المؤلفون: Han, Gyeo-Re, Goncharov, Artem, Eryilmaz, Merve, Joung, Hyou-Arm, Ghosh, Rajesh, Yim, Geon, Chang, Nicole, Kim, Minsoo, Ngo, Kevin, Veszpremi, Marcell, Liao, Kun, Garner, Omai B., Di Carlo, Dino, Ozcan, Aydogan

مصطلحات موضوعية: Physics - Medical Physics, Physics - Applied Physics, Physics - Biological Physics

الوصف: Successful integration of point-of-care testing (POCT) into clinical settings requires improved assay sensitivity and precision to match laboratory standards. Here, we show how innovations in amplified biosensing, imaging, and data processing, coupled with deep learning, can help improve POCT. To demonstrate the performance of our approach, we present a rapid and cost-effective paper-based high-sensitivity vertical flow assay (hs-VFA) for quantitative measurement of cardiac troponin I (cTnI), a biomarker widely used for measuring acute cardiac damage and assessing cardiovascular risk. The hs-VFA includes a colorimetric paper-based sensor, a portable reader with time-lapse imaging, and computational algorithms for digital assay validation and outlier detection. Operating at the level of a rapid at-home test, the hs-VFA enabled the accurate quantification of cTnI using 50 uL of serum within 15 min per test and achieved a detection limit of 0.2 pg/mL, enabled by gold ion amplification chemistry and time-lapse imaging. It also achieved high precision with a coefficient of variation of < 7% and a very large dynamic range, covering cTnI concentrations over six orders of magnitude, up to 100 ng/mL, satisfying clinical requirements. In blinded testing, this computational hs-VFA platform accurately quantified cTnI levels in patient samples and showed a strong correlation with the ground truth values obtained by a benchtop clinical analyzer. This nanoparticle amplification-based computational hs-VFA platform can democratize access to high-sensitivity point-of-care diagnostics and provide a cost-effective alternative to laboratory-based biomarker testing.
Comment: 23 Pages, 4 Figures, 1 Table

الوصول الحر: http://arxiv.org/abs/2402.11195Test

المؤلفون: Magaki, Shino, Zhang, Ting, Han, Karam, Hilda, Mirbaha, Yong, William H, Achim, Cristian, Fishbein, Gregory, Fishbein, Michael C, Garner, Omai, Salamon, Noriko, Williams, Christopher K, Valdes-Sueiras, Miguel A, Hsu, Jeffrey J, Kelesidis, Theodoros, Mathisen, Glenn E, Lavretsky, Helen, Singer, Elyse J, Vinters, Harry V

مصطلحات موضوعية: Medical Microbiology, Biomedical and Clinical Sciences, Neurodegenerative, HIV/AIDS, Neurosciences, Coronaviruses, Emerging Infectious Diseases, Sexually Transmitted Infections, Brain Disorders, Acquired Cognitive Impairment, Infectious Diseases, Mental Health, Infection, Good Health and Well Being, COVID-19, HIV, HIV-associated neurocognitive disorders, Long COVID, Neuropathology, Post-COVID conditions

الوصف: Human immunodeficiency virus (HIV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause significant neurologic disease. Central nervous system (CNS) involvement of HIV has been extensively studied, with well-documented invasion of HIV into the brain in the initial stage of infection, while the acute effects of SARS-CoV-2 in the brain are unclear. Neuropathologic features of active HIV infection in the brain are well characterized whereas neuropathologic findings in acute COVID-19 are largely non-specific. On the other hand, neuropathologic substrates of chronic dysfunction in both infections, as HIV-associated neurocognitive disorders (HAND) and post-COVID conditions (PCC)/long COVID are unknown. Thus far, neuropathologic studies on patients with HAND in the era of combined antiretroviral therapy have been inconclusive, and autopsy studies on patients diagnosed with PCC have yet to be published. Further longitudinal, multidisciplinary studies on patients with HAND and PCC and neuropathologic studies in comparison to controls are warranted to help elucidate the mechanisms of CNS dysfunction in both conditions.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/7zb101hmTest
https://escholarship.org/content/qt7zb101hm/qt7zb101hm.pdfTest

