU/g. For freshwater sites, that number was 201.7 CFU/g (0, 6400 CFU/g (p = 0.01)) and for coastal sites was 76.7 CFU/g (0, 3497.5 CFU/g). For coastal waters and all waters, the median was 0 CFU/ml (0, 1592 CFU/ml) and for freshwaters 6.7 (0, 310.0) CFU/ml (p < 0.001). The results advocate that beaches should be monitored for fungi for safer use and better management.
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Affiliation(s)
- J Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; Centre for Environmental and Marine Studies (CESAM) - Department of Animal Biology, University of Lisbon, Lisbon, Portugal.
| | - J P Gangneux
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - S Arikan-Akdagli
- Mycology Laboratory at Department of Medical Microbiology of Hacettepe University Medical School, Ankara, Turkey
| | - A Barac
- Clinical Centre of Serbia, Clinic for Infectious and Tropical Diseases, Faculty of Medicine, University of Belgrade, Serbia
| | - A C Bostanaru
- Ion Ionescu de la Brad University of Agricultural Sciences and Veterinary Medicine of Iasi, Romania
| | - S Brito
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - M Bull
- Quantal Bioscience, North Parramatta, Australia
| | - N Çerikçioğlu
- Mycology Laboratory at Department of Medical Microbiology of Marmara University Medical School, Istanbul, Turkey
| | - B Chapman
- Quantal Bioscience, North Parramatta, Australia
| | - M A Efstratiou
- Department of Marine Sciences, University of the Aegean, University Hill, Mytilene, Greece
| | - Ç Ergin
- Department of Medical Microbiology, Medical Faculty, Pamukkale University, Denizli, Turkey
| | - M Frenkel
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - A Gitto
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Ireland; UCD Earth Institute, University College Dublin, Ireland; UCD Conway Institute, University College Dublin, Ireland
| | - C I Gonçalves
- Department of Biology and Environment, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - H Guégan
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - N Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Slovenia
| | - M Güran
- Faculty of Medicine, Eastern Mediterranean University, Famagusta, Northern Cyprus, Mersin 10, Turkey
| | - L Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Disease and Microbiology, Sydney Medical School, Westmead Clinical School, Westmead Hospital, Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, Westmead Institute for Medical Research, The University of Sydney, Westmead, Australia
| | - E Jonikaitė
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
| | - M Kataržytė
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
| | - L Klingspor
- Division of Clinical Microbiology, Department of Laboratory Medicin, Karolinska Institutet, Stockholm, Sweden
| | - M Mares
- Ion Ionescu de la Brad University of Agricultural Sciences and Veterinary Medicine of Iasi, Romania
| | - W G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Ireland; UCD Earth Institute, University College Dublin, Ireland; UCD Conway Institute, University College Dublin, Ireland
| | - W J G Melchers
- Medical Microbiology, Radboud University Medical Centre (Radboudumc), Nijmegen, the Netherlands
| | - J Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - W Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Disease and Microbiology, Sydney Medical School, Westmead Clinical School, Westmead Hospital, Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, Westmead Institute for Medical Research, The University of Sydney, Westmead, Australia
| | - V Nastasa
- Ion Ionescu de la Brad University of Agricultural Sciences and Veterinary Medicine of Iasi, Romania
| | - M Novak Babič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Slovenia
| | - D Ogunc
- Department of Medical Microbiology, Akdeniz University Medical School, Antalya, Turkey
| | - B Ozhak
- Department of Medical Microbiology, Akdeniz University Medical School, Antalya, Turkey
| | - A Prigitano
- Department of Biomedical Sciences for Health, Università Degli Studi di Milano, Milan, Italy
| | - S Ranque
- Aix Marseille Univ, IHU-Méditerranée Infection, AP-HM, IRD, SSA, VITROME, Marseille, France
| | - R O Rusu
- Ion Ionescu de la Brad University of Agricultural Sciences and Veterinary Medicine of Iasi, Romania
| | - R Sabino
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - A Sampaio
- Department of Biology and Environment, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), UTAD, Vila Real, Portugal
| | - S Silva
- Department of Epidemiology, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - J H Stephens
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Ireland; UCD Earth Institute, University College Dublin, Ireland; UCD Conway Institute, University College Dublin, Ireland
| | - M Tehupeiory-Kooreman
- Medical Microbiology, Radboud University Medical Centre (Radboudumc), Nijmegen, the Netherlands
| | - A M Tortorano
- Department of Biomedical Sciences for Health, Università Degli Studi di Milano, Milan, Italy
| | - A Velegraki
- Mycology Research Laboratory and UOA/HCPF Culture Collection, Microbiology Department, Medical School, National and Kapodistrian University of Athens, Athens, Greece and Mycology Laboratory, BIOMEDICINE S.A., Athens, Greece
| | - C Veríssimo
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - G C Wunderlich
- Quantal Bioscience, North Parramatta, Australia; Molecular Mycology Research Laboratory, Centre for Infectious Disease and Microbiology, Sydney Medical School, Westmead Clinical School, Westmead Hospital, Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, Westmead Institute for Medical Research, The University of Sydney, Westmead, Australia
| | - E Segal
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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Buil JB, Brüggemann RJM, Bedin Denardi L, Melchers WJG, Verweij PE. In vitro interaction of isavuconazole and anidulafungin against azole-susceptible and azole-resistant Aspergillus fumigatus isolates. J Antimicrob Chemother 2021; 75:2582-2586. [PMID: 32516368 PMCID: PMC7443724 DOI: 10.1093/jac/dkaa185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 11/25/2019] [Revised: 02/24/2020] [Accepted: 04/15/2020] [Indexed: 01/01/2023] Open
Abstract
Background The voriconazole and echinocandin combination has been found to be synergistic in vitro and in vivo against most Aspergillus fumigatus isolates, both with a WT azole phenotype and an azole-resistant phenotype. The interaction between isavuconazole and echinocandins is less well studied. This is especially true for azole-resistant isolates. Objectives We investigated the in vitro interaction between isavuconazole and anidulafungin for 30 A. fumigatus isolates including 18 azole-resistant isolates with various isavuconazole resistance phenotypes. Methods The isavuconazole/anidulafungin interaction was studied by using an adapted EUCAST-based 2D (12 × 8) chequerboard broth microdilution colorimetric assay using XTT. The interaction was analysed by FIC index (FICi) analysis and Bliss independence (BI) interaction analysis. Results Both the FICi analysis and the BI analysis showed synergistic interaction between isavuconazole and anidulafungin for the majority of WT and azole-resistant isolates. As we did not see significant beneficial effects of combination therapy in TR46/Y121F/T289A isolates at clinically achievable drug concentrations, it is unlikely that TR46/Y121F/T289A infections would benefit from isavuconazole and anidulafungin combination therapy. Conclusions In regions with high azole resistance rates this combination may benefit patients with WT disease, azole-resistant invasive aspergillosis and those with mixed azole-susceptible and azole-resistant infection, but may not be beneficial for aspergillosis due to isolates with high isavuconazole resistance, such as TR46/Y121F/T289A isolates.
