Eric C. J. Claas
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View article: Risk of new HIV diagnosis by intersecting migration, socioeconomic, and mental health vulnerabilities in the Netherlands: a nationwide analysis of the ATHENA cohort and Statistics Netherlands registry data
Risk of new HIV diagnosis by intersecting migration, socioeconomic, and mental health vulnerabilities in the Netherlands: a nationwide analysis of the ATHENA cohort and Statistics Netherlands registry data Open
View article: Rapid and reliable species-level identification from clinical samples using 16S rRNA gene nanopore sequencing analysis
Rapid and reliable species-level identification from clinical samples using 16S rRNA gene nanopore sequencing analysis Open
The detection and identification of bacterial species in clinical samples are crucial for patient management and antibiotic treatment. When culture-based identification methods fail, 16 S rRNA gene next-generation sequencing (NGS) serves a…
View article: Intra-Host Evolution During Relapsing Parvovirus B19 Infection in Immunocompromised Patients
Intra-Host Evolution During Relapsing Parvovirus B19 Infection in Immunocompromised Patients Open
Background: Parvovirus B19 (B19V) can cause severe relapsing episodes of pure red cell aplasia in immunocompromised individuals, which are commonly treated with intravenous immunoglobulins (IVIGs). Few data are available on B19V intra-host…
View article: The added value of metagenomic next-generation sequencing in central nervous system infections: a systematic review of case reports
The added value of metagenomic next-generation sequencing in central nervous system infections: a systematic review of case reports Open
Background The diversity of pathogens causing central nervous system (CNS) infections presents a diagnostic challenge. Patient demographics and geographical location affect the likelihood of certain pathogens causing infection. Current dia…
View article: Diagnosing viral gastro-enteritis using the fully automated sample-in, result-out STARlet All in one system (AIOS)
Diagnosing viral gastro-enteritis using the fully automated sample-in, result-out STARlet All in one system (AIOS) Open
The STARlet All-In-One system is a modular platform that integrates the complete molecular diagnostic workflow from nucleic acid extraction of clinical samples to PCR set-up and amplification. The platform was evaluated in comparison with …
View article: Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics
Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics Open
View article: Comparison of the performance of two targeted metagenomic virus capture probe-based methods using reference control materials and clinical samples
Comparison of the performance of two targeted metagenomic virus capture probe-based methods using reference control materials and clinical samples Open
Viral enrichment by probe hybridization has been reported to significantly increase the sensitivity of viral metagenomics. This study compares the analytical performance of two targeted metagenomic virus capture probe-based methods: (i) Se…
View article: Automating the Illumina DNA library preparation kit for whole genome sequencing applications on the flowbot ONE liquid handler robot
Automating the Illumina DNA library preparation kit for whole genome sequencing applications on the flowbot ONE liquid handler robot Open
View article: Prospective and systematic screening for invasive aspergillosis in the ICU during the COVID-19 pandemic, a proof of principle for future pandemics
Prospective and systematic screening for invasive aspergillosis in the ICU during the COVID-19 pandemic, a proof of principle for future pandemics Open
The diagnostic performance of a prospective, systematic screening strategy for COVID-19 associated pulmonary aspergillosis (CAPA) during the COVID-19 pandemic was investigated. Patients with COVID-19 admitted to the ICU were screened for C…
View article: Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics
Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics Open
Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we p…
View article: A multicenter evaluation of the QIAstat-Dx meningitis-encephalitis syndromic test kit as compared to the conventional diagnostic microbiology workflow
A multicenter evaluation of the QIAstat-Dx meningitis-encephalitis syndromic test kit as compared to the conventional diagnostic microbiology workflow Open
Purpose Rapid diagnosis and treatment of infectious meningitis and encephalitis (ME) is critical to minimize morbidity and mortality. Recently, Qiagen introduced the CE-IVD QIAstat-Dx ME panel (QS-ME) for syndromic diagnostic testing of me…
View article: A core-genome multilocus sequence typing scheme for the detection of genetically related <i>Streptococcus pyogenes</i> clusters
A core-genome multilocus sequence typing scheme for the detection of genetically related <i>Streptococcus pyogenes</i> clusters Open
The recently observed increase in invasive Streptococcus pyogenes infections causes concern in Europe. However, conventional molecular typing methods lack discriminatory power to aid investigations of outbreaks caused by S. pyogenes . Ther…
View article: Multicenter performance evaluation of the Alinity m CMV assay for quantifying cytomegalovirus DNA in plasma samples
Multicenter performance evaluation of the Alinity m CMV assay for quantifying cytomegalovirus DNA in plasma samples Open
Monitoring of cytomegalovirus (CMV) viral load is critical for informing treatment decisions in order to prevent the severe health consequences of CMV infection or reactivation of latent CMV in immunocompromised individuals. This first fie…
View article: Multi-site performance evaluation of the Alinity m Molecular assay for quantifying Epstein-Barr virus DNA in plasma samples
Multi-site performance evaluation of the Alinity m Molecular assay for quantifying Epstein-Barr virus DNA in plasma samples Open
Detection and monitoring of acute infection or reactivation of Epstein-Barr virus (EBV) are critical for treatment decision-making and to reduce the risk of EBV-related malignancies and other associated diseases in immunocompromised indivi…
View article: Voclosporin and the Antiviral Effect Against SARS-CoV-2 in Immunocompromised Kidney Patients
Voclosporin and the Antiviral Effect Against SARS-CoV-2 in Immunocompromised Kidney Patients Open
View article: Comparison of the performance of two targeted metagenomic virus capture probe-based methods using synthetic viral sequences and clinical samples
Comparison of the performance of two targeted metagenomic virus capture probe-based methods using synthetic viral sequences and clinical samples Open
Viral enrichment by probe hybridization has been reported to significantly increase the sensitivity of viral metagenomics. This study compares the analytical performance of two targeted metagenomic virus capture probe-based methods: i) Seq…
View article: Panton-Valentine Leukocidin–Positive CC398 MRSA in Urban Clinical Settings, the Netherlands
Panton-Valentine Leukocidin–Positive CC398 MRSA in Urban Clinical Settings, the Netherlands Open
We report detection of Panton-Valentine leukocidin-positive clonal complex 398 human-origin methicillin-resistant Staphylococcus aureus L2 in the Netherlands. This hypervirulent lineage originated in the Asia-Pacific Region and could becom…
View article: Clinical performance of two new, fully integrated molecular platforms used for HIV-1, HBV and HCV viral load analysis, the NeuMoDx 288 and the Alinity m.