المؤلفون: Shah, Vishwesh, Yang, Xilin, Arnheim, Alyssa, Udani, Shreya, Tseng, Derek, Luo, Yi, Ouyang, Mengxing, Destgeer, Ghulam, Garner, Omai, Koydemir, Hatice, Ozcan, Aydogan, Di Carlo, Dino

المصدر: ACS Nano. 17(20)

مصطلحات موضوعية: ELISA, biomarker detection, droplet, low-cost sensors, portable reader, statistical quantitation, Humans, Biomarkers, Microfluidics, Vasodilator Agents, Enzyme-Linked Immunosorbent Assay, Heart Failure

الوصف: Compartmentalization, leveraging microfluidics, enables highly sensitive assays, but the requirement for significant infrastructure for their design, build, and operation limits access. Multimaterial particle-based technologies thermodynamically stabilize monodisperse droplets as individual reaction compartments with simple liquid handling steps, precluding the need for expensive microfluidic equipment. Here, we further improve the accessibility of this lab on a particle technology to resource-limited settings by combining this assay system with a portable multimodal reader, thus enabling nanoliter droplet assays in an accessible platform. We show the utility of this platform in measuring N-terminal propeptide B-type natriuretic peptide (NT-proBNP), a heart failure biomarker, in complex medium and patient samples. We report a limit of detection of ∼0.05 ng/mL and a linear response between 0.2 and 2 ng/mL in spiked plasma samples. We also show that, owing to the plurality of measurements per sample, swarm sensing acquires better statistical quantitation with a portable reader. Monte Carlo simulations show the increasing capability of this platform to differentiate between negative and positive samples, i.e., below or above the clinical cutoff for acute heart failure (∼0.1 ng/mL), as a function of the number of particles measured. Our platform measurements correlate with gold standard ELISA measurement in cardiac patient samples, and achieve lower variation in measurement across samples compared to the standard well plate-based ELISA. Thus, we show the capabilities of a cost-effective droplet-reader system in accurately measuring biomarkers in nanoliter droplets for diseases that disproportionately affect underserved communities in resource-limited settings.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/2s48994rTest

المؤلفون: Shaw, Bennett, von Bredow, Benjamin, Tsan, Allison, Garner, Omai, Yang, Shangxin

المصدر: Microorganisms. 11(10)

مصطلحات موضوعية: Mycobacterium tuberculosis complex, clinical evaluation, drug susceptibility testing, phylogenetic relatedness analysis, whole-genome sequencing

الوصف: The global rise of drug resistant tuberculosis has highlighted the need for improved diagnostic technologies that provide rapid and reliable drug resistance results. Here, we develop and validate a whole genome sequencing (WGS)-based test for identification of mycobacterium tuberculosis complex (MTB) drug resistance to rifampin, isoniazid, pyrazinamide, ethambutol, and streptomycin. Through comparative analysis of drug resistance results from WGS-based testing and phenotypic drug susceptibility testing (DST) of 38 clinical MTB isolates from patients receiving care in Los Angeles, CA, we found an overall concordance between methods of 97.4% with equivalent performance across culture media. Critically, prospective analysis of 11 isolates showed that WGS-based testing provides results an average of 36 days faster than phenotypic culture-based methods. We showcase the additional benefits of WGS data by investigating a suspected laboratory contamination event and using phylogenetic analysis to search for cryptic local transmission, finding no evidence of community spread amongst our patient population in the past six years. WGS-based testing for MTB drug resistance has the potential to greatly improve diagnosis of drug resistant MTB by accelerating turnaround time while maintaining accuracy and providing additional benefits for infection control, lab safety, and public health applications.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/98f9d6p7Test

المؤلفون: Goncharov, Artem, Joung, Hyou-Arm, Ghosh, Rajesh, Han, Gyeo-Re, Ballard, Zachary S., Maloney, Quinn, Bell, Alexandra, Aung, Chew Tin Zar, Garner, Omai B., Di Carlo, Dino, Ozcan, Aydogan

المصدر: Small (2023)

مصطلحات موضوعية: Physics - Medical Physics, Physics - Applied Physics, Physics - Biological Physics

