Biology subjects

de Jong, M. D.

Publications and source records attributed to de Jong, M. D..

9 recordsLinked to original sources

bioRxiv2025

MirAge, a novel Matrix Analyzer for fast DNA classification

SummaryTo understand the composition of metagenomics samples, fast computer tools analyze large datasets to compose a taxonomic overview. With large datasets, it is still a challenge to achieve high precision and sensitive results in fast manner. Here we show the new tool MirAge which implements a newly developed classification strategy for analyzing DNA and RNA samples. MirAge is a highly precise and sensitive tool which can be easily used to create results from large amount of data in a fast manner. The ability to combine different databases, run on complex High Performance Computing (HPC) environments and customize many settings shows MirAge to be versatile. AvailabilityThe software is freely available at https://github.com/mirdesign/mirage Contactmirage@mirdesign.nl

bioinformatics↗

bioRxiv2023

Deep profiling of antigen-specific B cells from different pathogens identifies novel compartments in the IgG memory B cell and antibody-secreting cell lineages

A better understanding of the bifurcation of human B cell differentiation into memory B cells (MBC) and antibody-secreting cells (ASC) and identification of MBC and ASC precursors is crucial to optimize vaccination strategies or block undesired antibody responses. To unravel the dynamics of antigen-induced B cell responses, we compared circulating B cells reactive to SARS-CoV-2 (Spike, RBD and Nucleocapsid) in COVID-19 convalescent individuals to B cells specific to Influenza-HA, RSV-F and TT, induced much longer ago. High-dimensional spectral flow cytometry indicated that the decision point between ASC- and MBC-formation lies in the CD43+CD71+IgG+ Activated B cell compartment, showing properties indicative of recent germinal center activity and recent antigen encounter. Within this Activated B cells compartment, CD86+ B cells exhibited close phenotypical similarity with ASC, while CD86- B cells were closely related to IgG+ MBCs. Additionally, different activation stages of the IgG+ MBC compartment could be further elucidated. The expression of CD73 and CD24, regulators of survival and cellular metabolic quiescence, discerned activated MBCs from resting MBCs. Activated MBCs (CD73-CD24lo) exhibited phenotypical similarities with CD86- IgG+ Activated B cells and were restricted to SARS-CoV-2 specificities, contrasting with the resting MBC compartment (CD73-/CD24hi) that exclusively encompassed antigen-specific B cells established long ago. Overall, these findings identify novel stages for IgG+ MBC and ASC formation and bring us closer in defining the decision point for MBC or ASC differentiation. ImportanceIn this study, researchers aimed to better understand human B cell differentiation and their role in establishing long-lived humoral immunity. Using high-dimensional flow cytometry, they studied B cells reactive to three SARS-CoV-2 antigens in individuals convalescent for COVID-19, and compared their phenotypes to B cells reactive to three distinct protein antigens derived from vaccines or viruses encountered months to decades before. Their findings showed that Activated B cells reflect recent germinal center graduates that may have diverse fates; with some feeding the pool of antibody-secreting cells and others fueling the resting memory B cell compartment. Activated B cells gradually differentiate into resting memory B cells through an activated MBC phase. Increased expression of the cellular metabolic regulators CD73 and CD24 in resting memory B cells distinguishes them from the activated memory B cells phase, and is likely involved in sustaining a durable memory of humoral immunity. These findings are crucial for the development of vaccines that provide lifelong protection and may show potential to define reactive B cells in diseases where the cognate-antigen is still unknown such as in autoimmunity, cancers, or novel viral outbreaks.

immunology↗

bioRxiv2022

Single-cell transcriptomics reveals subset-specific metabolic profiles underpinning the bronchial epithelial response to flagellin