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Affiliation(s)
- J B Buil
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - R J M Brüggemann
- Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands.,Department of Pharmacy, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L Bedin Denardi
- Programa de Pós-Graduação em Ciências Farmacêuticas, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Santa Maria, RS, Brasil
| | - W J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - P E Verweij
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
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36
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Lestrade PPA, Buil JB, van der Beek MT, Kuijper EJ, van Dijk K, Kampinga GA, Rijnders BJA, Vonk AG, de Greeff SC, Schoffelen AF, van Dissel J, Meis JF, Melchers WJG, Verweij PE. Paradoxal Trends in Azole-Resistant Aspergillus fumigatus in a National Multicenter Surveillance Program, the Netherlands, 2013-2018. Emerg Infect Dis 2021; 26:1447-1455. [PMID: 32568033 PMCID: PMC7323544 DOI: 10.3201/eid2607.200088] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We investigated the prevalence of azole resistance of Aspergillus fumigatus isolates in the Netherlands by screening clinical A. fumigatus isolates for azole resistance during 2013-2018. We analyzed azole-resistant isolates phenotypically by in vitro susceptibility testing and for the presence of resistance mutations in the Cyp51A gene. Over the 6-year period, 508 (11%) of 4,496 culture-positive patients harbored an azole-resistant isolate. Resistance frequency increased from 7.6% (95% CI 5.9%-9.8%) in 2013 (58/760 patients) to 14.7% (95% CI 12.3%-17.4%) in 2018 (112/764 patients) (p = 0.0001). TR34/L98H (69%) and TR46/Y121F/T289A (17%) accounted for 86% of Cyp51A mutations. However, the mean voriconazole MIC of TR34/L98H isolates decreased from 8 mg/L (2013) to 2 mg/L (2018), and the voriconazole-resistance frequency was 34% lower in 2018 than in 2013 (p = 0.0001). Our survey showed changing azole phenotypes in TR34/L98H isolates, which hampers the use of current PCR-based resistance tests.
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Wolters F, Grünberg M, Huber M, Kessler HH, Prüller F, Saleh L, Fébreau C, Rahamat-Langendoen J, Thibault V, Melchers WJG. European multicenter evaluation of Xpert® Xpress SARS-CoV-2/Flu/RSV test. J Med Virol 2021; 93:5798-5804. [PMID: 34050951 PMCID: PMC8242864 DOI: 10.1002/jmv.27111] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/07/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023]
Abstract
Rapid diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) are paramount for reducing the spread of the current pandemic. During additional seasonal epidemics with influenza A/B and respiratory syncytial virus (RSV), the clinical signs and symptoms cannot be distinguished easily from SARS‐CoV‐2. Therefore, a new assay combining four targets in the form of the new Xpert Xpress SARS‐CoV‐2/Flu/RSV assay was evaluated. The assay was compared to the Xpert Xpress SARS‐CoV‐2, Xpert Xpress Flu/RSV, Seegene Flu/RSV, influenza A/B r‐gene® and RSV/hMPV r‐gene®. A total of 295 nasopharyngeal and throat swabs were tested at four institutes throughout Europe including 72 samples positive for SARS‐CoV‐2, 65 for influenza A, 47 for influenza B, and 77 for RSV. The sensitivity of the new assay was above 95% for all targets, with the highest for SARS‐CoV‐2 (97.2%). The overall correlation of SARS‐CoV‐2 Ct values between Xpert Xpress SARS‐CoV‐2 assay and Xpert Xpress SARS‐CoV‐2/Flu/RSV assay was high. The agreement between Ct values above 30 showed the multiplex giving higher Ct values for SARS‐CoV‐2 on average than the singleplex assay. In conclusion, the new assay is a rapid and reliable alternative with less hands‐on time for the detection of not one, but four upper respiratory tract pathogens that may circulate at the same time.
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Affiliation(s)
- Femke Wolters
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maria Grünberg
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Harald H Kessler
- Molecular Diagnostics Laboratory, Diagnostic and Research Institute of Hygiene, Microbiology, and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Florian Prüller
- Clinical Institute of Medical and Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Lanja Saleh
- Institute of Clinical Chemistry, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Christine Fébreau
- Department of Virology, University Hospital of Rennes, Rennes, France
| | | | - Vincent Thibault
- Department of Virology, University Hospital of Rennes, Rennes, France
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
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Gits-Muselli M, White PL, Mengoli C, Chen S, Crowley B, Dingemans G, Fréalle E, L Gorton R, Guiver M, Hagen F, Halliday C, Johnson G, Lagrou K, Lengerova M, Melchers WJG, Novak-Frazer L, Rautemaa-Richardson R, Scherer E, Steinmann J, Cruciani M, Barnes R, Donnelly JP, Loeffler J, Bretagne S, Alanio A. The Fungal PCR Initiative's evaluation of in-house and commercial Pneumocystis jirovecii qPCR assays: Toward a standard for a diagnostics assay. Med Mycol 2021; 58:779-788. [PMID: 31758173 DOI: 10.1093/mmy/myz115] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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: 05/27/2019] [Revised: 10/22/2019] [Accepted: 10/31/2019] [Indexed: 01/04/2023] Open
Abstract
Quantitative real-time PCR (qPCR) is increasingly used to detect Pneumocystis jirovecii for the diagnosis of Pneumocystis pneumonia (PCP), but there are differences in the nucleic acids targeted, DNA only versus whole nucleic acid (WNA), and also the target genes for amplification. Through the Fungal PCR Initiative, a working group of the International Society for Human and Animal Mycology, a multicenter and monocenter evaluation of PCP qPCR assays was performed. For the multicenter study, 16 reference laboratories from eight different countries, performing 20 assays analyzed a panel consisting of two negative and three PCP positive samples. Aliquots were prepared by pooling residual material from 20 negative or positive- P. jirovecii bronchoalveolar lavage fluids (BALFs). The positive pool was diluted to obtain three concentrations (pure 1:1; 1:100; and 1:1000 to mimic high, medium, and low fungal loads, respectively). The monocenter study compared five in-house and five commercial qPCR assays testing 19 individual BALFs on the same amplification platform. Across both evaluations and for all fungal loads, targeting WNA and the mitochondrial small sub-unit (mtSSU) provided the earliest Cq values, compared to only targeting DNA and the mitochondrial large subunit, the major surface glycoprotein or the beta-tubulin genes. Thus, reverse transcriptase-qPCR targeting the mtSSU gene could serve as a basis for standardizing the P. jirovecii load, which is essential if qPCR is to be incorporated into clinical care pathways as the reference method, accepting that additional parameters such as amplification platforms still need evaluation.