الوصف: We demonstrate multiplexed computational sensing with a point-of-care serodiagnosis assay to simultaneously quantify three biomarkers of acute cardiac injury. This point-of-care sensor includes a paper-based fluorescence vertical flow assay (fxVFA) processed by a low-cost mobile reader, which quantifies the target biomarkers through trained neural networks, all within <15 min of test time using 50 microliters of serum sample per patient. This fxVFA platform is validated using human serum samples to quantify three cardiac biomarkers, i.e., myoglobin, creatine kinase-MB (CK-MB) and heart-type fatty acid binding protein (FABP), achieving less than 0.52 ng/mL limit-of-detection for all three biomarkers with minimal cross-reactivity. Biomarker concentration quantification using the fxVFA that is coupled to neural network-based inference is blindly tested using 46 individually activated cartridges, which showed a high correlation with the ground truth concentrations for all three biomarkers achieving > 0.9 linearity and < 15 % coefficient of variation. The competitive performance of this multiplexed computational fxVFA along with its inexpensive paper-based design and handheld footprint make it a promising point-of-care sensor platform that could expand access to diagnostics in resource-limited settings.
Comment: 17 Pages, 6 Figures

الوصول الحر: http://arxiv.org/abs/2301.10934Test

المؤلفون: Saleh, Tawny, Fuller, Trevon, Cambou, Mary C, Segura, Eddy R, Kamau, Edwin, Yang, Shangxin, Garner, Omai B, Nielsen-Saines, Karin

المصدر: Vaccines. 11(6)

مصطلحات موضوعية: Prevention, Pediatric, Biodefense, Emerging Infectious Diseases, Immunization, Vaccine Related, Lung, Clinical Research, Infectious Diseases, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Infection, Good Health and Well Being, youth, pediatric COVID-19, VOCs, SARS-CoV-2 disease severity, Los Angeles County, COVID-19 vaccination

الوصف: BackgroundOutcomes of SARS CoV-2 infection in infants, children and young adults are reported less frequently than in older populations. The evolution of SARS-CoV-2 cases in LA County youths followed at a large health network in southern California over two years was evaluated.MethodsA prospective cohort study of patients aged 0-24 years diagnosed with COVID-19 was conducted. Demographics, age distribution, disease severity, circulating variants of concern (VOCs), and immunization rates were compared between first and second pandemic years. Logistic regression estimated odds ratios (OR) and 95% confidence intervals (CI) of factors associated with severe/critical COVID-19.ResultsIn total, 61,208 patients 0-24 years of age were tested for SARS-CoV-2 by polymerase chain reaction (PCR); 5263 positive patients (8.6%) with available data were identified between March 2020 and March 2022. In Year 1, 5.8% (1622/28,088) of youths tested positive, compared to 11% (3641/33,120) in Year 2 (p < 0.001). Most youths had mild/asymptomatic illness over two years. SARS-CoV-2 positivity was >12% across all age groups in the second half of Year 2, when Omicron prevailed. Pulmonary disease was associated with higher risk of severe COVID-19 in both years (OR: 2.4, 95% CI: 1.4-4.3, p = 0.002, Year 1; OR: 11.3, 95% CI: 4.3-29.6, Year 2, p < 0.001). Receipt of at least one COVID-19 vaccine dose was protective against severe COVID-19 (OR: 0.3, 95% CI: 0.11-0.80, p < 0.05).ConclusionsDespite different VOCs and higher rates of test positivity in Year 2 compared to Year 1, most youths with COVID-19 had asymptomatic/mild disease. Underlying pulmonary conditions increased the risk of severe COVID-19, while vaccination was highly protective against severe disease in youths.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/5597x2hvTest

المؤلفون: Darboe, Saffiatou, Mirasol, Ruel, Adejuyigbe, Babapelumi, Muhammad, Abdul Khalie, Nadjm, Behzad, De St Maurice, Annabelle, Dogan, Tiffany L, Ceesay, Buntung, Umukoro, Solomon, Okomo, Uduak, Nwakanma, Davis, Roca, Anna, Secka, Ousman, Forrest, Karen, Garner, Omai B

المصدر: Antibiotics. 12(4)

مصطلحات موضوعية: Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, Antimicrobial Resistance, Clinical Research, Vaccine Related, Emerging Infectious Diseases, Infectious Diseases, Prevention, Infection, Good Health and Well Being, cumulative antibiogram, antimicrobial resistance, infection prevention and control, low- and middle-income countries, Escherichia coli (E, coli), Staphylococcus aureus (S, aureus), Klebsiella pnuemonaie (K, pneumoniae), bacteraemia, urinary tract infection, Escherichia coli, Klebsiella pnuemonaie, Staphylococcus aureus, Pharmacology and pharmaceutical sciences