Respiratory epithelial cells line the airways and represent the first line of defense against respiratory pathogens. The cellular heterogeneity of the airway wall has only recently been recognized by single-cell analyses. Here, we leveraged single-cell RNA sequencing of primary human bronchial epithelial cells growing in air-liquid interface to determine cell-specific changes evoked by flagellin, a protein driving the motility of many mucosal pathogens. We detected seven cell clusters in the human epithelium, including ciliated cells, ionocytes and several states of basal and secretory cells, of which only inflammatory basal cells and inflammatory secretory cells showed a proportional increase in response to flagellin. Only inflammatory secretory cells showed evidence of metabolic reprogramming toward aerobic glycolysis, and inhibition of the mTOR pathway specifically reduced this subset, prevented this metabolic shift, and reduced inflammatory gene transcription in these cells. This study expands our knowledge of the airways immune response to flagellated pathogens to single cell resolution and defines a novel target to modulate mucosal immunity during bacterial infections.

immunology↗

bioRxiv2021

The within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children

The evolution of influenza viruses is fundamentally shaped by within-host processes. However, the within-host evolutionary dynamics of influenza viruses remain incompletely understood, in part because most studies have focused on within-host virus diversity of infections in otherwise healthy adults based on single timepoint data. Here, we analysed the within-host evolution of 82 longitudinally-sampled individuals, mostly young children, infected with A/H3N2 or A/H1N1pdm09 viruses between 2007 and 2009. For A/H1N1pdm09 infections during the 2009 pandemic, nonsynonymous changes were common early in infection but decreased or remained constant throughout infection. For A/H3N2 viruses, early infection was dominated by purifying selection. However, as infections progressed, nonsynonymous variants increased in frequencies even though within-host virus titres decreased, leading to the maintenance of virus diversity via mutation-selection balance. Our findings suggest that this maintenance of genetic diversity in these children combined with their longer duration of infection may provide important opportunities for within-host virus evolution.

microbiology↗

bioRxiv2020

Informing epidemic (research) responses in a timely fashion by knowledge management - a Zika virus use case

The response of pathophysiological research to emerging epidemics often occurs after the epidemic and, as a consequence, has little to no impact on improving patient outcomes or on developing high-quality evidence to inform clinical management strategies during the epidemic. Rapid and informed guidance of epidemic (research) responses to severe infectious disease outbreaks requires quick compilation and integration of existing pathophysiological knowledge. As a case study we chose the Zika virus (ZIKV) outbreak that started in 2015 to develop a proof-of-concept knowledge repository. To extract data from available sources and build a computationally tractable and comprehensive molecular interaction map we applied generic knowledge management software for literature mining, expert knowledge curation, data integration, reporting and visualisation. A multi-disciplinary team of experts, including clinicians, virologists, bioinformaticians and knowledge management specialists, followed a pre-defined workflow for rapid integration and evaluation of available evidence. While conventional approaches usually require months to comb through the existing literature, the initial ZIKV KnowledgeBase (ZIKA KB) was completed within a few weeks. Recently we updated the ZIKA KB with additional curated data from the large amount of literature published since 2016 and made it publicly available through a web interface together with a step-by-step guide to ensure reproducibility of the described use case (S4). In addition, a detailed online user manual is provided to enable the ZIKV research community to generate hypotheses, share knowledge, identify knowledge gaps, and interactively explore and interpret data (S5). A workflow for rapid response during outbreaks was generated, validated and refined and is also made available. The process described here can be used for timely structuring of pathophysiological knowledge for future threats. The resulting structured biological knowledge is a helpful tool for computational data analysis and generation of predictive models and opens new avenues for infectious disease research. Availabilitywww.zikaknowledgebase.eu FundingEuropean Commissions Seventh Framework Research Programme project PREPARE (FP7-Health n{degrees}602525) and ZIKALLIANCE (MK, H2020; No 734548). Author summaryDuring the recent ZIKV outbreak there was little information about the interactions between Zika virus and the host, however, the massive research response lead to a steep increase in the number of relevant publications within a very short period of time. At the time, there was no structured and comprehensive database available for integrated molecular and physiological data and knowledge about ZIKV infection. Researchers had to manually review the literature (amounting to over 5000 articles on ZIKV during our last update of the ZIKA KB in September 2018) to extract information about host-pathogen interaction and affected molecular, cellular and organ pathways. We explored the use of automated literature analysis and a defined cooperative effort between experts from various scientific, biomedical and information-technology domains to rapidly compile existing pathophysiological knowledge as a potential tool to support investigations during an emergency. This tool is contrasted with conventional approaches that would take months to comb through the massive amount of existing literature. In addition to providing background information for research, scientific publications can be processed to transform textual information into complex networks, which can be integrated with existing knowledge resources to suggest novel hypotheses that potentially contribute to innovative infectious disease research approaches. This study shows that the knowledge extraction and mapping process required to inform clinical and research responses to an emerging epidemic can be efficiently and effectively executed with a dedicated and trained group of experts, a validated process and the necessary tools. Our results further provide an overview of ZIKV biology, allow prediction of drug efficacy and indentify specific host factors and signalling pathways affected by ZIKV.

