Biology subjects

van Crevel, R.

Publications and source records attributed to van Crevel, R..

12 recordsLinked to original sources

bioRxiv2026

Analytical concordance of targeted next-generation sequencing and whole-genome sequencing for Mycobacterium tuberculosis drug resistance and lineage determination in West Java, Indonesia

As drug-resistant tuberculosis (DR-TB) cases rise, resistance detection in a timely manner is essential to lead effective treatment and limit transmission. Targeted next-generation sequencing (tNGS) offers quick results with multiple important drugs covered, but assessments regarding its performance for DR-TB diagnostic use compared to whole genome sequencing (WGS) as the most comprehensive genomic-based tool are still limited. This cross-sectional study compared resistance profiles generated by Deeplex Myc-TB tNGS assay with WGS for 116 prospectively-collected rifampicin resistant TB samples from West Java, Indonesia. All 116 samples were subject to paired analysis, the clinical samples were split to be directly processed for tNGS and to be cultivated for culture-based WGS. Both WGS and tNGS were carried out using Illumina MiSeq platform. High concordance of tNGS and WGS were observed across thirteen anti-TB drugs evaluated, particularly for drugs included in the BPaLM regimen. Isoniazid had the lowest concordance of 86.73%. Of 116 samples, 31.03% (n = 36) had discrepant resistance calling from the two methods for one or more drugs, which came from 73 discordant variants identification. The most common source of discrepancy was when tNGS detected a resistance-conferring mutation while WGS did not (54.8%). tNGS could detect mixed infection better than WGS, but WGS was superior in identifying detailed major Mycobacterium tuberculosis lineage of the sample. tNGS showed a good level concordance with WGS in detecting resistance-conferring mutations in rifampicin-resistant TB samples, with a more rapid turnaround time. Continuous update to tNGS panel and mutation catalogue is needed to keep the tool clinically relevant. ImportanceDrug-resistant tuberculosis (DR-TB) continues to pose worldwide threat, and newer diagnostic tools to generate quick, comprehensive resistance profile are crucial to provide timely appropriate treatment. Targeted next-generation sequencing (tNGS) is a promising new alternative, but more evidence on its performance is needed to support programmatic adoption. By analysing DR-TB samples with both tNGS and whole genome sequencing (WGS) and evaluating their results agreement, this study shows that tNGS works just as well as WGS in detecting TB drug resistance-conferring mutations, confirming its potential for routine diagnostic use. This study also observed that while WGS is superior in identifying Mycobacterium tuberculosis lineage with high resolution, it did not detect mixed infection better than tNGS. Notably, this study demonstrated that tNGS is clinically relevant for DR-TB detection in a high burden setting, providing evidence for programmatic consideration in Indonesia and other settings with similar demographics and TB situation.

genomics↗

bioRxiv2026

A new stress-response pathway in Mycobacterium tuberculosis

Metabolic adaptations are key in the virulence of the pathogen Mycobacterium tuberculosis (Mtb). However, our current understanding of these adaptations is limited to common pathways in central carbon metabolism. Here we apply an untargeted bottom-up approach to discover unknown stress-responsive metabolites and their biosynthetic enzyme. We show that upon exposure to hypoxia, nitric oxide and activated macrophages, Mtb rapidly produces high levels of an unknown metabolite that we identify as 6-{gamma}-amino-butyric acid-trehalose (GABA-trehalose). Formation of millimolar GABA-trehalose levels under these stresses is driven by a rapid rise in GABA, which is also excreted. We demonstrate that GABA-trehalose is produced from GABA and trehalose by the uncharacterized ATP-grasp enzyme Rv1722, involving a carboxylate-hydroxyl ligation that is non-canonical for ATP-grasp enzymes. Phylogenetic analyses demonstrate that the gene rv1722 is present in most slow-growing mycobacteria but absent in most rapid-growing mycobacteria. While the role of GABA-trehalose in Mtb metabolism remains unclear, we postulate that the increased NADH/NAD+ ratio under hypoxia and nitric oxide exposure promotes GABA formation and inhibits its breakdown, leading to GABA accumulation and excretion. Rv1722-driven coupling of GABA and trehalose constitutes an alternative to excretion that conserves carbon and nitrogen. Taken together, our bottom-up approach reveals a new stress-response pathway in Mtb that rapidly produces large quantities of GABA-trehalose. These findings extend our knowledge of the metabolic adaptations that a major human pathogen utilizes in response to immune system-imposed stresses.