الوصف: Antimicrobial resistance is a global health threat and efforts to mitigate it is warranted, thus the need for local antibiograms to improve stewardship. This study highlights the process that was used to develop an antibiogram to monitor resistance at a secondary-level health facility to aid empirical clinical decision making in a sub-Saharan African county. This retrospective cross-sectional descriptive study used 3 years of cumulative data from January 2016 to December 2018. Phenotypic data was manually imputed into WHONET and the cumulative antibiogram constructed using standardized methodologies according to CLSI M39-A4 guidelines. Pathogens were identified by standard manual microbiological methods and antimicrobial susceptibility testing was performed using Kirby-Bauer disc diffusion method according to CLSI M100 guidelines. A total of 14,776 non-duplicate samples were processed of which 1163 (7.9%) were positive for clinically significant pathogens. Among the 1163 pathogens, E. coli (n = 315) S. aureus (n = 232), and K. pneumoniae (n = 96) were the leading cause of disease. Overall, the susceptibility for E. coli and K. pneumoniae from all samples were: trimethoprim-sulfamethoxazole (17% and 28%), tetracycline (26% and 33%), gentamicin (72% and 46%), chloramphenicol (76 and 60%), and ciprofloxacin (69% and 59%), and amoxicillin/clavulanic (77% and 54%) respectively. Extended spectrum beta-lactamase (ESBL) resistance was present in 23% (71/315) vs. 35% (34/96) respectively. S. aureus susceptibility for methicillin was 99%. This antibiogram has shown that improvement in combination therapy is warranted in The Gambia.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/35x2w9wgTest

المؤلفون: Rodriguez-Watson, Carla V, Sheils, Natalie E, Louder, Anthony M, Eldridge, Elizabeth H, Lin, Nancy D, Pollock, Benjamin D, Gatz, Jennifer L, Grannis, Shaun J, Vashisht, Rohit, Ghauri, Kanwal, Valo, Gina, Chakravarty, Aloka G, Lasky, Tamar, Jung, Mary, Lovell, Stephen L, Major, Jacqueline M, Kabelac, Carly, Knepper, Camille, Leonard, Sandy, Embi, Peter J, Jenkinson, William G, Klesh, Reyna, Garner, Omai B, Patel, Ayan, Dahm, Lisa, Barin, Aiden, Cooper, Dan M, Andriola, Tom, Byington, Carrie L, Crews, Bridgit O, Butte, Atul J, Allen, Jeff

المصدر: PLOS ONE. 18(2)

مصطلحات موضوعية: General Science & Technology

الوصف: Background As diagnostic tests for COVID-19 were broadly deployed under Emergency Use Authorization, there emerged a need to understand the real-world utilization and performance of serological testing across the United States. Methods Six health systems contributed electronic health records and/or claims data, jointly developed a master protocol, and used it to execute the analysis in parallel. We used descriptive statistics to examine demographic, clinical, and geographic characteristics of serology testing among patients with RNA positive for SARS-CoV-2. Results Across datasets, we observed 930,669 individuals with positive RNA for SARS-CoV-2. Of these, 35,806 (4%) were serotested within 90 days; 15% of which occurred 30%) in some datasets—limiting our ability to examine differences in serological testing by race. In datasets where race/ethnicity information was available, we observed a greater distribution of White individuals among those serotested; however, the time between RNA and serology tests appeared shorter in Black compared to White individuals. Test manufacturer data was available in half of the datasets contributing to the analysis. Conclusion Our results inform the underlying context of serotesting during the first year of the COVID-19 pandemic and differences observed between claims and EHR data sources–a critical first step to understanding the real-world accuracy of serological tests. Incomplete reporting of race/ethnicity data and a limited ability to link test manufacturer data, lab results, and clinical data challenge the ability to assess the real-world performance of SARS-CoV-2 tests in different contexts and the overall U.S. response to current and future disease pandemics.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/8rx9p907Test

المؤلفون: Salem-Bango, Zackary, Price, Travis K, Chan, June L, Chandrasekaran, Sukantha, Garner, Omai B, Yang, Shangxin

المصدر: Journal of fungi (Basel, Switzerland). 9(2)