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Affiliation(s)
- Maud Gits-Muselli
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, Paris, France.,Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, Paris, France
| | - P Lewis White
- Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, UK
| | | | - Sharon Chen
- Clinical Mycology reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, and the University of Sydney, Australia
| | - Brendan Crowley
- Department of Virology, St James's Hospital, Dublin, Ireland
| | | | - Emilie Fréalle
- CHU Lille, Laboratoire de Parasitologie-Mycologie, F-59000 Lille, France & Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Centre for Infection and Immunity of Lille, F-59000 Lille, France
| | - Rebecca L Gorton
- Regional UK Clinical Mycology Network (UK CMN) Laboratory, Dept. Infection Sciences, Health Services Laboratories (HSL) LLP, London, UK
| | - Malcom Guiver
- Public Health Laboratory, National Infection Service Public Health England, Manchester University NHS Foundation Trust, Manchester, UK
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands.,Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Catriona Halliday
- Clinical Mycology reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, and the University of Sydney, Australia
| | | | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, KU Leuven, and Department of Laboratory Medicine and National Reference Centre for Mycosis, Excellence Centre for Medical Mycology (ECMM), University Hospitals Leuven, Leuven, Belgium
| | - Martina Lengerova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Willem J G Melchers
- Radboud University Medical Centre, Department of Medical Microbiology, Nijmegen, The Netherlands
| | - Lily Novak-Frazer
- Mycology Reference Centre Manchester, Manchester University NHS Foundation Trust; and Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Riina Rautemaa-Richardson
- Department of Infectious Diseases and the Mycology Reference Centre Manchester, Manchester University NHS Foundation Trust; and Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Emeline Scherer
- Department of Parasitology-Mycology, University Hospital of Besançon, Besançon, France
| | - Joerg Steinmann
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Klinikum Nürnberg, Paracelsus Medical University, Nuremberg, Germany.,Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Mario Cruciani
- Infectious Diseases Unit, San Bonifacio Hospital, Verona, Italy
| | | | | | - Juergen Loeffler
- University Hospital Wuerzburg, Medical Hospital II, C11, Wuerzburg, Germany
| | - Stéphane Bretagne
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, Paris, France.,Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, Paris, France
| | - Alexandre Alanio
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, Paris, France.,Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, Paris, France
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Buil JB, van Zanten ARH, Bentvelsen RG, Rijpstra TA, Goorhuis B, van der Voort S, Wammes LJ, Janson JA, Melchers M, Heusinkveld M, Melchers WJG, Kuijper EJ, Verweij PE. Case series of four secondary mucormycosis infections in COVID-19 patients, the Netherlands, December 2020 to May 2021. Euro Surveill 2021; 26:2100510. [PMID: 34114540 PMCID: PMC8193993 DOI: 10.2807/1560-7917.es.2021.26.23.2100510] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/10/2021] [Indexed: 12/14/2022] Open
Abstract
We describe four secondary fungal infections caused by Mucorales species in COVID-19 patients. Three COVID-19 associated mucormycosis (CAM) occurred in ICU, one outside ICU. All were men aged > 50 years, three died. Clinical presentations included pulmonary, rhino-orbital cerebral and disseminated infection. Infections occurred in patients with and without diabetes mellitus. CAM is an emerging disease and our observations underscore the need to be aware of invasive mucormycosis, including in COVID-19 patients without (poorly controlled) diabetes mellitus and outside ICU.
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Affiliation(s)
- Jochem B Buil
- Department of Medical Microbiology, Radboud University Medical Center, and Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, the Netherlands
| | | | - Robbert G Bentvelsen
- Microvida Laboratory for Microbiology, Amphia Hospital, Breda, the Netherlands
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tom A Rijpstra
- Department of Intensive Care, Amphia Hospital, Breda, the Netherlands
| | - Bram Goorhuis
- Department of Infectious Diseases, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Sanne van der Voort
- Department of Infectious Diseases, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Linda J Wammes
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jeroen A Janson
- Department of Intensive Care, Leiden University Medical Center, Leiden, the Netherlands
| | - Max Melchers
- Department of Intensive Care, Gelderse Vallei Hospital, Ede, the Netherlands
| | - Moniek Heusinkveld
- Department of Medical Microbiology, Gelderse Vallei Hospital, Ede, the Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, and Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, the Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
- Center for Infectious Disease Research, Diagnostics and Laboratory Surveillance National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Paul E Verweij
- Department of Medical Microbiology, Radboud University Medical Center, and Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, the Netherlands
- Center for Infectious Disease Research, Diagnostics and Laboratory Surveillance National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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40
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Keijmel SP, Kuipers S, van der Jagt MFP, Melchers WJG, Kouijzer IJE, Oever JT. Mycotic aneurysm of the infrarenal abdominal aorta infected by Mycoplasma hyorhinis diagnosed with direct 16S ribosomal DNA sequencing. Clin Microbiol Infect 2021; 27:1356-1357. [PMID: 33901664 DOI: 10.1016/j.cmi.2021.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/06/2021] [Accepted: 04/13/2021] [Indexed: 10/21/2022]
Affiliation(s)
- Stephan P Keijmel
- Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Medical Centre, Nijmegen, the Netherlands.
| | - Saskia Kuipers
- Department of Medical Microbiology and Radboud Centre for Infectious Diseases, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Michel F P van der Jagt
- Department of Vascular and Transplant Surgery, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology and Radboud Centre for Infectious Diseases, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Ilse J E Kouijzer
- Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Jaap Ten Oever
- Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Medical Centre, Nijmegen, the Netherlands.
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Coolen JPM, den Drijver EPM, Verweij JJ, Schildkraut JA, Neveling K, Melchers WJG, Kolwijck E, Wertheim HFL, Kluytmans JAJW, Huynen MA. Genome-wide analysis in Escherichia coli unravels a high level of genetic homoplasy associated with cefotaxime resistance. Microb Genom 2021; 7:000556. [PMID: 33843573 PMCID: PMC8208684 DOI: 10.1099/mgen.0.000556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 03/11/2021] [Indexed: 11/18/2022] Open
Abstract
Cefotaxime (CTX) is a third-generation cephalosporin (3GC) commonly used to treat infections caused by Escherichia coli. Two genetic mechanisms have been associated with 3GC resistance in E. coli. The first is the conjugative transfer of a plasmid harbouring antibiotic-resistance genes. The second is the introduction of mutations in the promoter region of the ampC β-lactamase gene that cause chromosome-encoded β-lactamase hyperproduction. A wide variety of promoter mutations related to AmpC hyperproduction have been described. However, their link to CTX resistance has not been reported. We recultured 172 cefoxitin-resistant E. coli isolates with known CTX minimum inhibitory concentrations and performed genome-wide analysis of homoplastic mutations associated with CTX resistance by comparing Illumina whole-genome sequencing data of all isolates to a PacBio sequenced reference chromosome. We mapped the mutations on the reference chromosome and determined their occurrence in the phylogeny, revealing extreme homoplasy at the -42 position of the ampC promoter. The 24 occurrences of a T at the -42 position rather than the wild-type C, resulted from 18 independent C>T mutations in five phylogroups. The -42 C>T mutation was only observed in E. coli lacking a plasmid-encoded ampC gene. The association of the -42 C>T mutation with CTX resistance was confirmed to be significant (false discovery rate <0.05). To conclude, genome-wide analysis of homoplasy in combination with CTX resistance identifies the -42 C>T mutation of the ampC promotor as significantly associated with CTX resistance and underlines the role of recurrent mutations in the spread of antibiotic resistance.