pathology↗

bioRxiv2020

Internal Control for process monitoring of clinical metagenomic next-generation sequencing of urine samples

BackgroundProcess control for clinical metagenomic next-generation sequencing (mNGS) is not yet widely applied, while technical sources of bias are plentiful. We present an easy-to-use internal control (IC) method focussing on technical process control applied to metagenomics in clinical diagnostics. MethodsDNA of nine urine samples was sequenced in the absence and presence of Thermus thermophilus DNA as IC in incremental concentrations (0.5-2-5%). Between aliquots of each sample, we compared the IC relative abundance (RA), and after in silico subtraction of IC reads, the microbiota and the RA of pathogens. The optimal IC spike-in concentration was defined as the lowest concentration still detectable in all samples. ResultsThe RA of IC correlated linearly with the spiked IC concentration (r2=0.99). IC added in a concentration of 0.5% of total DNA concentration was detectable in all samples, regardless of human/bacterial composition and after in silico removal gave the smallest difference in RA of pathogens compared to the unspiked aliquot of the sample. The microbiota of sample aliquots sequenced in the presence and absence of IC was highly similar after in silico removal of IC reads (median BC-dissimilarity per sample of 0.059), provided samples had sufficient bacterial read counts. ConclusionT. thermophilus DNA at a percentage of 0.5% of the total DNA concentration can be applied for the process control of mNGS of urine samples. We demonstrated negligible alterations in sample microbial composition after in silico subtraction of IC sequence reads. This approach contributes toward implementation of mNGS in the clinical microbiology laboratory.

microbiology↗

bioRxiv2019

Disparate evolution of virus populations in upper and lower airways of mechanically ventilated patients

In routine surveillance and diagnostic testing, influenza virus samples are typically collected only from the upper respiratory tract (URT) due to the invasiveness of sample collection from the lower airways. Very little is known about virus variation in the lower respiratory tract (LRT) and it remains unclear if the virus populations at different sites of the human airways may develop to have divergent genetic signatures. We used deep sequencing of serially obtained matched nasopharyngeal swabs and endotracheal aspirates from four mechanically ventilated patients with influenza A/H3N2 infections. A physical barrier separating both compartments of the respiratory tract introduced as part of the medical procedures enabled us to track and compare the genetic composition of the virus populations during isolated evolution in the same host. Amino acid variants reaching majority proportions emerged during the course of infection in both nasopharyngeal swabs and endotracheal aspirates, and amino acid variation was observed in all influenza virus proteins. Genetic variation of the virus populations differed between the URT and LRT and variants were frequently uniquely present in either URT or LRT virus populations of a patient. These observations indicate that virus populations in spatially distinct parts of the human airways may follow different evolutionary trajectories. Selectively sampling from the URT may therefore fail to detect potentially important emerging variants.\n\nImportanceInfluenza viruses are rapidly mutating pathogens that easily adapt to changing environments. Although advances in sequencing technology make it possible to identify virus variants at very low proportions of the within-host virus population, several aspects of intrahost viral evolution have not been studied because sequentially collected samples and samples from the lower respiratory tract are not routinely obtained for influenza surveillance or clinical diagnostic purposes. Importantly, how virus populations evolve in different parts of the human respiratory tract remains unknown. Here we used serial clinical specimens collected from mechanically ventilated influenza patients to compare how virus populations develop in the upper and lower respiratory tract. We show that virus populations in the upper and lower respiratory tract may evolve along distinct evolutionary pathways, and that current sampling and surveillance regimens likely capture only part of the complete intrahost virus variation.

