Browsing by Subject "infectious disease"

Now showing 1 - 8 of 8

Open Access
A Decade On: Systematic Review of ClinicalTrials.gov Infectious Disease Trials, 2007-2017.
(Open forum infectious diseases, 2019-06) Jaffe, Ian S; Chiswell, Karen; Tsalik, Ephraim L
Background:Registration of interventional trials of Food and Drug Administration-regulated drug and biological products and devices became a legal requirement in 2007; the vast majority of these trials are registered in ClinicalTrials.gov. An analysis of ClinicalTrials.gov offers an opportunity to define the clinical research landscape; here we analyze 10 years of infectious disease (ID) clinical trial research. Methods:Beginning with 166 415 interventional trials registered in ClinicalTrials.gov from 2007-2017, ID trials were selected by study conditions and interventions. Relevance to ID was confirmed through manual review, resulting in 13 707 ID trials and 152 708 non-ID trials. Results:ID-related trials represented 6.9%-9.9% of all trials with no significant trend over time. ID trials tended to be more focused on treatment and prevention, with a focus on testing drugs, biologics, and vaccines. ID trials tended to be large, randomized, and nonblinded with a greater degree of international enrollment. Industry was the primary funding source for 45.2% of ID trials. Compared with the global burden of disease, human immunodeficiency virus/AIDS and hepatitis C trials were overrepresented, and lower respiratory tract infection trials were underrepresented. Hepatitis C trials fluctuated, keeping with a wave of new drug development. Influenza vaccine trials peaked during the 2009 H1N1 swine influenza outbreak. Conclusions:This study presents the most comprehensive characterization of ID clinical trials over the past decade. These results help define how clinical research aligns with clinical need. Temporal trends reflect changes in disease epidemiology and the impact of scientific discovery and market forces. Periodic review of ID clinical trials can help identify gaps and serve as a mechanism to realign resources.
Open Access
A phylogenetic transform enhances analysis of compositional microbiota data.
(Elife, 2017-02-15) Silverman, Justin D; Washburne, Alex D; Mukherjee, Sayan; David, Lawrence A
Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abundance data. Here, we introduce the PhILR transform, which incorporates microbial evolutionary models with the isometric log-ratio transform to allow off-the-shelf statistical tools to be safely applied to microbiota surveys. We demonstrate that analyses of community-level structure can be applied to PhILR transformed data with performance on benchmarks rivaling or surpassing standard tools. Additionally, by decomposing distance in the PhILR transformed space, we identified neighboring clades that may have adapted to distinct human body sites. Decomposing variance revealed that covariation of bacterial clades within human body sites increases with phylogenetic relatedness. Together, these findings illustrate how the PhILR transform combines statistical and phylogenetic models to overcome compositional data challenges and enable evolutionary insights relevant to microbial communities.
Open Access
Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut.
(eLife, 2018-06-19) Reese, Aspen T; Cho, Eugenia H; Klitzman, Bruce; Nichols, Scott P; Wisniewski, Natalie A; Villa, Max M; Durand, Heather K; Jiang, Sharon; Midani, Firas S; Nimmagadda, Sai N; O'Connell, Thomas M; Wright, Justin P; Deshusses, Marc A; David, Lawrence A
How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact host and microbial function, change redox state and how this contributes to post-antibiotic succession. We showed gut redox potential increased within hours of an antibiotic dose in mice. Host and microbial functioning changed under treatment, but shifts in redox potentials could be attributed specifically to bacterial suppression in a host-free ex vivo human gut microbiota model. Redox dynamics were linked to blooms of the bacterial family Enterobacteriaceae. Ecological succession to pre-treatment composition was associated with recovery of gut redox, but also required dispersal from unaffected gut communities. As bacterial competition for electron acceptors can be a key ecological factor structuring gut communities, these results support the potential for manipulating gut microbiota through managing bacterial respiration.
Open Access
Comparison of a Blood Self-Collection System with Routine Phlebotomy for SARS-CoV-2 Antibody Testing.
(Diagnostics (Basel, Switzerland), 2022-07) Wixted, Douglas; Neighbors, Coralei E; Pieper, Carl F; Wu, Angie; Kingsbury, Carla; Register, Heidi; Petzold, Elizabeth; Newby, L Kristin; Woods, Christopher W
The Coronavirus Disease 2019 (COVID-19) pandemic forced researchers to reconsider in-person assessments due to transmission risk. We conducted a pilot study to evaluate the feasibility of using the Tasso-SST (Tasso, Inc, Seattle, Washington) device for blood self-collection for use in SARS-CoV-2 antibody testing in an ongoing COVID-19 prevalence and immunity research study. 100 participants were recruited between January and March 2021 from a previously identified sub-cohort of the Cabarrus County COVID-19 Prevalence and Immunity (C3PI) Study who were under-going bimonthly COVID-19 antibody testing. Participants were given a Tasso-SST kit and asked to self-collect blood during a scheduled visit where trained laboratory personnel performed routine phlebotomy. All participants completed an after-visit survey about their experience. Overall, 70.0% of participants were able to collect an adequate sample for testing using the device. Among those with an adequate sample, there was a high concordance in results between the Tasso-SST and phlebotomy blood collection methods (Cohen’s kappa coefficient = 0.88, Interclass correlation coefficient 0.98 [0.97, 0.99], p < 0.0001). The device received a high-level (90.0%) of acceptance among all participants. Overall, the Tasso-SST could prove to be a valuable tool for seroprevalence testing. However, future studies in larger, diverse populations over longer periods may provide a better understanding of device usability and acceptance among older participants and those with comorbidities in various use scenarios.
Open Access
Epidemiology of surgical site infections after solid organ transplants in the period 2015-2019: A single-center retrospective cohort study.
