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Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon
Get PDFBackground: Resistance to antimalarial drugs remains a major obstacle to malaria elimination. Multiplexed, targeted amplicon sequencing is being adopted for surveilling resistance and dissecting the genetics of complex malaria infections. Moreover, genotyping of parasites and detection of molecular markers drug resistance in resource-limited regions requires opensource protocols for processing samples, using accessible reagents, and rapid methods for processing numerous samples including pooled sequencing. Methods: Plasmodium falciparum Streamlined Multiplex Antimalarial Resistance and Relatedness Testing (Pf-SMARRT) is a PCR-based amplicon panel consisting of 15 amplicons targeting antimalarial resistance mutations and 9 amplicons targeting hypervariable regions. This assay uses oligonucleotide primers in two pools and a non-proprietary library and barcoding approach. Results: We evaluated Pf-SMARRT using control mocked dried blood spots (DBS) at varying levels of parasitemia and a mixture of 3D7 and Dd2 strains at known frequencies, showing the ability to genotype at low parasite density and recall within-sample allele frequencies. We then piloted Pf-SMARRT to genotype 100 parasite isolates collected from uncomplicated malaria cases at three health facilities in Dschang, Western Cameroon. Antimalarial resistance genotyping showed high levels of sulfadoxine-pyrimethamine resistance mutations, including 31% prevalence of the DHPS A613S mutation. No K13 candidate or validated artemisinin partial resistance mutations were detected, but one low-level non-synonymous change was observed. Pf-SMARRT’s hypervariable targets, used to assess complexity of infections and parasite diversity and relatedness, showed similar levels and patterns compared to molecular inversion probe (MIP) sequencing. While there was strong concordance of antimalarial resistance mutations between individual samples and pools, low-frequency variants in the pooled samples were often missed. Conclusion: Overall, Pf-SMARRT is a robust tool for assessing parasite relatedness and antimalarial drug resistance markers from both individual and pooled samples. Control samples support that accurate genotyping as low as 1 parasite per microliter is routinely possible
Prior heat waves improve survival of field but not domesticated populations of tobacco hornworm exposed to repeated bacterial infections
Get PDFIn insects and other invertebrates, prior pathogen exposures can improve immune responses and survival to subsequent infections through immune priming. Alternatively, stress and metabolic costs of multiple infections can impair host immunity and survival. The effects of high‐temperature extremes on host–pathogen interactions are not well understood despite the increasing occurrence of heat waves caused by climate change. The response of insects to heat waves and pathogens depends on recent evolutionary history with selective pressures. Domestication of insect pests has occurred in lab colonies of model species, reducing selective pressures for immune and heat stress responses. Lab strains are often used in immunological or heat stress experiments to represent wild field strains, but the efficacy of this approach is seldom evaluated. Using the tobacco hornworm ( Manduca sexta ), we tested the impact of a heat wave during initial pathogen exposure on survival of a secondary infection with Bacillus thuringiensis bacteria. We used a domesticated lab population and a naturally occurring field population of M. sexta to evaluate the impacts of recent domestication on immune and thermal responses. A heat wave during initial infection significantly increased survival of the secondary B. thuringiensis infection in the field, but not the lab population of M. sexta. In the field population, survival of the repeated infection was temperature dependent: exposure to an initial infection event reduced survival of the secondary infection at the control temperature regime, consistent with a stress effect. However, a heat wave during the initial infection event increased survival of the secondary infection, consistent with immune priming effects. The results of this study demonstrate that (a) insect response to thermal stress and pathogens can depend on recent domestication and (b) responses of hosts to repeat pathogen exposures can be temperature‐dependent, suggesting that cross‐talk between the heat stress and immune memory pathways may have important consequences for host–pathogen outcomes under heat wave events. Read the free Plain Language Summary for this article on the Journal blog
Social Anxiety, Negative Affect, and Hearing Difficulties in Adults.
Get PDFSubjective ratings of communication function reflect both auditory sensitivity and the situational, social, and emotional consequences of communication difficulties. Listeners interact with people and their environment differently, have various ways of handling stressful situations, and have diverse communication needs. Therefore, understanding the relationship between auditory and mental health factors is crucial for the holistic diagnosis and treatment of communication difficulty, particularly as mental health and communication function may have bidirectional effects. The goal of this study was to evaluate the degree to which social anxiety and negative affect (encompassing generalized anxiety, depression, and anger) contributed to subjective communication function (hearing handicap) in adult listeners. A cross-sectional online survey was administered via REDCap. Primary measures were brief assessments of social anxiety, negative affect, and subjective communication function measures. Participants were 628 adults (408 women, 220 men), ages 19 to 87 years (mean = 43) living in the United States. Results indicated that individuals reporting higher social anxiety and higher negative affect also reported poorer communication function. Multiple linear regression analysis revealed that both negative affect and social anxiety were significant and unique predictors of subjective communication function. Social anxiety and negative affect both significantly, and uniquely, contribute to how much someone feels a hearing loss impacts their daily communication function. Further examination of social anxiety and negative affect in older adults with hearing loss may help researchers and clinicians understand the complex interactions between mental health and sensory function during everyday communication, in this rapidly growing clinical population
Identification of Social Risk‐Related Referrals in Discrete Primary Care Electronic Health Record Data: Lessons Learned From a Novel Methodology
Get PDFOBJECTIVE: To assess the utility of using discrete primary care electronic health record (EHR) data to identify social risk referrals in a national network of community-based clinics. DATA SOURCES AND STUDY SETTING: Primary data were abstracted from the OCHIN network EHR (June 2016 to February 2022) of 1459 community-based clinics across the United States. STUDY DESIGN: Structured data elements included 913 commonly used smartphrases and 53 procedure codes that were considered potential indicators of social risk referrals. Using stratified purposive sampling, we compared these discrete data with clinical notes to assess concordance of social risk referral documentation, and of the prevalence, types, and outcomes of such referrals. DATA COLLECTION/EXTRACTION METHODS: Smartphrases were classified into three categories (likely, possible, or unlikely to indicate a social risk referral); 50 chart notes were sampled for each of the 25 most frequently used smartphrases in each category, and for 53 of the most frequently used procedure codes. A total of 6104 chart notes were reviewed. PRINCIPAL FINDINGS: In 59% of chart notes where discrete data suggested a social risk referral occurred, there was no documentation of this in the note. Primary domains addressed were food insecurity (38%), financial stress (18%) and housing needs (18%). Common referral activities included providing contact information (26%), help with assistance applications (17%), and direct provision of resources (16%). Documentation indicated the patient received resources in 29% of notes. CONCLUSIONS: EHR documentation of social risk referrals in structured data fields is inconsistent. Further work should establish best practices, especially given emerging policies that tie payments to documentation of social risk screening and intervention provision. Community health centers may struggle to use data elements such as smartphrases and procedure codes to monitor and report on their social risk referrals until standardized coding practices are established and effectively implemented
Confocal Microscopy Lecture
No full textThis presentation was used for instruction in the graduate-level course in microscopy at UNC-CH (CBPH710) starting in February 2025, and for training for new confocal users at the Microscopy Services Laboratory (MSL).
A video of Dr. Pablo Ariel going through this presentation is available on the MSL YouTube page, here.
The Future of Optical Astronomy with the Skynet Robotic Telescope Network
Get PDFThe Skynet Robotic Telescope Network (Skynet) is a global network of autonomous, queue-based robotic telescopes that is used as a data collection platform for a wide variety of fields within astronomy and astronomy education. Originally consisting of six telescopes dedicated for rapid response observations of gamma-ray burst afterglows, Skynet has grown to include ~20 optical telescopes across four continents. As part of a complete overhaul of Skynet’s software stack, we have created new observational modes and models, as well as new scheduling capabilities, which complement a wide variety of scientific uses. All Skynet observing modes will be available through a public API, allowing automatic response to transient alert systems or external scripting. The new observation modes include the option to collect discrete datasets with multiple telescopes in parallel, which will be crucial to rapid response observations to a transient phenomena, as well as the ability to observe targets with multiple telescopes sequentially, a useful option for extended photometric or spectroscopic monitoring campaigns of time-dependent systems. New observation models will also allow for flexible observation requests based on a target signal-to-noise-ratio, and alongside future work to build in automated photometry, allow the possibility of adaptive exposure times based on photometric data collected in real time. Finally, the addition of an observing schedule event manager to the network will allow for the use of Skynet telescopes for target-of-opportunity observations, as well as exclusive access to particular telescopes at specific times. These capabilities will allow Skynet telescopes to be used for simultaneous observations of exoplanet transits, time-sensitive observations of solar system objects, and transient observations, while still maintaining the queue-based observing system of the network during other times. Along with the overhaul of the system’s hardware management and integration software, allowing for new instruments such as optical spectrographs and polarimeters, the overhaul of Skynet’s optical observing system will greatly increase the network’s scientific capabilities
