Biology subjects

Davidson, R. M.

Publications and source records attributed to Davidson, R. M..

3 recordsLinked to original sources

bioRxiv2023

Transcriptional adaptation of drug-tolerant Mycobacterium tuberculosis in mice

Transcriptome evaluation of Mycobacterium tuberculosis in the lungs of laboratory animals during long-term treatment has been limited by extremely low abundance of bacterial mRNA relative to eukaryotic RNA. Here we report a targeted amplification RNA sequencing method called SEARCH-TB. After confirming that SEARCH-TB recapitulates conventional RNA-seq in vitro, we applied SEARCH-TB to Mycobacterium tuberculosis-infected BALB/c mice treated for up to 28 days with the global standard isoniazid, rifampin, pyrazinamide, and ethambutol regimen. We compared results in mice with 8-day exposure to the same regimen in vitro. After treatment of mice for 28 days, SEARCH-TB suggested broad suppression of genes associated with bacterial growth, transcription, translation, synthesis of rRNA proteins and immunogenic secretory peptides. Adaptation of drug-stressed Mycobacterium tuberculosis appeared to include a metabolic transition from ATP-maximizing respiration towards lower-efficiency pathways, modification and recycling of cell wall components, large-scale regulatory reprogramming, and reconfiguration of efflux pumps expression. Despite markedly different expression at pre-treatment baseline, murine and in vitro samples had broadly similar transcriptional change during treatment. The differences observed likely indicate the importance of immunity and pharmacokinetics in the mouse. By elucidating the long-term effect of tuberculosis treatment on bacterial cellular processes in vivo, SEARCH-TB represents a highly granular pharmacodynamic monitoring tool with potential to enhance evaluation of new regimens and thereby accelerate progress towards a new generation of more effective tuberculosis treatment.

microbiology↗

bioRxiv2021

NK cell metabolic adaptation to infection promotes survival and viral clearance.

Natural killer (NK) cells are essential for early protection against virus infection, and must metabolically adapt to the energy demands of activation. Here, we found upregulation of the metabolic adaptor hypoxia inducible factor-1 (HIF-1) is a feature of NK cells during murine cytomegalovirus (MCMV) infection in vivo. HIF-1-deficient NK cells failed to control viral load, causing increased morbidity. No defects were found in effector functions of HIF-1 KO NK cells however, their numbers were significantly reduced. Loss of HIF-1 did not affect NK cell proliferation during in vivo infection and in vitro cytokine stimulation. Instead, we found HIF1-deficient NK cells showed increased expression of the pro-apoptotic protein Bim and glucose metabolism was impaired during cytokine stimulation in vitro. Similarly, during MCMV infection HIF1-deficient NK cells upregulated Bim and had increased caspase activity. Thus, NK cells require HIF-1-dependent metabolic functions to repress Bim expression and sustain cell numbers for an optimal virus response.

immunology↗

bioRxiv2019

Population Genomics of Nontuberculous Mycobacteria Recovered from United States Cystic Fibrosis Patients

Nontuberculous mycobacteria (NTM) pose a threat to individuals with cystic fibrosis (CF) due to an increased prevalence of pulmonary infections, innate drug resistance of the bacteria, and potential transmission between CF patients. To explore the genetic diversity of NTM isolated from CF patients within the United States (US) and to identify potential transmission events, we sequenced and analyzed the genomes of 341 NTM isolates from 191 CF patients as part of a nationwide surveillance study. The most abundant species in the isolate cohort were Mycobacterium abscessus (59.5%), followed by species in the Mycobacterium avium complex (37.5%). Phylogenomic analyses of the three M. abscessus subspecies revealed that more than half of CF patients had isolates in one of four dominant clones, including two dominant clones of M. abscessus subspecies abscessus and two dominant clones of M. abscessus subspecies massiliense. M. avium isolates from US CF patients, however, do not have dominant clones and are phylogenetically diverse. Longitudinal NTM isolates were compared to determine genome-wide single nucleotide polymorphisms (SNPs) that occur within patients over time. This information was used to compare between and within-patient SNP distributions, to quantitatively define SNP thresholds suggestive of transmission, and calculate a posterior probability of recent transmission given the SNP distance between two isolates from different patients. Out of 114 patients with M. abscessus subspecies, ten clusters of highly similar isolates from 26 patients were identified. Among the 26 patients in the M. abscessus clusters, 12 attended the same CF care centers. No highly similar isolate clusters were observed in M. avium. Our study reveals the contrasting genomic diversity and epidemiology of two major NTM taxa and the potential for between-patient exposure and cross-transmission of these emerging pathogens.

microbiology↗