Stefan A. Boers
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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: Value of collaborative investigation by hospital infection control, public health services and a national reference laboratory during an increase in puerperal sepsis
Value of collaborative investigation by hospital infection control, public health services and a national reference laboratory during an increase in puerperal sepsis Open
Background In a Dutch tertiary care hospital, two cases of puerperal sepsis were diagnosed within 16 days in June-July 2022. The subsequent outbreak investigation emphasizes the value of collaboration between hospital infection control, re…
View article: Metagenomic and transcriptomic investigation of pediatric acute liver failure cases reveals a common pathway predominated by monocytes
Metagenomic and transcriptomic investigation of pediatric acute liver failure cases reveals a common pathway predominated by monocytes Open
In 2022, a cluster of severe childhood hepatitis was detected primarily in Europe and North America, leading to a global alert by the World Health Organization. An association with adeno-associated virus 2 (AAV2) in conjunction with human …
View article: Community-Acquired Pneumonia Caused by Avian <i>Chlamydia abortus</i>, the Netherlands
Community-Acquired Pneumonia Caused by Avian <i>Chlamydia abortus</i>, the Netherlands Open
We report avian Chlamydia abortus pneumonia in an immunocompetent elderly patient in the Netherlands after environmental exposure to wild aquatic birds, including seabirds. New molecular surveillance studies are needed in wild and captive …
View article: A Targeted LC-MRM3 Proteomic Approach for the Diagnosis of SARS-CoV-2 Infection in Nasopharyngeal Swabs
A Targeted LC-MRM3 Proteomic Approach for the Diagnosis of SARS-CoV-2 Infection in Nasopharyngeal Swabs Open
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: Implications of ad-hoc molecular typing for infection control measures in a multi-cluster, multi-phenotypic Serratia marcescens outbreak in a neonatal intensive care unit
Implications of ad-hoc molecular typing for infection control measures in a multi-cluster, multi-phenotypic Serratia marcescens outbreak in a neonatal intensive care unit Open
The use of ad-hoc cgMLST provided timely data for rational decision-making during an S. marcescens outbreak at the NICU. Antibiotic phenotyping alone was found not to be suitable for studying clonal spread during this outbreak with S. marc…
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: Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny Open
The SARS-CoV-2 genome occupies a unique place in infection biology – it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has bee…
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: 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: Indistinguishable monocyte pathway activation in adeno-associated virus positive and negative paediatric liver explants
Indistinguishable monocyte pathway activation in adeno-associated virus positive and negative paediatric liver explants Open
Adeno-associated virus 2 (AAV2) has recently been epidemiologically associated with severe childhood hepatitis, however the pathogenesis remains unclear. Here, we report excessive activation of monocyte pathways in liver explant tissue fro…
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: Influence of transition from open bay units to single room units in a neonatal intensive care unit on hospital transmission of multi-drug-resistant Enterobacterales
Influence of transition from open bay units to single room units in a neonatal intensive care unit on hospital transmission of multi-drug-resistant Enterobacterales Open
After transition to SRUs, there was no decrease in the number of clusters of MDROs with an epidemiological link, suggesting that nursing infants in an NICU with an SRU design is not, in itself, protective against the acquisition of MDROs.
View article: Improved Diagnostics in Bacterial Neonatal Meningitis Using a Next-Generation Sequencing Platform
Improved Diagnostics in Bacterial Neonatal Meningitis Using a Next-Generation Sequencing Platform Open
View article: A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2
A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2 Open
View article: The diagnostic value of nasal microbiota and clinical parameters in a multi-parametric prediction model to differentiate bacterial versus viral infections in lower respiratory tract infections
The diagnostic value of nasal microbiota and clinical parameters in a multi-parametric prediction model to differentiate bacterial versus viral infections in lower respiratory tract infections Open
Background The ability to accurately distinguish bacterial from viral infection would help clinicians better target antimicrobial therapy during suspected lower respiratory tract infections (LRTI). Although technological developments make …
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: A Comparison of Five Illumina, Ion Torrent, and Nanopore Sequencing Technology-Based Approaches for Whole Genome Sequencing of Sars-Cov-2
A Comparison of Five Illumina, Ion Torrent, and Nanopore Sequencing Technology-Based Approaches for Whole Genome Sequencing of Sars-Cov-2 Open
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: Convalescent Plasma in a Patient with Protracted COVID-19 and Secondary Hypogammaglobulinemia Due to Chronic Lymphocytic Leukemia: Buying Time to Develop Immunity?
Convalescent Plasma in a Patient with Protracted COVID-19 and Secondary Hypogammaglobulinemia Due to Chronic Lymphocytic Leukemia: Buying Time to Develop Immunity? Open
It is not exactly clear yet which type of immune response prevails to accomplish viral clearance in coronavirus disease 2019 (COVID-19). Studying a patient with chronic lymphocytic leukemia and hypogammaglobulinemia who suffered from COVID…
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: On-site rapid molecular testing, mobile sampling teams and <i>eHealth</i> to support primary care physicians during the COVID-19 pandemic
On-site rapid molecular testing, mobile sampling teams and <i>eHealth</i> to support primary care physicians during the COVID-19 pandemic Open
Objectives We evaluated the effects of on-site rapid molecular testing at a drive-through sampling facility, deployment of mobile sampling teams and implementation of an online eHealth platform as supportive measures for general practition…
View article: Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota
Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota Open
Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumi…
View article: Comparison of Illumina Versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota
Comparison of Illumina Versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota Open
Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumi…
View article: Multicenter Evaluation of QIAstat-Dx Respiratory Panel V2 for Detection of Viral and Bacterial Respiratory Pathogens
Multicenter Evaluation of QIAstat-Dx Respiratory Panel V2 for Detection of Viral and Bacterial Respiratory Pathogens Open
QIAstat-Dx Respiratory Panel V2 (RP) is a novel molecular-method-based syndromic test for the simultaneous and rapid (∼70-min) detection of 18 viral and 3 bacterial pathogens causing respiratory infections. This report describes the first …
View article: Successful High-Dosage Monotherapy of Tigecycline in a Multidrug-Resistant Klebsiella pneumoniae Pneumonia–Septicemia Model in Rats
Successful High-Dosage Monotherapy of Tigecycline in a Multidrug-Resistant Klebsiella pneumoniae Pneumonia–Septicemia Model in Rats Open
Background: Recent scientific reports on the use of high dose tigecycline monotherapy as a “drug of last resort” warrant further research into the use of this regimen for the treatment of severe multidrug-resistant, Gram-negative bacterial…