biochemistry↗

bioRxiv2026

Lineage 2-Beijing Mycobacterium tuberculosis strains suppress BCG-trained innate immunity early after infection

Genetically distinct lineages of Mycobacterium tuberculosis differ in their virulence, transmissibility, and immune evasion capacity. The modern Lineage 2-Beijing (L2-B) clade of Mtb, which is highly prevalent in Asia and now globally distributed, is associated with resistance to the bacille Calmette Guerin (BCG) vaccine. Using a murine BCG vaccination model followed by aerosol challenge with geographically matched L2-B or Lineage 4 clinical isolates, we examined how L2-B circumvents vaccine-induced immunity. BCG-trained alveolar macrophages showed impaired control of L2-B growth in vitro. Spatial transcriptomic profiling of infected lungs revealed broad transcriptional reprogramming, including selective suppression of pathways essential for macrophage activation and trained innate immunity. Similar immune dysregulation was observed in peripheral blood from BCG-vaccinated household contacts of L2-B smear-positive TB patients. Together, these findings suggest mechanisms of lineage-specific immune evasion in TB, highlight key components of BCG-induced protection, and support re-evaluation of current TB vaccine strategies.

immunology↗

bioRxiv2025

HIV-specific CD8+ T-cell responses soon after treatment initiation during acute HIV infection are associated with viral reservoir decline

Antiretroviral therapy (ART) initiated in the acute phase of HIV infection (AHI) results in a smaller viral reservoir. However, the impact of early HIV-specific T-cell responses on long- term reservoir dynamics is less well characterized. Therefore, we measured the size of the viral reservoir and functionality of HIV-specific CD8+ T-cell responses after the acute phase at 24 and 156 weeks after ART initiation in individuals who started treatment during AHI. A significant reduction in total and defective HIV DNA and a trend towards a reduction in intact HIV DNA were observed between 24 and 156 weeks. Functional CD8+ T-cell responses against HIV peptides Env, Gag, Nef, and Pol were maintained over three years after treatment initiation. The proliferative capacity of HIV-specific CD8+ T cells at 24 weeks of ART was predictive of the degree of reduction in total and defective HIV DNA between 24 and 156 weeks, suggesting HIV-specific CD8+ T-cells may at least partially drive the decline of the viral reservoir. Therefore, enforcing HIV-specific immune responses as early as possible after diagnosis of AHI should be a central focus of HIV cure strategies.

immunology↗

bioRxiv2024

Immune correlates of early clearance of Mycobacterium tuberculosis among tuberculosis household contacts in Indonesia

Some individuals, even when heavily exposed to an infectious tuberculosis patient, do not develop a specific T-cell response as measured by interferon-gamma release assay (IGRA). This could be explained by an IFN-{gamma}-independent adaptive immune response, or an effective innate host response clearing Mycobacterium tuberculosis (Mtb) without adaptive immunity. In heavily exposed Indonesian tuberculosis household contacts (n=1347), a persistently IGRA negative status was associated with presence of a BCG scar, and - especially among BCG-vaccinated individuals - with altered innate immune cells dynamics, higher heterologous (Escherichia coli-induced) proinflammatory cytokine production, and higher inflammatory proteins in the IGRA mitogen tube. Neither circulating concentrations of Mtb-specific antibodies nor functional antibody activity associated with IGRA status at baseline or follow-up. In a cohort of adults in a low tuberculosis incidence setting, BCG vaccination induced heterologous innate cytokine production, but only marginally affected Mtb-specific antibody profiles. Our findings suggest that a more efficient host innate immune response, rather than a humoral response, mediates early clearance of Mtb. The protective effect of BCG vaccination against Mtb infection may be linked to innate immune priming, also termed trained immunity.

