ABSTRACT
OBJECTIVES: To determine the association of the use of the multiplex assay meningitis/encephalitis panel with clinical management of suspected meningitis. METHODS: A cross-sectional study was conducted with children 0 to 18 years of age who received a lumbar puncture within 48 hours of admission for an infectious workup. Patient demographic and presenting information, laboratory studies, and medication administration were collected. The primary measure was length of stay (LOS) with secondary measures: time on antibiotics, time to narrowing antibiotics, and acyclovir doses. LOS and antibiotic times were stratified for outcomes occurring before 36 hours. Logistic regression analysis was used to account for potential confounding factors associated with both the primary and secondary outcomes. A value of P < .05 was considered statistically significant. RESULTS: Meningitis panel use was associated with a higher likelihood of a patient LOS <36 hours (P = .04; odds ratio = 1.7; 95% confidence interval [CI]: 1.03-2.87), a time to narrowing antibiotics <36 hours (P = .008; odds ratio = 1.89; 95% CI: 1.18-2.87), and doses of acyclovir (P < .001; incidence rate ratio = 0.37; 95% CI: 0.26-0.53). When controlling for potential confounding factors, these associations persisted. CONCLUSIONS: Use of the meningitis panel was associated with a decreased LOS, time to narrowing of antibiotics, and fewer acyclovir doses. This likely is a result of the rapid turnaround time as compared with cerebrospinal fluid cultures. Additional studies to examine the outcomes related to this change in management are warranted.
Subject(s)
Encephalitis, Herpes Simplex/diagnosis , Enterovirus Infections/diagnosis , Meningitis, Bacterial/diagnosis , Meningitis, Pneumococcal/diagnosis , Meningitis, Viral/diagnosis , Roseolovirus Infections/diagnosis , Acyclovir/therapeutic use , Anti-Bacterial Agents/therapeutic use , Antiviral Agents/therapeutic use , Cross-Sectional Studies , Encephalitis, Herpes Simplex/cerebrospinal fluid , Encephalitis, Herpes Simplex/drug therapy , Enterovirus Infections/cerebrospinal fluid , Enterovirus Infections/drug therapy , Female , Humans , Infant , Infant, Newborn , Length of Stay/statistics & numerical data , Male , Meningitis, Bacterial/cerebrospinal fluid , Meningitis, Bacterial/drug therapy , Meningitis, Pneumococcal/cerebrospinal fluid , Meningitis, Pneumococcal/drug therapy , Meningitis, Viral/cerebrospinal fluid , Meningitis, Viral/drug therapy , Real-Time Polymerase Chain Reaction , Retrospective Studies , Roseolovirus Infections/cerebrospinal fluid , Roseolovirus Infections/drug therapy , Spinal PunctureABSTRACT
The rate of transcription elongation plays an important role in the timing of expression of full-length transcripts as well as in the regulation of alternative splicing. In this study, we coupled Bru-seq technology with 5,6-dichlorobenzimidazole 1-ß-D-ribofuranoside (DRB) to estimate the elongation rates of over 2000 individual genes in human cells. This technique, BruDRB-seq, revealed gene-specific differences in elongation rates with a median rate of around 1.5 kb/min. We found that genes with rapid elongation rates showed higher densities of H3K79me2 and H4K20me1 histone marks compared to slower elongating genes. Furthermore, high elongation rates had a positive correlation with gene length, low complexity DNA sequence, and distance from the nearest active transcription unit. Features that negatively correlated with elongation rate included the density of exons, long terminal repeats, GC content of the gene, and DNA methylation density in the bodies of genes. Our results suggest that some static gene features influence transcription elongation rates and that cells may alter elongation rates by epigenetic regulation. The BruDRB-seq technique offers new opportunities to interrogate mechanisms of regulation of transcription elongation.
Subject(s)
Epigenesis, Genetic , Genome, Human , RNA Polymerase II/metabolism , Transcription Elongation, Genetic , Base Composition , DNA Methylation , Exons , Histones/genetics , Histones/metabolism , Humans , MCF-7 Cells , RNA Polymerase II/genetics , Terminal Repeat SequencesABSTRACT
The anti-cancer drug camptothecin inhibits replication and transcription by trapping DNA topoisomerase I (Top1) covalently to DNA in a "cleavable complex". To examine the effects of camptothecin on RNA synthesis genome-wide we used Bru-Seq and show that camptothecin treatment primarily affected transcription elongation. We also observed that camptothecin increased RNA reads past transcription termination sites as well as at enhancer elements. Following removal of camptothecin, transcription spread as a wave from the 5'-end of genes with no recovery of transcription apparent from RNA polymerases stalled in the body of genes. As a result, camptothecin preferentially inhibited the expression of large genes such as proto-oncogenes, and anti-apoptotic genes while smaller ribosomal protein genes, pro-apoptotic genes and p53 target genes showed relative higher expression. Cockayne syndrome group B fibroblasts (CS-B), which are defective in transcription-coupled repair (TCR), showed an RNA synthesis recovery profile similar to normal fibroblasts suggesting that TCR is not involved in the repair of or RNA synthesis recovery from transcription-blocking Top1 lesions. These findings of the effects of camptothecin on transcription have important implications for its anti-cancer activities and may aid in the design of improved combinatorial treatments involving Top1 poisons.