Clinical performance of two new, fully integrated molecular platforms used for HIV-1, HBV and HCV viral load analysis, the NeuMoDx 288 and the Alinity m. Open
The Alinity m and NeuMoDx HCV assay have a comparable performance. Quantification differences in the HIV-1 assay were mostly apparent in the lower VLs and under-quantification of the NeuMoDx HBV assay was observed.
View article: Livestock-associated methicillin-resistant Staphylococcus aureus epidemiology, genetic diversity, and clinical characteristics in an urban region
Livestock-associated methicillin-resistant Staphylococcus aureus epidemiology, genetic diversity, and clinical characteristics in an urban region Open
Objectives While Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA), defined as CC398, is a well-known pathogen among those working with livestock, there are indications that LA-MRSA prevalence among the general pop…
View article: Next-generation sequencing in routine clinical microbiology and infectious diseases: an ESGMD-ESGEM ESCMID postgraduate course
Next-generation sequencing in routine clinical microbiology and infectious diseases: an ESGMD-ESGEM ESCMID postgraduate course Open
View article: Evaluation of the sample-to-result, random access NeuMoDx platform for viral load testing of Cytomegalovirus and Epstein Barr virus in clinical specimens
Evaluation of the sample-to-result, random access NeuMoDx platform for viral load testing of Cytomegalovirus and Epstein Barr virus in clinical specimens Open
View article: Performance of five metagenomic classifiers for virus pathogen detection using respiratory samples from a clinical cohort
Performance of five metagenomic classifiers for virus pathogen detection using respiratory samples from a clinical cohort Open
Viral metagenomics is increasingly being applied in clinical diagnostic settings for detection of pathogenic viruses. While a number of benchmarking studies have been published on the use of metagenomic classifiers for abundance and divers…
View article: External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories
External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories Open
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…
View article: Viral metagenomic sequencing in the diagnosis of meningoencephalitis: a review of technical advances and diagnostic yield
Viral metagenomic sequencing in the diagnosis of meningoencephalitis: a review of technical advances and diagnostic yield Open
The last decade has shown major advances in technical possibilities for using mNGS in diagnostic settings including cloud-based analysis. An additional advance may be the current established infrastructure of platforms for bioinformatic an…
View article: Increasing diagnostic possibilities using the geneLEAD VIII platform for detection of SARS-CoV-2
Increasing diagnostic possibilities using the geneLEAD VIII platform for detection of SARS-CoV-2 Open
View article: Evaluation of the Genmark ePlex® and QIAstat-Dx® respiratory pathogen panels in detecting bacterial targets in lower respiratory tract specimens
Evaluation of the Genmark ePlex® and QIAstat-Dx® respiratory pathogen panels in detecting bacterial targets in lower respiratory tract specimens Open
View article: Viral metagenomic sequencing in a cohort of international travellers returning with febrile illness
Viral metagenomic sequencing in a cohort of international travellers returning with febrile illness Open
View article: Longitudinal monitoring of DNA viral loads in transplant patients using quantitative metagenomic next-generation sequencing
Longitudinal monitoring of DNA viral loads in transplant patients using quantitative metagenomic next-generation sequencing Open
Introduction Immunocompromised patients are prone to reactivations of multiple latent DNA viruses. Viral load monitoring by single-target quantitative PCRs (qPCR) is the current cornerstone for virus quantification. In this study, a metage…
View article: Hospital transmission of borderline oxacillin-resistant Staphylococcus aureus evaluated by whole-genome sequencing
Hospital transmission of borderline oxacillin-resistant Staphylococcus aureus evaluated by whole-genome sequencing Open
Introduction. Staphylococcus aureus is a major cause of hospital infections worldwide. Awareness towards methicillin-resistant S. aureus (MRSA) infections is high but attention towards borderline oxacillin-resistant S. aureus (BORSA) is li…
View article: Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples
Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples Open
A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardiza…