A5085255857- Tuberculosis Research and Epidemiology
- Mycobacterium research and diagnosis
- Clostridium difficile and Clostridium perfringens research
- Bacterial Identification and Susceptibility Testing
- Viral gastroenteritis research and epidemiology
- Biosensors and Analytical Detection
- Antibiotic Resistance in Bacteria
- Antifungal resistance and susceptibility
- Fungal Infections and Studies
- Infectious Diseases and Tuberculosis
- Antimicrobial Resistance in Staphylococcus
- Gut microbiota and health
- Microscopic Colitis
- Pneumonia and Respiratory Infections
- Infectious Diseases and Mycology
- SARS-CoV-2 and COVID-19 Research
- COVID-19 Clinical Research Studies
- Enterobacteriaceae and Cronobacter Research
- Respiratory viral infections research
- Pneumocystis jirovecii pneumonia detection and treatment
- Bacterial biofilms and quorum sensing
- Antibiotics Pharmacokinetics and Efficacy
- Bacteriophages and microbial interactions
- Diagnosis and treatment of tuberculosis
- Spectroscopy Techniques in Biomedical and Chemical Research
Stanford University
2016-2025
Stanford Medicine
2016-2025
Stanford Health Care
2016-2025
Palo Alto University
2019-2024
City Of Hope National Medical Center
2021
Office of Infectious Diseases
2018
Palo Alto Institute
2017
Stratford University
2017
Ministry of Health
2017
Lucile Packard Children's Hospital
2010-2016
Raman optical spectroscopy promises label-free bacterial detection, identification, and antibiotic susceptibility testing in a single step. However, achieving clinically relevant speeds accuracies remains challenging due to weak signal from cells numerous species phenotypes. Here we generate an extensive dataset of spectra apply deep learning approaches accurately identify 30 common pathogens. Even on low signal-to-noise spectra, achieve average isolate-level exceeding 82% treatment...
The rapid spread of COVID-19 across the world has revealed major gaps in our ability to respond new virulent pathogens. Rapid, accurate, and easily configurable molecular diagnostic tests are imperative prevent global diseases. CRISPR-based approaches proving be useful as field-deployable solutions. In one basic form this assay, CRISPR-Cas12 enzyme complexes with a synthetic guide RNA (gRNA). This complex becomes activated only when it specifically binds target DNA cleaves it. thereafter...
Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA has emerged as an attractive diagnostic modality allowing broad-range pathogen detection, noninvasive sampling, and earlier diagnosis. However, little is known about its real-world clinical impact used in routine practice.We performed a retrospective cohort study all patients for whom mNGS (Karius test) was indications at 5 United States institutions over 1.5 years. Comprehensive records review performed, standardized...
Diagnosis of life-threatening deep-seated infections currently requires invasive sampling the infected tissue to provide a microbiologic diagnosis. These procedures can lead high morbidity in patients and add healthcare costs. Here we describe novel next-generation sequencing assay that was used detect pathogen-derived cell-free DNA peripheral blood with biopsy-proven fungal infections. The noninvasive nature this approach could rapid, actionable treatment information for when biopsy is not possible.
Abstract Despite the advantages of providing an early presumptive diagnosis, fungal classification by histopathology can be difficult and may lead to diagnostic error. To assess accuracy histologic diagnosis infections vs culture (“gold standard”), we performed a 10-year retrospective review at our institution. Of 47 338 positive mold yeast cultures with concurrent surgical pathology evaluation without known history infection, 37 (79%) were correctly identified based on morphologic features...
Adaptive immunity to Mycobacterium tuberculosis controls progressive bacterial growth and disease but does not eradicate infection. Among CD4+ T cells in the lungs of M. tuberculosis-infected mice, we observed that few produced IFN-γ without ex vivo restimulation. Therefore, hypothesized one mechanism whereby avoids elimination is by limiting activation effector at site infection lungs. To test this hypothesis, adoptively transferred Th1-polarized specific for Ag85B peptide 25 (P25TCRTh1...