immunology↗

bioRxiv2022

cis-eQTL mapping of TB-T2D comorbidity elucidates the involvement of African ancestry in TB susceptibility

The validation of genome-wide association signals for tuberculosis (TB) susceptibility and the development of type 2 diabetes (T2D) across diverse populations remain problematic. The ancestry-specific variants (coding and non-coding) that contribute to previously identified differentially expressed genes (DEG) in patients with TB, T2D and comorbid TB-T2D, remain unknown. Identifying ancestry-specific expression quantitative trait loci (eQTLs) can aid in distinguishing the most probable disease-causing variants for population-specific therapeutic interventions. Therefore, this study conducted cis-eQTL mapping in TB, T2D and TB-T2D patients to identify variants associated with DEG. Both genotyping (Infinium H3A array with [~]2.3 M markers) and RNA sequencing data of 96 complex multi-way admixed South Africans were used for this purpose. Importantly, both global-and local ancestry adjustment were included in statistical analysis to account for complex admixture. Unique gene-variant pairs were associated with TB-T2D on chromosome 7p22 whilst adjusting for Bantu-speaking African ancestry (PRKAR1B:rs4464850; P=7.68e-07) and Khoe-San ancestry (PRKAR1B:rs117842122; P=3.66e-07). In addition, IFITM3 (a biomarker for the development of TB) was associated with three SNPs (rs11025530, rs3808990, and rs10896664) on chromosome 11p15 while adjusting for Khoe-San ancestry. Our results also indicated that the upregulation of the NLRP6 inflammasome is strongly associated with people with TB-T2D while adjusting for Khoe-San ancestry. Three African-specific eGenes (NLRP6, IFITM3 and PRKAR1B) would have been missed if local ancestry adjustment was not conducted. This study determined a list of ancestry-specific eQTLs in TB-T2D patients that could potentially guide the search for new therapeutic targets for TB-T2D in African populations. Author SummaryThe limitation of genome-wide association study (GWAS) is that the particular biological pathway impacted by a variant might not be evident. eQTL mapping can be conducted to determine the impact that a genetic variant might have on the expression of a specific gene in a biological pathway. In this study the use of cis-eQTL mapping was explored to elucidate the underlying genetic variants that regulate gene expression between TB-T2D and T2D patients, and between TB patients and healthy controls with multi-way genetic admixture from South Africa. Using RNA sequencing data and newly genotyped dataset of 96 individuals (Illumina Infinium H3Africa array with [~]2.5 M markers), we were able to identify ancestry-specific eQTLs. eQTLs of indigenous Khoe-San ancestral origin were identified in genetic regions previously implicated in TB and T2D in African populations. If local ancestry was not incorporated in the cis-eQTL mapping analysis these important African-specific eQTLs would have been missed. Our results provide a list of possible ancestry-specific causal variants associated with TB-T2 comorbidity that could guide the search for new therapeutic targets for African-specific populations. Including populations with complex ancestry and admixture in genetic studies is necessary to improve the quality of genetic research in sub-Saharan African groups.

genetics↗

bioRxiv2021

An optimized protocol for dual RNA-Seq of human macrophages infected with Mycobacterium avium

