Biology subjects

Phu, N. H.

Publications and source records attributed to Phu, N. H..

4 recordsLinked to original sources

bioRxiv2023

Whole blood transcriptional profiles and the pathogenesis of tuberculous meningitis

BackgroundMortality and morbidity from tuberculous meningitis (TBM) are frequent and strongly associated with the inflammatory response to Mycobacterium tuberculosis infection. However, the mechanisms driving the associations are uncertain. We sought to identify the gene modules, hubs and pathways associated with the pathogenesis and mortality from TBM, and to identify which best-predicted death. MethodsWe used whole blood RNA sequencing to obtain transcriptional profiles from 281 Vietnamese adults with TBM (207 HIV-negative; 74 HIV-positive), 295 with pulmonary TB (PTB), and 30 healthy controls. The TBM cohort was divided randomly into a discovery cohort (n=142) and a validation cohort (n=139). Weighted gene co-expression network analysis identified clusters of genes (or modules) and hub genes associated with death or disease severity. An overrepresentation analysis identified pathways associated with TBM mortality, with a consensus analysis identifying consensual patterns between HIV-positive and HIV-negative individuals. A multivariate elastic-net Cox regression model selected the candidate predictors of TBM mortality, then model prediction performance using logistic regression and internal bootstrap validation to choose best predictors. ResultsOverall, TBM mortality was associated with increased neutrophil activation and decreased T and B cell activation pathways. Death from TBM was associated with increased angiogenesis in HIV-positive adults, and with activated TNF signaling and down-regulated extracellular matrix organization in HIV-negative adults. PTB and TBM have similar transcriptional profiles compared to healthy controls, although inflammatory genes were more activated in HIV-positive than HIV-negative TBM. The expression of four hub genes - MCEMP1, NELL2, ZNF354C and CD4 - were strongly predictive of death from TBM (AUC 0.80 and 0.86 for HIV-negative and HIV-positive, respectively). ConclusionsWhole blood transcriptional profiling revealed that TBM is associated with a characteristic systemic inflammatory response, similar to that invoked by pulmonary tuberculosis, but with key gene modules, hubs and pathways strongly associated with death. Our analysis suggests a novel 4-gene biomarker for predicting death from TBM, but also opens a new window into TBM pathogenesis that may reveal novel therapeutic targets for this lethal disease.

molecular biology↗

bioRxiv2020

Elevated cerebrospinal fluid cytokine levels in tuberculous meningitis predict survival in response to dexamethasone

Adjunctive treatment with anti-inflammatory corticosteroids like dexamethasone increases survival in tuberculosis meningitis. Dexamethasone responsiveness associates with a C/T variant in Leukotriene A4 Hydrolase (LTA4H), which regulates expression of the pro-inflammatory mediator leukotriene B4 (LTB4). TT homozygotes, with increased LTB4, have the highest survival when treated with dexamethasone and the lowest survival without. While the T allele is present in only a minority of the worlds population, corticosteroids confer modest survival benefit worldwide. Using Bayesian methods, we examined how pre-treatment levels of cerebrospinal fluid (CSF) pro-inflammatory cytokines affect survival in dexamethasone-treated tuberculous meningitis. LTA4H TT homozygosity was associated with global cytokine increases, including TNF. Association between higher cytokine levels and survival extended to non-TT patients, suggesting that other genetic variants may also induce dexamethasone-responsive pathological inflammation. These findings warrant studies that tailor dexamethasone therapy to pre-treatment CSF cytokine concentrations, while searching for additional genetic loci shaping the inflammatory milieu.

immunology↗

bioRxiv2020

Most-probable number based minimum duration of killing assay for determining the spectrum of rifampicin susceptibility in clinical M. tuberculosis isolates

Accurate antibiotic susceptibility testing is essential for successful tuberculosis treatment. Recent studies have highlighted the limitations of minimum inhibitory concentrations (MIC) based phenotypic susceptibility methods in detecting other aspects of antibiotic susceptibilities in bacteria. Duration and peak of antibiotic exposure, at or above the MIC required for killing the bacterial population, has emerged as another important factor for determining the antibiotic susceptibility. This is broadly defined as antibiotic tolerance. Antibiotic tolerance can further facilitate the emergence of antibiotic resistance. Currently there are limited methods to quantify antibiotic tolerance among clinical M. tuberculosis isolates. In this study, we develop a most-probable number (MPN) based minimum duration of killing (MDK) assay to quantify the spectrum of M. tuberculosis rifampicin susceptibility within subpopulations, based on time duration of rifampicin exposure required for killing the bacterial population. MDK90-99 and MDK99.99 defined as the minimum time duration of antibiotic exposure at or above MIC required for killing 90-99% and 99.99% of the initial (pre-treatment) bacterial population respectively. Results from the rifampicin MDK assay applied to 28 laboratory and clinical M. tuberculosis isolates showed that there is variation in rifampicin susceptibility among isolates. Rifampicin MDK99/99.99 time for isolates varied from less than 2 to 10 days. MDK duration was correlated with larger sub-populations of M. tuberculosis from clinical isolates that were rifampicin tolerant. Our study demonstrates the utility of MDK assays to measure the variation in antibiotic tolerance among clinical M. tuberculosis isolates and further expands clinically important aspects of antibiotic susceptibility testing.

microbiology↗

bioRxiv2020

Diagnostic Cerebrospinal Fluid Biomarker Discovery and Validation in Patients with Central Nervous System Infections

BackgroundCentral nervous system (CNS) infections are common causes of morbidity and mortality worldwide. Rapid, accurate identification of the likely cause is essential for clinical management and the early initiation of antimicrobial therapy, which potentially improves clinical outcome. MethodsWe applied liquid chromatography tandem mass-spectrometry on 45 cerebrospinal fluid (CSF) samples from a cohort of adults with/without CNS infections to discover potential diagnostic protein biomarkers. We then validated the diagnostic performance of a selected biomarker candidate in an independent cohort of 364 consecutively treated adults with CNS infections admitted to a referral hospital in southern Vietnam. ResultsIn the discovery cohort, we identified lipocalin 2 (LCN2) as a potential biomarker of bacterial meningitis. The analysis of the validation cohort showed that LCN2 could discriminate bacterial meningitis from other CNS infections, including tuberculous meningitis, cryptococcal meningitis and viral/antibody-mediated encephalitis (sensitivity: 0.88 (95% confident interval (CI): 0.77-0.94), specificity: 0.91 (95%CI: 0.88-0.94) and diagnostic odd ratio: 73.8 (95%CI: 31.8-171.4)). LCN2 outperformed other CSF markers (leukocytes, glucose, protein and lactate) commonly used in routine care worldwide. The combination of LCN2 and these four routine CSF markers resulted in the highest diagnostic performance for bacterial meningitis (area under receiver-operating-characteristic-curve 0.96; 95%CI: 0.93-0.99). ConclusionsOur results suggest that LCN2 is a sensitive and specific biomarker for discriminating bacterial meningitis from a broad spectrum of CNS infections. A prospective study is needed to further assess the diagnostic utility of LCN2 in the diagnosis and management of CNS infections.

microbiology↗