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Affiliation(s)
- Jordy P. M. Coolen
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Evert P. M. den Drijver
- Department of Infection Control, Amphia Ziekenhuis, Breda, The Netherlands
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - Jaco J. Verweij
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - Jodie A. Schildkraut
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eva Kolwijck
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heiman F. L. Wertheim
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan A. J. W. Kluytmans
- Department of Infection Control, Amphia Ziekenhuis, Breda, The Netherlands
- Laboratory for Microbiology, Microvida, Breda, The Netherlands
- Julius Center for Health Sciences and Primary Care, UMCU, Utrecht, The Netherlands
| | - Martijn A. Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
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Baltussen TJH, Coolen JPM, Verweij PE, Dijksterhuis J, Melchers WJG. Identifying Conserved Generic Aspergillus spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics. J Fungi (Basel) 2021; 7:270. [PMID: 33916245 PMCID: PMC8067318 DOI: 10.3390/jof7040270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 02/22/2021] [Revised: 03/27/2021] [Accepted: 03/29/2021] [Indexed: 12/26/2022] Open
Abstract
Aspergillus spp. is an opportunistic human pathogen that may cause a spectrum of pulmonary diseases. In order to establish infection, inhaled conidia must germinate, whereby they break dormancy, start to swell, and initiate a highly polarized growth process. To identify critical biological processes during germination, we performed a cross-platform, cross-species comparative analysis of germinating A. fumigatus and A. niger conidia using transcriptional data from published RNA-Seq and Affymetrix studies. A consensus co-expression network analysis identified four gene modules associated with stages of germination. These modules showed numerous shared biological processes between A. niger and A. fumigatus during conidial germination. Specifically, the turquoise module was enriched with secondary metabolism, the black module was highly enriched with protein synthesis, the darkgreen module was enriched with protein fate, and the blue module was highly enriched with polarized growth. More specifically, enriched functional categories identified in the blue module were vesicle formation, vesicular transport, tubulin dependent transport, actin-dependent transport, exocytosis, and endocytosis. Genes important for these biological processes showed similar expression patterns in A. fumigatus and A. niger, therefore, they could be potential antifungal targets. Through cross-platform, cross-species comparative analysis, we were able to identify biologically meaningful modules shared by A. fumigatus and A. niger, which underscores the potential of this approach.
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Affiliation(s)
- Tim J. H. Baltussen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
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Loopik DL, Koenjer LM, Siebers AG, Melchers WJG, Bekkers RLM. Benefit and burden in the Dutch cytology-based vs high-risk human papillomavirus-based cervical cancer screening program. Am J Obstet Gynecol 2021; 224:200.e1-200.e9. [PMID: 32800820 DOI: 10.1016/j.ajog.2020.08.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 04/22/2020] [Revised: 07/16/2020] [Accepted: 08/11/2020] [Indexed: 01/11/2023]
Abstract
BACKGROUND In 2017, the Dutch cervical cancer screening program had replaced the primary cytology-based screening with primary high-risk human papillomavirus-based screening, including the opportunity to participate through self-sampling. Evaluation and balancing benefit (detection of high-grade cervical intraepithelial neoplasia) and burden of screening (unnecessary referrals, invasive diagnostics, and overtreatment) is needed. OBJECTIVE This study aimed to compare the referral rates, detection of high-grade cervical intraepithelial neoplasia, overdiagnosis, and overtreatment in the new high-risk human papillomavirus-based screening program, including physician-sampled and self-sampled material, with the previous cytology-based screening program in the Netherlands. STUDY DESIGN A retrospective cohort study was conducted within the Dutch population-based cervical cancer screening program. Screenees with referrals for colposcopy between 2014 and 2015 (cytology-based screening) and 2017 and 2018 (high-risk human papillomavirus-based screening) were included. Data were retrieved from the Dutch Pathology Registry (PALGA) and compared between the 2 screening programs. The main outcome measures were referral rate, detection of high-grade cervical intraepithelial neoplasia or worse, overdiagnosis (cervical intraepithelial neoplasia grade 1 or less in the histologic specimen), and overtreatment (cervical intraepithelial neoplasia grade 1 or less in the treatment specimen). RESULTS Of the women included in the study, 19,109 received cytology-based screening, and 26,171 received high-risk human papillomavirus-based screening. Referral rates increased from 2.5% in cytology-based screening to 4.2% in high-risk human papillomavirus-based screening (+70.2%). Detection rates increased to 46.2% for cervical intraepithelial neoplasia grade 2 or worse, 32.2% for cervical intraepithelial neoplasia grade 3 or worse, and 31.0% for cervical cancer, and overdiagnosis increased to 143.4% with high-risk human papillomavirus-based screening. Overtreatment rates were similar in both screening periods. The positive predictive value of referral for detection of cervical intraepithelial neoplasia grade 2 or worse in high-risk human papillomavirus-based screening was 34.6% compared with 40.2% in cytology-based screening. Women screened through self-sampling were at higher risk of cervical intraepithelial neoplasia grade 2 or worse detection (odds ratio, 1.38; 95% confidence interval, 1.20-1.59) and receiving treatment (odds ratio, 1.31; 95% confidence interval, 1.16-1.48) than those screened through physician-sampling. CONCLUSION Compared with cytology-based screening, high-risk human papillomavirus-based screening increases detection of high-grade cervical intraepithelial neoplasia, with 462 more cervical intraepithelial neoplasia grade 2 or worse cases per 100,000 women but at the expense of 850 more cases per 100,000 women with invasive diagnostics indicating cervical intraepithelial neoplasia grade 1 or less.
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Affiliation(s)
- Diede L Loopik
- Department of Obstetrics and Gynaecology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Lisanne M Koenjer
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Albert G Siebers
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands; PALGA Foundation, Houten, the Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ruud L M Bekkers
- Department of Obstetrics and Gynaecology, Catharina Hospital, Eindhoven, the Netherlands; Department of Obstetrics and Gynaecology, GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
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Seidel D, Cornely O, Zarrouk M, Koehler P, Meis JF, Salmanton-García J, Vehreschild JJ, Christner M, Gräfe SK, Falces-Romero I, Lagrou K, Maertens J, Reséndiz- Sharpe A, Racil Z, Weinbergerová B, Valerio M, Muñoz P, Blennow O, Rammaert B, Ostojic A, Govic YL, Lass-Flörl C, Rössler S, van Dijk K, de Jong N, Steinmann J, Desoubeaux G, Alakel N, Klimko N, Schalk E, Brenier-Pinchart MP, Garcia-Vidal C, Bergeron A, Cho SY, Melchers WJG, Vehreschild MJGT, Verweij PE. 1598. Clinical implications of azole-resistant vs. azole-susceptible invasive aspergillosis in hematological malignancy (CLARITY) – a multicenter study. Open Forum Infect Dis 2020. [PMCID: PMC7778089 DOI: 10.1093/ofid/ofaa439.1778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/13/2022] Open
Abstract
Abstract
Background
Advances in the survival of patients with invasive aspergillosis (IA) are jeopardized by the emergence of azole resistance in Aspergillus fumigatus, which has been associated with high probability of azole treatment failure. The clinical implications of azole-resistant IA compared to azole-susceptible IA remain unclear. Thus, we seek to describe the epidemiology and to determine the efficacy of antifungal therapy in patients with documented azole-resistant IA compared to azole-susceptible IA in patients with hematological malignancy.
Methods
For proven and probable IA (EORTC/MSG 2019) caused by A. fumigatus in patients with hematological malignancies retrospective data were documented, comprising demographics, diagnosis, treatment, response, and outcome. Sites provided susceptibility results or respective isolates for analysis in a central laboratory.