Recently, dual RNA-sequencing (RNA-Seq) has been identified as a powerful tool to study host-pathogen interactions, which is particularly interesting for intracellular pathogens such as mycobacteria. However, due to the complexity of obtaining human host cells, many models rely on the usage of host cells derived from animals or cell lines, which does not accurately mimic the situation in the patient. Furthermore, due to the severe disbalance in host and pathogen RNA content, it is difficult to obtain sufficient sequencing depth for the infecting pathogen. Here, we present an optimized method to perform dual RNA-sequencing on human monocyte-derived macrophages (hMDMs) infected with Mycobacterium avium (M. avium). It is likely that, with slight modifications in multiplicity of infection (MOI) to account for differences in virulence, this methodology will be applicable for other difficult-to-lyse intracellular mycobacteria.

genomics↗

bioRxiv2020

Metformin enhances anti-mycobacterial responses by educating immunometabolic circuits of CD8+ T cells

Diabetic patients taking metformin have lower risk for Mycobacterium tuberculosis (Mtb) infection, progression from infection to tuberculosis (TB) disease, TB morality and TB recurrence. However, a detailed mechanistic understanding of metformins protective immunological benefits on host resistance to TB is lacking. In this study, using mass cytometry we show that metformin treatment expands memory-like antigen-inexperienced CD8+CXCR3+ T cells in naive mice, and in healthy and diabetic humans. Metformin-educated CD8+ T cells have increased (i) mitochondrial mass, oxidative phosphorylation, and fatty acid oxidation; (ii) survival capacity; and (iii) anti-mycobacterial properties. CD8+ T cells from CXCR3-/- mice did not exhibit metformin-mediated metabolic programming. In BCG-vaccinated mice and guinea pigs, metformin enhanced immunogenicity and protective efficacy against Mtb challenge. Collectively, our results demonstrate an important role of CD8+ T cells in metformin-derived host metabolic-fitness towards Mtb infection.

immunology↗

bioRxiv2020

A Bayesian analysis of the association between Leukotriene A4 Hydrolase genotype and survival probability of tuberculous meningitis patients treated with adjunctive dexamethasone

Tuberculous meningitis (TBM) remains the most devastating form of tuberculosis (TB) with high mortality despite effective antimicrobial treatment. As mortality has been linked to excessive inflammation, anti-inflammatory glucocorticoids are now routinely used as adjunctive treatment with antimicrobial therapy. However, they reduce mortality by only ~ 30%, raising the possibility that only a subset of TBM deaths are caused by inflammatory pathophysiology. Studies in Vietnam found that the survival benefit of adjunctive glucocorticoids was limited to individuals with a common promoter variant in the leukotriene A4 hydrolase (LTA4H) gene encoding an enzyme that regulates inflammatory eicosanoid expression. The variant constitutes a C/T transition with TT homozygotes having increased expression over CT heterozygotes and CC homozygotes. In Vietnam, the LTA4H TT genotype predicted survival, consistent with dexamethasone benefiting only those individuals with a dysregulated hyper-inflammatory response. However, a study of TBM patients in Indonesia did not find the LTA4H TT genotype to confer a significant survival benefit. Given the potential of personalized life-saving anti-inflammatory therapies guided by LTA4H genotype, we have used Bayesian methods to analyze the data from both studies. Bayesian analysis reveals that the LTA4H TT genotype confers survival benefit in both the Vietnam and Indonesia cohorts that begins within days and continues long-term. However, its benefit is nullified in the most severe cases where other factors cause early mortality. LTA4H TT genotype is associated with increased survival in HIV-positive patients also. Thus, our analysis extends the association of LTA4H genotype with TBM survival to populations outside of Vietnam and to HIV-positive patients. Patient LTA4H genotyping used in conjunction with disease severity assessment may help to target glucocorticoids to patients most likely to benefit from this broadly-acting immunosuppressive regimen despite its significant adverse effects.