(American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, 2022-09) Carugati, Manuela; Arif, Sana; Sudan, Debra Lynn; Collins, Bradley Henry; Haney, John Carroll; Schroder, Jacob Niall; Reynolds, John Michael; Lewis, Sarah Stamps; Yarrington, Michael Edwards; Miller, Rachel Ann; Alexander, Barbara Dudley
Surgical site infections (SSI) are severe complications of solid organ transplant (SOT). This retrospective study assessed the epidemiology of and outcomes associated with invasive primary SSI (IP-SSI) occurring within 3 months of transplantation in adult SOT recipients at Duke University over a 5-year period (2015-2019). Among 2073 consecutive SOT recipients, 198 IP-SSI were identified. The IP-SSI rate declined over the period (14.4% in 2015 vs. 8.3% in 2019) and was higher among multi-organ compared with single-organ transplants (33.9% vs. 8.1%, p < .01). SOT recipients with IP-SSI had longer hospital stays than patients without SSI (30.0 vs. 17.0 days, p < .01). Transplant hospitalization (9.6% vs. 2.2%, p < .01), 6-month (11.6% vs. 3.3%, p < .01), and 1-year mortality (15.7% vs. 5.8%, p < .01) were higher in SOT recipients with IP-SSI than in those without. While Gram-positive bacteria were the most common pathogens, urogenital Mollicute and atypical Mycobacteria were identified as an unexpected cause of IP-SSI, particularly among lung transplant recipients. The median time to IP-SSI was 24.0 (IQR 13.8-48.3) days, although the time to IP-SSI varied based on organ transplanted and the causative pathogen. IP-SSI is an important and potentially modifiable complication of SOT, associated with prolonged hospitalizations and reduced survival, particularly in the lung transplant population.
Open Access
Epstein-Barr virus ensures B cell survival by uniquely modulating apoptosis at early and late times after infection.
(Elife, 2017-04-20) Price, Alexander M; Dai, Joanne; Bazot, Quentin; Patel, Luv; Nikitin, Pavel A; Djavadian, Reza; Winter, Peter S; Salinas, Cristina A; Barry, Ashley Perkins; Wood, Kris C; Johannsen, Eric C; Letai, Anthony; Allday, Martin J; Luftig, Micah A
Latent Epstein-Barr virus (EBV) infection is causally linked to several human cancers. EBV expresses viral oncogenes that promote cell growth and inhibit the apoptotic response to uncontrolled proliferation. The EBV oncoprotein LMP1 constitutively activates NFκB and is critical for survival of EBV-immortalized B cells. However, during early infection EBV induces rapid B cell proliferation with low levels of LMP1 and little apoptosis. Therefore, we sought to define the mechanism of survival in the absence of LMP1/NFκB early after infection. We used BH3 profiling to query mitochondrial regulation of apoptosis and defined a transition from uninfected B cells (BCL-2) to early-infected (MCL-1/BCL-2) and immortalized cells (BFL-1). This dynamic change in B cell survival mechanisms is unique to virus-infected cells and relies on regulation of MCL-1 mitochondrial localization and BFL-1 transcription by the viral EBNA3A protein. This study defines a new role for EBNA3A in the suppression of apoptosis with implications for EBV lymphomagenesis.
Open Access
Haplotype Association Mapping Identifies a Candidate Gene Region in Mice Infected With Staphylococcus aureus.
(G3 (Bethesda), 2012-06) Johnson, Nicole V; Ahn, Sun Hee; Deshmukh, Hitesh; Levin, Mikhail K; Nelson, Charlotte L; Scott, William K; Allen, Andrew; Fowler, Vance G; Cowell, Lindsay G
Exposure to Staphylococcus aureus has a variety of outcomes, from asymptomatic colonization to fatal infection. Strong evidence suggests that host genetics play an important role in susceptibility, but the specific host genetic factors involved are not known. The availability of genome-wide single nucleotide polymorphism (SNP) data for inbred Mus musculus strains means that haplotype association mapping can be used to identify candidate susceptibility genes. We applied haplotype association mapping to Perlegen SNP data and kidney bacterial counts from Staphylococcus aureus-infected mice from 13 inbred strains and detected an associated block on chromosome 7. Strong experimental evidence supports the result: a separate study demonstrated the presence of a susceptibility locus on chromosome 7 using consomic mice. The associated block contains no genes, but lies within the gene cluster of the 26-member extended kallikrein gene family, whose members have well-recognized roles in the generation of antimicrobial peptides and the regulation of inflammation. Efficient mixed-model association (EMMA) testing of all SNPs with two alleles and located within the gene cluster boundaries finds two significant associations: one of the three polymorphisms defining the associated block and one in the gene closest to the block, Klk1b11. In addition, we find that 7 of the 26 kallikrein genes are differentially expressed between susceptible and resistant mice, including the Klk1b11 gene. These genes represent a promising set of candidate genes influencing susceptibility to Staphylococcus aureus.
Open Access
Hemorrhagic Herpes Simplex Virus Type 1 Nephritis: An Unusual Cause of Acute Allograft Dysfunction.
(Am J Transplant, 2017-01) Hemmersbach-Miller, M; Duronville, J; Sethi, S; Miller, SE; Howell, DN; Henshaw, N; Alexander, BD; Roberts, JK
Interstitial nephritis due to viruses is well-described after solid organ transplantation. Viruses implicated include cytomegalovirus; BK polyomavirus; Epstein-Barr virus; and, less commonly, adenovirus. We describe a rare case of hemorrhagic allograft nephritis due to herpes simplex virus type 1 at 10 days after living donor kidney transplantation. The patient had a favorable outcome with intravenous acyclovir and reduction of immunosuppression.