Results
Sites in 16 countries worldwide enrolled 187 cases diagnosed with IA between 2010 and 2019; 31 (16.6%) were resistant to at least one of the clinical azoles. Fungal isolates were available from 42 cases. A mixed fungal infection was reported for 32 patients (17.1%), most were related to non-fumigatus Aspergillus and non-Aspergillus molds (n=22, 69%). Most patients were male (66.8%) and overall the majority of patients were in the age groups between 50 and 89 years (71%). Amphotericin B was used for treatment in 24 (77%) patients with azole-resistant IA, compared to 76 (49%) in the azole-susceptible group (lipid-based formulation in 98%); only five (16%) patients with azole-resistant IA were treated with an azole alone vs. 57 (36%) of those with azole-susceptible IA. Overall, all-cause mortality rate was higher for patients with azole-resistant compared to azole-susceptible IA (74.2% vs. 53.8%, log rank P=0.004), the 8 patients with an azole-resistant IA treated in the intensive care unit died within 1 month (Figure 1). Details on underlying disease and survival are given in Table 1.
Table 1. Underlying hematological malignancy and clinical outcome of patients with azole-resistant and azole-susceptible invasive aspergillosis
Figure 1. Intensive care unit 1-year survival probability for patients with azole-resistant and azole-susceptible invasive aspergillosis
Conclusion
Azole-resistance in IA is associated with worse outcome, especially in critically ill patients. Susceptibility testing should be considered in patients with a suspected azole-resistant IA to support treatment decisions.
Disclosures
Danila Seidel, PhD, Basilea (Other Financial or Material Support, travel grant) Oliver Cornely, Prof., Actelion (Grant/Research Support)Actelion (Other Financial or Material Support, Personal fees)Al Jazeera Pharmaceuticals (Consultant)Allecra Therapeutics (Other Financial or Material Support, Personal fees)Amplyx (Other Financial or Material Support, Personal fees)Amplyx (Grant/Research Support)Astellas (Grant/Research Support)Astellas (Other Financial or Material Support, Personal fees)Basilea (Other Financial or Material Support, Personal fees)Basilea (Grant/Research Support)Biosys UK Limited (Other Financial or Material Support, Personal fees)Cidara (Other Financial or Material Support, Personal fees)Cidara (Grant/Research Support)Da Volterra (Grant/Research Support)Da Volterra (Other Financial or Material Support, Personal fees)Entasis (Other Financial or Material Support, Personal fees)F2G (Other Financial or Material Support)F2G (Grant/Research Support)Gilead (Grant/Research Support)Gilead (Other Financial or Material Support, Personal fees)Grupo Biotoscana (Other Financial or Material Support, Personal fees)Janssen Pharmaceuticals (Grant/Research Support)Matinas (Other Financial or Material Support, Personal fees)Medicines Company (Grant/Research Support)MedPace (Grant/Research Support)MedPace (Other Financial or Material Support, Personal fees)Melinta Therapeutics (Grant/Research Support)Menarini Ricerche (Other Financial or Material Support, Personal fees)Merck/MSD (Other Financial or Material Support, Personal fees)Merck/MSD (Grant/Research Support)Mylan Pharmaceuticals (Consultant)Nabriva Therapeutics (Other Financial or Material Support, Personal fees)Octapharma (Other Financial or Material Support, Personal fees)Paratek Pharmaceuticals (Other Financial or Material Support, Personal fees)Pfizer (Other Financial or Material Support, Personal fees)Pfizer (Grant/Research Support)PSI (Other Financial or Material Support, Personal fees)Rempex (Other Financial or Material Support, Personal fees)Roche Diagnostics (Other Financial or Material Support, Personal fees)Scynexis (Other Financial or Material Support, Personal fees)Scynexis (Grant/Research Support)Seres Therapeutics (Other Financial or Material Support, Personal fees)Tetraphase (Other Financial or Material Support, Personal fees) Philipp Koehler, MD, Akademie für Infektionsmedizin e.V., (Other Financial or Material Support, Personal fees)Astellas Pharma GmbH (Other Financial or Material Support, Personal fees)Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany (Other Financial or Material Support, Other)Gilead Sciences GmbH (Other Financial or Material Support, Personal fees)GPR Academy Ruesselsheim (Speaker’s Bureau)Miltenyi Biotec GmbH (Other Financial or Material Support, Non-financial support)MSD Sharp & Dohme GmbH (Other Financial or Material Support, Personal fees)Noxxon N.V. (Speaker’s Bureau)University Hospital, LMU Munich (Other Financial or Material Support, Personal fees) Katrien Lagrou, n/a, FUJIFILM WAKO (Speaker’s Bureau)Gilead (Consultant, Speaker’s Bureau)MSD (Consultant, Speaker’s Bureau, Other Financial or Material Support, travel grant)Pfizer (Speaker’s Bureau, travel grant)SMB Laboratoires Brussels (Consultant) Zdenek Racil, n/a, Astellas (Grant/Research Support, Speaker’s Bureau, travel grant) Blandine Rammaert, n/a, Gilead (Speaker’s Bureau, Other Financial or Material Support, travel grant)Merck/MSD (Speaker’s Bureau)Pfizer (Other Financial or Material Support, travel grant) Nikolay Klimko, n/a, Astellas (Speaker’s Bureau)Gilead (Speaker’s Bureau)Merck/MSD (Speaker’s Bureau)Pfizer (Speaker’s Bureau) Sung-Yeon Cho, MD, Gilead (Grant/Research Support, Speaker’s Bureau)Merck Sharp & Dohme (Grant/Research Support, Speaker’s Bureau)Pfizer (Grant/Research Support, Speaker’s Bureau)
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Affiliation(s)
- Danila Seidel
- University Hospital of Cologne, Cologne, Nordrhein-Westfalen, Germany
| | - Oliver Cornely
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Nordrhein-Westfalen, Germany
| | - Marouan Zarrouk
- University Hospital of Cologne, Cologne, Nordrhein-Westfalen, Germany
| | - Philipp Koehler
- University Hospital of Cologne, Cologne, Nordrhein-Westfalen, Germany
| | - Jacques F Meis
- Canisius Wilhelmina Hospital, Nijmegen, The Netherlands, Nijmegen, Gelderland, Netherlands
| | - Jon Salmanton-García
- University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, NRW
| | - Jörg Janne Vehreschild
- University Hospital of Cologne, ECMM Excellence Center, Cologne, Germany, Cologne, Nordrhein-Westfalen, Germany
| | - Martin Christner
- Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany, Hamburg, Hamburg, Germany
| | - Stefanie K Gräfe
- University Hospital of Cologne, ECMM Excellence Center, Cologne, Germany, University of Hamburg, Faculty of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany., Cologne, Nordrhein-Westfalen, Germany
| | | | - Katrien Lagrou
- KU Leuven, Leuven, Belgium, Leuven, Vlaams-Brabant, Belgium
| | - Johan Maertens
- KU Leuven, Leuven, Belgium, Leuven, Vlaams-Brabant, Belgium
| | | | - Zdenek Racil
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic, Prague, Hlavni mesto Praha, Czech Republic
| | - Barbora Weinbergerová
- Faculty Hospital Brno, Brno, Czech Republic, Brno, Hlavni mesto Praha, Czech Republic
| | - Maricela Valerio