microbiology↗

bioRxiv2017

Metagenomic sequencing to replace semi-quantitative urine culture for detection of urinary tract infections: a proof of concept

ABSTRACTSemi-quantitative bacterial culture is the standard method to diagnose urinary tract infections (UTI), but bacterial growth rate limits diagnostic speed and it is unreliable when patients have been pre-treated with antibiotics. Metagenomics could increase diagnostic speed and accuracy by sequencing the microbiome and resistome directly from urine samples, bypassing culture. However, a semi-quantitative approach - as needed for diagnosing UTIs - has not been established.\n\nMetagenomics was deployed to identify and semi-quantify bacterial presence indicative of UTI, predict antimicrobial susceptibility (AMR), and results were compared to semi-quantitative culture. Whole genome sequencing of the corresponding uropathogens was done for comparison. Analysis time and cost were tracked.\n\nForty-one consecutive urine samples underwent metagenomic analysis. All culture positive samples contained >200ng of DNA, suggestive of a threshold below which UTI could be ruled out solely based on DNA quantity. A semi-quantitative Diagnostic Index (DI) was created by multiplying the total DNA quantity by the relative abundance of uropathogens per urine sample. The DI allowed discrimination of UTI from non-UTI samples in all but 1 case. Metagenomic detection of AMR determinants correctly predicted the phenotype of uropathogens in 20 of 32 cases. The metagenomic work-flow was 31h and cost {euro}116 per sample, but could be reduced to 4.5h and {euro}5 for low-DNA-yield non-UTI samples.\n\nThe genomic determinants of AMR and their distribution across uropathogens need to be better understood for prediction of AMR phenotypes by metagenomics. The introduction of the DI demonstrates the potential of semi-quantitative metagenomics to replace culture as rapid diagnostic method for UTI.

microbiology↗

bioRxiv2017

Global Phylogenetic Analysis Of Escherichia coli And Plasmids Carrying The mcr-1 Gene Indicates Bacterial Diversity But Plasmid Restriction

To understand the dynamics behind the worldwide spread of the mcr-1 gene, we determined the population structure of Escherichia coli and of mobile genetic elements (MGEs) carrying the mcr-1 gene. After a systematic review of the literature we included 65 E. coli whole genome sequences (WGS), adding 6 recently sequenced travel related isolates, and 312 MLST profiles. We included 219 MGEs described in 7 Enterobacteriaceae species isolated from human, animal and environmental samples. Despite a high overall diversity, 2 lineages were observed in the E. coli population that may function as reservoirs of the mcr-1 gene, the largest of which was linked to ST10, a sequence type known for its ubiquity in human faecal samples and in food samples. No genotypic clustering by geographical origin or isolation source was observed. Amongst a total of 13 plasmid incompatibility types, the Incl2, lncX4 and IncHI2 plasmids accounted for more than 90% of MGEs carrying the mcr-1 gene. We observed significant geographical clustering with regional spread of lncHI2 plasmids in Europe and Incl2 in Asia. These findings point towards promiscuous spread of the mcr-1 gene by efficient horizontal gene transfer dominated by a limited number of plasmid incompatibility types.

microbiology↗