مصطلحات موضوعية: 28S rRNA, ITS, beta-tubulin, fungal infections, fungal species identification, k-mer tree, next-generation sequencing, whole-genome sequencing, Infectious Diseases, Genetics, Human Genome, Biotechnology, Detection, screening and diagnosis, 4.2 Evaluation of markers and technologies, Good Health and Well Being

الوصف: Using next-generation sequencing (NGS), we developed and validated a whole-genome sequencing (WGS)-based clinical test for fungal species identification on clinical isolates. The identification is mainly based on the fungal ribosomal internal transcribed spacer (ITS) region as the primary marker, and additional marker and genomic analysis applied for species within the Mucorales family (using the 28S rRNA gene) and Aspergillus genus (using the beta-tubulin gene and k-mer tree-based phylogenetic clustering). The validation study involving 74 unique fungal isolates (22 yeasts, 51 molds, and 1 mushroom-forming fungus) showed high accuracy, with 100% (74/74) concordance on the genus-level identifications and 89.2% (66/74) concordance on the species level. The 8 discrepant results were due to either the limitation of conventional morphology-based methodology or taxonomic changes. After one year of implementation in our clinical laboratory, this fungal NGS test was utilized in 29 cases; the majority of them were transplant and cancer patients. We demonstrated the utility of this test by detailing five case studies, in which accurate fungal species identification led to correct diagnosis, treatment adjustment or was ruled out for hospital acquired infection. This study provides a model for validation and implementation of WGS for fungal identification in a complex health system that serves a large immunocompromised patient population.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/9k40x96fTest

المؤلفون: Rodriguez-Watson, Carla VM, Louder, Anthony ME, Kabelac, Carly H, Frederick, Christopher MD, Sheils, Natalie ED, Eldridge, Elizabeth HL, Lin, Nancy DJ, Pollock, Benjamin D, Gatz, Jennifer L, Grannis, Shaun J, Vashisht, Rohit, Ghauri, Kanwal J, Knepper, Camille, Leonard, Sandy, Embi, Peter JB, Jenkinson, Garrett, Klesh, Reyna, Garner, Omai B, Patel, Ayan M, Dahm, Lisa, Barin, Aiden L, Cooper, Dan MO, Andriola, Tom J, Byington, Carrie L, Crews, Bridgit O, Butte, Atul J, Allen, Jeff

المصدر: PLOS ONE. 18(2)

مصطلحات موضوعية: General Science & Technology

الوصف: Background Real-world performance of COVID-19 diagnostic tests under Emergency Use Authorization (EUA) must be assessed. We describe overall trends in the performance of serology tests in the context of real-world implementation. Methods Six health systems estimated the odds of seropositivity and positive percent agreement (PPA) of serology test among people with confirmed SARS-CoV-2 infection by molecular test. In each dataset, we present the odds ratio and PPA, overall and by key clinical, demographic, and practice parameters. Results A total of 15,615 people were observed to have at least one serology test 14–90 days after a positive molecular test for SARS-CoV-2. We observed higher PPA in Hispanic (PPA range: 79–96%) compared to non-Hispanic (60–89%) patients; in those presenting with at least one COVID-19 related symptom (69–93%) as compared to no such symptoms (63–91%); and in inpatient (70–97%) and emergency department (93–99%) compared to outpatient (63–92%) settings across datasets. PPA was highest in those with diabetes (75–94%) and kidney disease (83–95%); and lowest in those with auto-immune conditions or who are immunocompromised (56–93%). The odds ratios (OR) for seropositivity were higher in Hispanics compared to non-Hispanics (OR range: 2.59–3.86), patients with diabetes (1.49–1.56), and obesity (1.63–2.23); and lower in those with immunocompromised or autoimmune conditions (0.25–0.70), as compared to those without those comorbidities. In a subset of three datasets with robust information on serology test name, seven tests were used, two of which were used in multiple settings and met the EUA requirement of PPA ≥87%. Tests performed similarly across datasets. Conclusion Although the EUA requirement was not consistently met, more investigation is needed to understand how serology and molecular tests are used, including indication and protocol fidelity. Improved data interoperability of test and clinical/demographic data are needed to enable rapid assessment of the real-world performance of in vitro diagnostic tests.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/15t5p8b2Test