- Hospital General Universitario Gregorio Marañón. Clinical Microbiology and Infectious Diseases Department. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Madrid, Spain
| | - Patricia Muñoz
- Hospital General Universitario Gregorio Marañón. Clinical Microbiology and Infectious Diseases Department, Madrid, Spain, Madrid, Madrid, Spain
| | - Ola Blennow
- Karolinska University Hospital, Stockholm, Stockholms Lan, Sweden
| | - Blandine Rammaert
- CHU Poitiers, Infectious Disease, Poitiers, France, Poitier, Poitou-Charentes, France
| | - Alen Ostojic
- University Hospital Centre Zagreb, Zagreb, Croatia, Zagreb, Zagrebacka, Croatia
| | - Yohann Le Govic
- University Hospital Angers, Angers, France, Angers, Nord-Pas-de-Calais, France
| | | | - Susann Rössler
- Technische Universität Dresden, Institute of Medical Microbiology and Hygiene, Dresden, Germany, Dresden, Sachsen, Germany
| | - Karin van Dijk
- Amsterdam UMC, location VUmc, The Netherlands, Amsterdam, Noord-Holland, Netherlands
| | - Nick de Jong
- Amsterdam UMC, location VUmc, The Netherlands, Amsterdam, Noord-Holland, Netherlands
| | - Jörg Steinmann
- Paracelsus Medical University, Nuremberg, Bayern, Germany
| | | | - Nael Alakel
- University Hospital Dresden, Dresden, Sachsen, Germany
| | - Nikolay Klimko
- North-Western State Medical University named after I.I. Mechnikov, St. Petersburg, Adygeya, Russia
| | - Enrico Schalk
- Otto-von-Guericke University, Magdeburg, Thuringen, Germany
| | | | - Carolina Garcia-Vidal
- Hospital Clinic, Department of Hematology, Barcelona, Spain, Barcelona, Catalonia, Spain
| | - Anne Bergeron
- Université Paris Diderot, APHP Saint-Louis Hospital, Paris, France, Paris, Ile-de-France, France
| | - Sung-Yeon Cho
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea, Seoul, Seoul-t’ukpyolsi, Republic of Korea
| | - Willem J G Melchers
- Radboud University Medical Center, Nijmegen, The Netherlands, Nijmegen, Noord-Holland, Netherlands
| | | | - Paul E Verweij
- Radboud University Medical Center, Nijmegen, The Netherlands, Nijmegen, Noord-Holland, Netherlands
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Visser WCH, de Jong H, Melchers WJG, Mulders PFA, Schalken JA. Commercialized Blood-, Urinary- and Tissue-Based Biomarker Tests for Prostate Cancer Diagnosis and Prognosis. Cancers (Basel) 2020; 12:E3790. [PMID: 33339117 PMCID: PMC7765473 DOI: 10.3390/cancers12123790] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 01/24/2023] Open
Abstract
In the diagnosis and prognosis of prostate cancer (PCa), the serum prostate-specific antigen test is widely used but is associated with low specificity. Therefore, blood-, urinary- and tissue-based biomarker tests have been developed, intended to be used in the diagnostic and prognostic setting of PCa. This review provides an overview of commercially available biomarker tests developed to be used in several clinical stages of PCa management. In the diagnostic setting, the following tests can help selecting the right patients for initial and/or repeat biopsy: PHI, 4K, MiPS, SelectMDx, ExoDx, Proclarix, ConfirmMDx, PCA3 and PCMT. In the prognostic setting, the Prolaris, OncotypeDx and Decipher test can help in risk-stratification of patients regarding treatment decisions. Following, an overview is provided of the studies available comparing the performance of biomarker tests. However, only a small number of recently published head-to-head comparison studies are available. In contrast, recent research has focused on the use of biomarker tests in relation to the (complementary) use of multiparametric magnetic resonance imaging in PCa diagnosis.
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Affiliation(s)
- Wieke C. H. Visser
- Department of Product Development, MDxHealth BV, 6534 AT Nijmegen, The Netherlands; (H.d.J.); (W.J.G.M.)
| | - Hans de Jong
- Department of Product Development, MDxHealth BV, 6534 AT Nijmegen, The Netherlands; (H.d.J.); (W.J.G.M.)
| | - Willem J. G. Melchers
- Department of Product Development, MDxHealth BV, 6534 AT Nijmegen, The Netherlands; (H.d.J.); (W.J.G.M.)
- Department of Medical Microbiology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Peter F. A. Mulders
- Department of Urology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands; (P.F.A.M.); (J.A.S.)
| | - Jack A. Schalken
- Department of Urology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands; (P.F.A.M.); (J.A.S.)
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Resendiz-Sharpe A, Hokken MWJ, Mercier T, Merckx R, Verhagen K, Dewitte L, Melchers WJG, Verweij PE, Maertens J, Lagrou K. Hmg1 Gene Mutation Prevalence in Triazole-Resistant Aspergillus fumigatus Clinical Isolates. J Fungi (Basel) 2020; 6:jof6040227. [PMID: 33081232 PMCID: PMC7711918 DOI: 10.3390/jof6040227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 09/01/2020] [Revised: 10/02/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022] Open
Abstract
Recently, mutations in the 3-hydroxy-3-methylglutaryl-coenzyme-A-reductase-encoding gene (hmg1), a gene involved in ergosterol production, were associated with triazole-resistance in Aspergillus fumigatus. In this study, we determined the prevalence and characteristics of hmg1 mutations in a collection of clinical triazole-resistant A. fumigatus isolates collected during 2001–2019 from two international mycology reference centers: the Belgian National Reference Center for Mycosis and the Center of Expertise in Mycology Radboudumc/CWZ. Clinical isolates with and without cyp51A gene mutations and randomly selected wild-type (WT) controls were included. Isolates were characterized by in vitro susceptibility testing, cyp51A and hmg1 sequencing, and short tandem repeat typing. Available clinical records were analyzed for previous triazole exposure. In 23 isolates (24%) of the 95 triazole-resistant A. fumigatus isolates, hmg1 gene mutations were observed; including 5/23 (22%) isolates without cyp51A gene mutations and 18/72 (25%) with cyp51A mutations. Four previously described hmg1 gene mutations (E105K, G307R/D, G466V, and S541G) and two novel mutations (W273S and L304P) were found; 4/23 (17%) in the sterol-sensing-domain region. No triazole-antifungal exposure was reported in 75% (9/12) of patients harboring an isolate with hmg1 gene mutations. Three of 39 WT isolates (8%) contained a hmg1 gene mutation; E105K (2-isolates) and S541G. Hmg1 gene mutations were predominantly found in A. fumigatus with cyp51A mutations with voriconazole MICs ≥ 8 mg/L.
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Affiliation(s)
- Agustin Resendiz-Sharpe
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Bacteriology and Mycology, KU Leuven, 3000 Leuven, Belgium; (A.R.-S.); (T.M.); (R.M.); (L.D.); (J.M.)
| | - Margriet W. J. Hokken
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Radboud Institute for Molecular Life Sciences, 6525 Nijmegen, The Netherlands; (M.W.J.H.); (K.V.); (W.J.G.M.); (P.E.V.)
| | - Toine Mercier
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Bacteriology and Mycology, KU Leuven, 3000 Leuven, Belgium; (A.R.-S.); (T.M.); (R.M.); (L.D.); (J.M.)