molecular biology↗

bioRxiv2019

Persistent DNA Hyper-methylation Dampens Host Anti-Mycobacterial Immunity

Mycobacterium tuberculosis (Mtb) has co-evolved with humans for millennia and developed multiple mechanisms to evade host immunity. Restoring host immunity in order to shorten existing therapy and improve outcomes will require identifying the full complement by which host immunity is inhibited. Perturbing host DNA methylation is a mechanism induced by chronic infections such as HIV, HPV, LCMV and schistosomiasis to evade host immunity. Here, we evaluated the DNA methylation status of TB patients and their asymptomatic household contacts demonstrating that TB patients have DNA hyper-methylation of the IL-2-STAT5, TNF-NF-{varkappa}B and IFN-{gamma} signaling pathways. By MSRE-qPCR, multiple genes of the IL-12-IFN-{gamma} signaling pathway (IL12B, IL12RB2, TYK2, IFNGR1, JAK1 and JAK2) were hyper-methylated in TB patients. The DNA hyper-methylation of these pathways is associated with decreased immune responsiveness with decreased mitogen induced upregulation of IFN-{gamma}, TNF, IL-6 and IL-1{beta} production. The DNA hyper-methylation of the IL-12-IFN-{gamma} pathway was associated with decreased IFN-{gamma} induced gene expression and decreased IL-12 inducible up-regulation of IFN-{gamma}. This work demonstrates that immune cells from TB patients are characterized by DNA hyper-methylation of genes critical to mycobacterial immunity resulting in decreased mycobacteria-specific and non-specific immune responsiveness.

immunology↗

bioRxiv2018

Associations between impulsivity, risk behavior and HIV, HBV, HCV and syphilis seroprevalence among female prisoners in Indonesia: A cross-sectional study

HIV, hepatitis B and C, and syphilis share common transmission routes of which primarily unsafe sexual contact and injecting drug use are important. Impulsivity is a major factor contributing to this transmission risk behavior, however comprehensive studies within female, prison, and Asian populations are scarce. This cross-sectional study aims to delineate the contributions of different aspects of impulsivity to transmission risk behavior, among female inmates living in a prison in Jakarta (N=214). The relationships between various aspects of impulsivity, risky behavior and seropositivity were tested using analyses of variance and logistic regression analyses. Motor impulsivity was related to alcohol use, reward-related impulsivity to drug use, and cognitive/goal-directed impulsivity to sexual risk behavior. Finally, goal-directed impulsivity was also directly associated with seropositivity. Specific aspects of impulsivity are associated with different types of risky behaviors in Indonesian female prisoners, what can be relevant for future studies on infection prevention strategies for such a population.

epidemiology↗

bioRxiv2018

A double-blinded randomised placebo-controlled phase II trial to evaluate high dose rifampicin for tuberculous meningitis: a dose finding study

BackgroundHigh doses of rifampicin may help tuberculous meningitis (TBM) patients to survive. Pharmacokinetic-pharmacodynamic evaluations suggested that rifampicin doses higher than 13 mg/kg intravenously or 20 mg/kg orally (as previously studied) are warranted to maximize treatment response.\n\nMethodsIn a double-blinded, randomised, placebo-controlled phase II trial, we assigned 60 adult TBM patients in Bandung, Indonesia, to standard 450 mg, 900 mg or 1350 mg (10, 20 and 30 mg/kg) oral rifampicin combined with other TB drugs for 30 days. Endpoints included pharmacokinetic measures, adverse events and survival.\n\nResultsA double and triple dose of oral rifampicin led to three and five-fold higher geometric mean total exposures in plasma in the critical early days (2{+/-}1) of treatment (AUC0-24h: 53{middle dot}5 mg.h/L vs 170{middle dot}6 mg.h/L vs. 293{middle dot}5 mg.h/L, p<0{middle dot}001), with proportional increases in CSF concentrations and without an increase in the incidence of grade 3/4 adverse events. Six-month mortality was 7/20 (35%, 9/20 (45%) and 3/20 (15%) in the 10, 20 and 30 mg/kg groups, respectively (p=0{middle dot}12).\n\nConclusionsTripling the standard dose caused a large increase in rifampicin exposure in plasma and CSF and was safe. Survival benefit with this dose should now be evaluated in a larger phase III clinical trial.

clinical trials↗