Usefulness of lumbar puncture educational videos for older people with HIV
Get PDFVideo-based education offers opportunities to enhance patients' medical literacy and to reduce anxiety and hesitation for patients undergoing diagnostic procedures such as lumbar puncture (LP). Multiple studies centered on LP education have demonstrated that video-based education can reduce anxiety regarding possible adverse events, while increasing literacy regarding the procedure itself for clinical purposes. Our study sought to assess the impact of video-based education on knowledge of and willingness to undergo an LP among older people with HIV (PWH). We enrolled PWH age ≥ 50 years who regularly attend our Infectious Diseases clinic between March 3 and November 16, 2023. Participants watched a patient-centered educational video explaining the LP procedure and completed a questionnaire both pre- and post-video assessing demographics, general awareness and prior experience with an LP, specific knowledge, attitudes and perceptions toward an LP and willingness to undergo an LP. Our study included 99 PWH with mean (standard deviation, SD) age of 58.8 (5.7) years, one-third females and 60% African American/Black race. After watching the video, participants were significantly more likely to correctly identify technical details of the procedure (excluding those who had previously had an LP, 83.7% pre-video vs. 95.9% post-video) and common complications of an LP; agree that LPs can result in back pain (p < 0.001) and headaches (p < 0.001). There was no significant difference in participants' willingness to undergo an LP for diagnostic or research purposes. Only 5% said that they would never have an LP under any circumstance after watching the video. Other educational interventions, such as in-person demonstrations or models, may help mitigate fears of LP. Our study provides important insight into the knowledge and perceptions of PWH when asked to undergo an LP and demonstrates that video-based education may not be sufficient to mitigate fears surrounding LP procedures, or a lack of interest or time for participating in an LP
Microbial contamination of therapeutic contact lenses after photorefractive keratectomy: a prospective analysis
Get PDFPurpose The objective of this study was to examine bacterial contamination in therapeutic contact lenses (TCLs) utilized following photorefractive keratectomy (PRK) and to identify factors correlated to positive culture outcomes. Methods This prospective study comprised 120 eyes from 60 patients who underwent bilateral PRK surgery at Farabi Eye Hospital in 2022. TCLs, applied postoperatively, were collected between the fifth and seventh days, placed in sterile containers with culture media, and analyzed for microbial growth. The documentation included patient demographic information, refractive status, preoperative conditions, culture results, and antibiotic susceptibility data. Results The results indicated microbial growth was detected in seven lenses, which accounts for 5.8% of the total number of lenses (120 TCLs). Coagulase-negative staphylococci (CoNS) (4 lenses, 2 methicillin-resistant staphylococci (MRS)), Escherichia coli (E. coli) (1 lens), diphtheroid (1 lens), and micrococcus species (1 lens) were the isolated organisms. The patients did not experience any instances of microbial keratitis during the study period. Patients with positive cultures demonstrated a significantly higher mean age (35.00 ± 7.09 years, P-value = 0.036). No significant gender disparities were identified (P-value = 0.263). Conclusion The incidence of microbial contamination in postoperative TCLs following PRK was minimal, with no occurrence of microbial keratitis. Older ages correlated with positive culture outcomes, highlighting the necessity for customized postoperative care approaches
Contribution of Limited Molecular Testing to Low Ehrlichiosis Diagnosis in High Incidence Area, North Carolina, USA
Get PDFIndirect immunofluorescence antibody assays have been the primary method for laboratory diagnosis of ehrlichiosis. Detection of Ehrlichia spp. DNA by using PCR is now widely available through commercial laboratories. To prepare for Ehrlichia spp. PCR introduction, we assessed ehrlichiosis testing practices, quantified the proportion of samples eligible for PCR testing, and estimated the potential effect of implementing PCR at the University of North Carolina health system in North Carolina, USA, which is in an area with a high-incidence of ehrlichiosis. We found <1% of patient samples underwent PCR testing, even though rates of serodiagnostic algorithm completion (testing of acute and convalescent samples) were low (18.4%). Our findings show a need to educate providers on diagnostic and treatment guidelines for ehrlichiosis and raise awareness of the availability and advantage of PCR testing
The changing demographics and severity in hospitalized patients across COVID-19 variants: A national cohort study
Get PDFIntroduction: The respiratory syndrome coronavirus (SARS-CoV-2) has undergone genetic evolution and led to variants of concern that vary in transmissibility and clinical severity. Methods: This retrospective cohort analysis studied 232,364 hospitalized COVID-19-positive patients in the National COVID Cohort Collaborative [April 27, 2020 and June 25, 2022]. The primary outcomes were to compare demographics and need for mechanical ventilation and 30-day mortality across variants including Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529). Results: The severity of SARS-CoV-2 decreased in the omicron-subsequent wave with decreased utilization of mechanical ventilation and decreased 30-day mortality among patients with comorbidities like diabetes mellitus, obesity, and liver disease. Although with each subsequent wave, the sex distribution remained equal and constant, there was an increase in rates of diabetes, liver disease, and respiratory disease amongst patients hospitalized with COVID-19 over the COVID waves despite the decreasing 30-day mortality and mechanical ventilation. Conclusions: Despite changes in demographics over time, more recent COVID waves were associated with decreasing severity and mortality. These observations will help guide specific and effective resource allocation and patient care