- Department of Hematology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Rita Merckx
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Bacteriology and Mycology, KU Leuven, 3000 Leuven, Belgium; (A.R.-S.); (T.M.); (R.M.); (L.D.); (J.M.)
| | - Kamiel Verhagen
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Radboud Institute for Molecular Life Sciences, 6525 Nijmegen, The Netherlands; (M.W.J.H.); (K.V.); (W.J.G.M.); (P.E.V.)
| | - Lisa Dewitte
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Bacteriology and Mycology, KU Leuven, 3000 Leuven, Belgium; (A.R.-S.); (T.M.); (R.M.); (L.D.); (J.M.)
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Radboud Institute for Molecular Life Sciences, 6525 Nijmegen, The Netherlands; (M.W.J.H.); (K.V.); (W.J.G.M.); (P.E.V.)
- Center of Expertise in Mycology, Radboudumc/CWZ, 6525 Nijmegen, The Netherlands
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Radboud Institute for Molecular Life Sciences, 6525 Nijmegen, The Netherlands; (M.W.J.H.); (K.V.); (W.J.G.M.); (P.E.V.)
- Center of Expertise in Mycology, Radboudumc/CWZ, 6525 Nijmegen, The Netherlands
| | - Johan Maertens
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Bacteriology and Mycology, KU Leuven, 3000 Leuven, Belgium; (A.R.-S.); (T.M.); (R.M.); (L.D.); (J.M.)
- Department of Hematology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Bacteriology and Mycology, KU Leuven, 3000 Leuven, Belgium; (A.R.-S.); (T.M.); (R.M.); (L.D.); (J.M.)
- Department of Laboratory Medicine and National Reference Center for Mycosis, Excellence Center for Medical Mycology (ECMM), University Hospitals Leuven, 3000 Leuven, Belgium
- Correspondence: ; Tel.: +32-016-34-70-98
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Lestrade PP, Bentvelsen RG, Schauwvlieghe AFAD, Schalekamp S, van der Velden WJFM, Kuiper EJ, van Paassen J, van der Hoven B, van der Lee HA, Melchers WJG, de Haan AF, van der Hoeven HL, Rijnders BJA, van der Beek MT, Verweij PE. Voriconazole Resistance and Mortality in Invasive Aspergillosis: A Multicenter Retrospective Cohort Study. Clin Infect Dis 2020; 68:1463-1471. [PMID: 30307492 DOI: 10.1093/cid/ciy859] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [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: 05/06/2018] [Accepted: 10/04/2018] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Triazole resistance is an increasing problem in invasive aspergillosis (IA). Small case series show mortality rates of 50%-100% in patients infected with a triazole-resistant Aspergillus fumigatus, but a direct comparison with triazole-susceptible IA is lacking. METHODS A 5-year retrospective cohort study (2011-2015) was conducted to compare mortality in patients with voriconazole-susceptible and voriconazole-resistant IA. Aspergillus fumigatus culture-positive patients were investigated to identify patients with proven, probable, and putative IA. Clinical characteristics, day 42 and day 90 mortality, triazole-resistance profiles, and antifungal treatments were investigated. RESULTS Of 196 patients with IA, 37 (19%) harbored a voriconazole-resistant infection. Hematological malignancy was the underlying disease in 103 (53%) patients, and 154 (79%) patients were started on voriconazole. Compared with voriconazole-susceptible cases, voriconazole resistance was associated with an increase in overall mortality of 21% on day 42 (49% vs 28%; P = .017) and 25% on day 90 (62% vs 37%; P = .0038). In non-intensive care unit patients, a 19% lower survival rate was observed in voriconazole-resistant cases at day 42 (P = .045). The mortality in patients who received appropriate initial voriconazole therapy was 24% compared with 47% in those who received inappropriate therapy (P = .016), despite switching to appropriate antifungal therapy after a median of 10 days. CONCLUSIONS Voriconazole resistance was associated with an excess overall mortality of 21% at day 42 and 25% at day 90 in patients with IA. A delay in the initiation of appropriate antifungal therapy was associated with increased overall mortality.
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Affiliation(s)
- Pieter P Lestrade
- Department of Medical Microbiology, Radboud University Medical Center
- Center of Expertise in Mycology Radboud University Medical Center/CWZ, Nijmegen
| | | | | | - Steven Schalekamp
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen
| | - Walter J F M van der Velden
- Center of Expertise in Mycology Radboud University Medical Center/CWZ, Nijmegen
- Department of Hematology, Radboud University Medical Center, Nijmegen
| | - Ed J Kuiper
- Department of Medical Microbiology, Leiden University Medical Center
| | | | | | - Henrich A van der Lee
- Department of Medical Microbiology, Radboud University Medical Center
- Center of Expertise in Mycology Radboud University Medical Center/CWZ, Nijmegen
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center
- Center of Expertise in Mycology Radboud University Medical Center/CWZ, Nijmegen
| | - Anton F de Haan
- Department of Health Evidence, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hans L van der Hoeven
- Center of Expertise in Mycology Radboud University Medical Center/CWZ, Nijmegen
- Department of Intensive Care, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bart J A Rijnders
- Department of Medical Microbiology and Infectious Disease, Erasmus Medical Center, Rotterdam
| | | | - Paul E Verweij
- Department of Medical Microbiology, Radboud University Medical Center
- Center of Expertise in Mycology Radboud University Medical Center/CWZ, Nijmegen
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van de Ven SEM, Derikx LAAP, Nagtegaal ID, van Herpen CM, Takes RP, Melchers WJG, Pierik M, van den Heuvel T, Verhoeven RHA, Hoentjen F, Nissen LHC. Laryngeal Carcinoma in Patients With Inflammatory Bowel Disease: Clinical Outcomes and Risk Factors. Inflamm Bowel Dis 2020; 26:1060-1067. [PMID: 31559415 PMCID: PMC7301406 DOI: 10.1093/ibd/izz210] [Citation(s) in RCA: 2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) patients are at increased risk for developing extra-intestinal malignancies, mainly due to immunosuppressive medication. The risk of developing head and neck cancer in immunosuppressed transplant patients is increased. The relation between IBD patients and laryngeal cancer (LC) remains unclear. We aimed (1) to identify risk factors in IBD patients for LC development and (2) to compare clinical characteristics, outcome, and survival of LC in IBD patients with the general population. METHODS All IBD patients with LC (1993-2011) were retrospectively identified using the Dutch Pathology Database. We performed 2 case-control studies: (1) to identify risk factors, we compared patients with IBD and LC (cases) with the general IBD population; (2) to analyze LC survival, we compared cases with controls from the general LC population. RESULTS We included 55 cases, 1800 IBD controls, and 2018 LC controls. Cases were more frequently male compared with IBD controls (P < 0.001). For ulcerative colitis (UC), cases were older at IBD diagnosis (P < 0.001). Crohn's disease (CD) cases were more frequently tobacco users (P < 0.001) and more often had stricturing (P = 0.006) and penetrating (P = 0.008) disease. We found no survival difference. Immunosuppressive medication had no impact on survival. CONCLUSIONS Male sex was a risk factor for LC in IBD patients. Older age at IBD diagnosis was a risk factor for UC to develop LC. Tobacco use and stricturing and penetrating disease were risk factors for LC development in CD patients. Inflammatory bowel disease was not associated with impaired survival of LC. Immunosuppressive medication had no influence on survival.