We investigated feasibility and accuracy of an interferon-γ release assay (IGRA) for detection T-cell responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Whole blood IGRA accurately distinguished between convalescent uninfected healthy donors with a predominantly CD4+ response. SARS-CoV-2 may serve as useful diagnostic tool in managing the disease 2019 pandemic.
A high-throughput screen against the Clostridium difficile toxin B cysteine protease domain identified a drug in clinical trials that reduced C. pathology mouse model.
Identification of fungi causing invasive fungal disease (IFD) is critical for guiding antifungal therapy. We describe the performance and clinical impact a targeted panfungal polymerase chain reaction (PCR) amplicon sequencing assay culture-independent diagnosis IFD.Between January 2009 September 2016, 233 specimens, consisting fresh formalin-fixed, paraffin-embedded (FFPE) tissues sterile body fluids with known IFD based on reference method results (n = 117), specimens negative culture, but...
Surface-enhanced Raman spectroscopy (SERS) is a promising cellular identification and drug susceptibility testing platform, provided it can be performed in controlled liquid environment that maintains cell viability. We investigate bacterial liquid-SERS, studying plasmonic electrostatic interactions between gold nanorods bacteria enable uniformly enhanced SERS. synthesize five nanorod sizes with longitudinal plasmon resonances ranging from 670 to 860 nm characterize SERS signatures of...
Abstract Bacterial bloodstream infections are a major cause of morbidity and mortality among patients undergoing hematopoietic cell transplantation (HCT). Although previous research has demonstrated that pathogens may translocate from the gut microbiome into to infections, mechanisms by which HCT acquire in their have not yet been described. Here, we use linked-read short-read metagenomic sequencing analyze 401 stool samples collected 149 adults hospitalized same unit over three years, many...
Identifying pathogens in complex samples such as blood, urine, and wastewater is critical to detect infection inform optimal treatment. Surface-enhanced Raman spectroscopy (SERS) machine learning (ML) can distinguish among multiple pathogen species, but processing fluid sensitively specifically remains an outstanding challenge. Here, we develop acoustic bioprinter digitize into millions of droplets, each containing just a few cells, which are identified with SERS ML. We demonstrate rapid...
Human norovirus (HuNoV) is a leading cause of disease globally, yet actual incidence unknown. HuNoV infections are not reportable in the United States, and surveillance limited to tracking severe illnesses or outbreaks. Wastewater monitoring for has been done previously results indicate it present wastewater influent concentrations associated with communities contributing wastewater. However, work mostly monthly samples liquid at one few treatment plants (WWTPs).
Enteric infections are important causes of morbidity and mortality, yet clinical surveillance is limited. Wastewater-based epidemiology (WBE) has been used to study community circulation individual enteric viruses panels respiratory diseases, but there limited work studying the concurrent a suite viruses. A retrospective WBE was carried out at two wastewater treatment plants located in California, United States. Using digital droplet polymerase chain reaction (PCR), we measured...
Abstract Background Syndromic molecular panels for the diagnosis of gastroenteritis, meningitis/encephalitis, and pneumonia are becoming routinely used patient care throughout world. Content These rapid, sample-to-answer assays have great potential to improve care, infection control, antimicrobial stewardship. However, diagnostic stewardship is essential their optimal use accuracy, interventions can be applied at all phases process. Summary The aim this review article describe effective...
Tuberculosis (TB) is the world’s deadliest infectious disease, with over 1.5 million deaths and 10 new cases reported anually. The causative organism Mycobacterium tuberculosis (Mtb) can take nearly 40 d to culture, a required step determine pathogen’s antibiotic susceptibility. Both rapid identification susceptibility testing of Mtb are essential for effective patient treatment combating antimicrobial resistance. Here, we demonstrate rapid, culture-free, incubation-free drug test TB using...
Rationale: North American occupational health programs that switched from the tuberculin skin test (TST) to IFN-γ release assays for latent tuberculosis screening are reporting challenges with interpretation of serial testing results in healthcare workers (HCWs). However, limited data exist on reproducibility assay low-risk HCWs.Objectives: To evaluate short-term QuantiFERON-TB Gold In-Tube (QFT) a large cohort HCWs and define QFT cutoff yielding conversion rate equivalent historical TST...