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Affiliation(s)
- Steffi E M van de Ven
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Lauranne A A P Derikx
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carla M van Herpen
- Department of Medical Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Robert P Takes
- Department of Otolaryngology and Head and Neck Surgery, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marieke Pierik
- Department of Gastroenterology and Hepatology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Tim van den Heuvel
- Department of Gastroenterology and Hepatology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Rob H A Verhoeven
- Department of Research & Development, Netherlands Comprehensive Cancer Organization, Utrecht, the Netherlands
| | - Frank Hoentjen
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - L H C Nissen
- Department of Gastroenterology and Hepatology, Jeroen Bosch Hospital, ‘s-Hertogenbosch, the Netherlands,Address correspondence to: Loes H. C. Nissen, PhD, Department of Gastroenterology and Hepatology, Jeroen Bosch Hospital, Henri Dunantstraat 1, Postbox 90153, 5200 ME ‘s-Hertogenbosch, the Netherlands ()
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van de Laar RLO, Hofhuis W, Duijnhoven RG, Polinder S, Melchers WJG, van Kemenade FJ, Bekkers RLM, Van Beekhuizen HJ. Adjuvant VACcination against HPV in surgical treatment of Cervical Intra-epithelial Neoplasia (VACCIN study) a study protocol for a randomised controlled trial. BMC Cancer 2020; 20:539. [PMID: 32517663 PMCID: PMC7285539 DOI: 10.1186/s12885-020-07025-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 04/14/2020] [Accepted: 06/01/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Cervical cancer is caused by Human Papilloma viruses (HPV) and is preceded by precursor stages: Cervical Intraepithelial Neoplasia (CIN). CIN is mostly found in women in their reproductive age and treated with a Loop Electrosurgical Excision Procedure (LEEP). The recurrence or residual disease rate after treatment is up to 17%. These women have a lifelong increased risk of recurrent CIN, cervical cancer and other HPV related malignancies. Furthermore, LEEP treatments are associated with complications such as premature birth. Limited data show that prophylactic HPV vaccination at the time of LEEP reduces recurrence rates, therefore leading to a reduction in repeated surgical interventions and side effect like preterm birth. The primary study objective is to evaluate the efficacy of the nonavalent HPV vaccination in women with a CIN II-III (high-grade squamous intraepithelial lesion (HSIL) lesion who will undergo a LEEP in preventing recurrent CIN II-III after 24 months. METHODS This study is a randomised, double blinded, placebo controlled trial in 750 patients without prior HPV vaccination or prior treatment for CIN and with histologically proven CIN II-III (independent of their hrHPV status) for whom a LEEP is planned. Included patients will be randomised to receive either three injections with nonavalent (9 HPV types) HPV vaccine or placebo injections (NaCL 0.9%) as a comparator. Treatment and follow-up will be according the current Dutch guidelines. Primary outcome is recurrence of a CIN II or CIN III lesion at 24 months. A normal PAP smear with negative hrHPV test serves as surrogate for absence of CIN. At the start and throughout the study HPV typing, quality of life and cost effectiveness will be tested. DISCUSSION Although prophylactic HPV vaccines are highly effective, little is known about the effectivity of HPV vaccines on women with CIN. Multiple LEEP treatments are associated with complications. We would like to evaluate the efficacy of HPV vaccination in addition to LEEP treatment to prevent residual or recurrent cervical dysplasia and decrease risks of repeated surgical treatment. TRIAL REGISTRATION Medical Ethical Committee approval number: NL66775.078.18. Affiliation: Erasmus Medical Centre. Dutch trial register: NL 7938. Date of registration 2019-08-05.
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Affiliation(s)
- R L O van de Laar
- Department of Gynecologic Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, PO Box: 2040, 3000 CA, Rotterdam, The Netherlands.
| | - W Hofhuis
- Department of Obstetrics and Gynaecology, Franciscus Gasthuis, PO Box: 10900, 3004 BA, Rotterdam, The Netherlands
| | - R G Duijnhoven
- Clinical trials unit of the Dutch Society for Obstetrics and Gynecology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, Netherlands
| | - S Polinder
- Department of Public Health, Center for Medical Decision Sciences, Erasmus MC- University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - W J G Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, PO Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - F J van Kemenade
- Department of Pathology, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, 3000 CA, The Netherlands
| | - R L M Bekkers
- Department of Obstetrics and Gynecology, Catharina Hospital, PO Box 1350, 5602 ZA, Eindhoven, the Netherlands.,GROW School for Oncology and Developmental Biology, Maastricht University, Eindhoven, the Netherlands
| | - H J Van Beekhuizen
- Department of Gynecologic Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, PO Box: 2040, 3000 CA, Rotterdam, The Netherlands
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Ballard E, Yucel R, Melchers WJG, Brown AJP, Verweij PE, Warris A. Antifungal Activity of Antimicrobial Peptides and Proteins against Aspergillus fumigatus. J Fungi (Basel) 2020; 6:jof6020065. [PMID: 32443413 PMCID: PMC7345740 DOI: 10.3390/jof6020065] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/12/2020] [Accepted: 05/15/2020] [Indexed: 01/06/2023] Open
Abstract
Antimicrobial peptides and proteins (AMPs) provide an important line of defence against invading microorganisms. However, the activity of AMPs against the human fungal pathogen Aspergillus fumigatus remains poorly understood. Therefore, the aim of this study was to characterise the anti-Aspergillus activity of specific human AMPs, and to determine whether A. fumigatus can possess resistance to specific AMPs, as a result of in-host adaptation. AMPs were tested against a wide range of clinical isolates of various origins (including cystic fibrosis patients, as well as patients with chronic and acute aspergillosis). We also tested a series of isogenic A. fumigatus isolates obtained from a single patient over a period of 2 years. A range of environmental isolates, obtained from soil in Scotland, was also included. Firstly, the activity of specific peptides was assessed against hyphae using a measure of fungal metabolic activity. Secondly, the activity of specific peptides was assessed against germinating conidia, using imaging flow cytometry as a measure of hyphal growth. We showed that lysozyme and histones inhibited hyphal metabolic activity in all the A. fumigatus isolates tested in a dose-dependent fashion. In addition, imaging flow cytometry revealed that histones, β-defensin-1 and lactoferrin inhibited the germination of A. fumigatus conidia.
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Affiliation(s)
- Eloise Ballard
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
| | - Raif Yucel
- Iain Fraser Cytometry Centre (IFCC), Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
- Cytomics Centre, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK;
| | - Willem J. G. Melchers
- Centre for Expertise in Mycology and Department of Medical Microbiology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands; (W.J.G.M.); (P.E.V.)
| | - Alistair J. P. Brown
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
- MRC Centre for Medical Mycology at the University of Exeter, Exeter 4EX 4QD, UK;
| | - Paul E. Verweij
- Centre for Expertise in Mycology and Department of Medical Microbiology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands; (W.J.G.M.); (P.E.V.)
| | - Adilia Warris
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
- MRC Centre for Medical Mycology at the University of Exeter, Exeter 4EX 4QD, UK;
- Correspondence: ; Tel.: +44-1392-727-593
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