Steve Miller
A5081374859- Mycobacterium research and diagnosis
- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- Genomics and Phylogenetic Studies
- Bacterial Identification and Susceptibility Testing
- Respiratory viral infections research
- Bacterial Infections and Vaccines
- Cytomegalovirus and herpesvirus research
- Bacteriophages and microbial interactions
- Infective Endocarditis Diagnosis and Management
- Viral gastroenteritis research and epidemiology
- Cancer Genomics and Diagnostics
- Animal Virus Infections Studies
- Infectious Diseases and Mycology
- Mosquito-borne diseases and control
- Pneumonia and Respiratory Infections
- Gut microbiota and health
- COVID-19 Clinical Research Studies
- Antibiotic Resistance in Bacteria
- Reproductive tract infections research
- Biosensors and Analytical Detection
- Glioma Diagnosis and Treatment
- Microbial infections and disease research
- Medical Imaging and Pathology Studies
- Antifungal resistance and susceptibility
University of California, San Francisco
2015-2024
University of Arts
2023
Cornell University
2023
Akron Children's Hospital
2023
Illumina (United States)
2023
Lindsay Unified School District
2023
Manhattan Institute for Policy Research
2023
New York Proton Center
2023
Communities In Schools of Orange County
2023
Oregon Medical Research Center
2023
A 14-year-old boy with severe combined immunodeficiency presented three times to a medical facility over period of 4 months fever and headache that progressed hydrocephalus status epilepticus necessitating medically induced coma. Diagnostic workup including brain biopsy was unrevealing. Unbiased next-generation sequencing the cerebrospinal fluid identified 475 3,063,784 sequence reads (0.016%) corresponding leptospira infection. Clinical assays for leptospirosis were negative. Targeted...
Metagenomic next-generation sequencing (NGS) of cerebrospinal fluid (CSF) has the potential to identify a broad range pathogens in single test.In 1-year, multicenter, prospective study, we investigated usefulness metagenomic NGS CSF for diagnosis infectious meningitis and encephalitis hospitalized patients. All positive tests on were confirmed by orthogonal laboratory testing. Physician feedback was elicited teleconferences with clinical microbial board surveys. Clinical effect evaluated...
During human CMV infection, there is a preferential expansion of natural killer (NK) cells expressing the activating CD94–NKG2C receptor complex, implicating this in recognition CMV-infected cells. We hypothesized that NK expanded response to pathogens will be marked by expression CD57, carbohydrate antigen expressed on highly mature within CD56 dim CD16 + cell compartment. Here we demonstrate unique subset coexpressing and CD57 donors. These NKG2C hi degranulated stimulation through their...
Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, diagnosis of infectious diseases. However, practical deployment technology is hindered by bioinformatics challenge analyzing results accurately a clinically relevant timeframe. Here we describe SURPI (“sequence-based ultrarapid identification”), computational pipeline...
Context.— Metagenomic sequencing can be used for detection of any pathogens using unbiased, shotgun next-generation (NGS), without the need sequence-specific amplification. Proof-of-concept has been demonstrated in infectious disease outbreaks unknown causes and patients with suspected infections but negative results conventional tests. NGS tests hold great promise to improve diagnostics, especially immunocompromised critically ill patients. Objective.— To discuss challenges provide example...
Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection has been successfully tested in proof-of-concept case studies patients with acute illness of unknown etiology but to date largely confined research settings. Here, we developed and validated a clinical mNGS assay diagnosis infectious causes meningitis encephalitis from cerebrospinal fluid (CSF) licensed microbiology laboratory. A customized bioinformatics pipeline, SURPI+, was rapidly analyze data, generate an automated...
According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics identification infection humans have not been extensively adopted. Time-consuming culture-based methods forefront clinical detection. The 16S rRNA gene, a marker bacterial species, is ubiquitous members this domain and, thanks ever-expanding databases...
Lower respiratory tract infections (LRTIs) lead to more deaths each year than any other infectious disease category. Despite this, etiologic LRTI pathogens are infrequently identified due limitations of existing microbiologic tests. In critically ill patients, noninfectious inflammatory syndromes resembling LRTIs further complicate diagnosis. To address the need for improved diagnostics, we performed metagenomic next-generation sequencing (mNGS) on tracheal aspirates from 92 adults with...
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology SARS-CoV-2 Northern from late January to mid-March 2020, using samples 36 patients spanning nine counties and Grand Princess cruise ship. Phylogenetic analyses revealed cryptic introduction at least seven different lineages into California, including epidemic WA1 strains...
Metagenomic next-generation sequencing (NGS) was used to diagnose an unusual and fatal case of progressive encephalitis in immunocompromised adult presenting at disease onset as bilateral hearing loss. The confirmatory studies revealed neuroinvasive infection the brain by astrovirus belonging a recently discovered VA/HMO clade.
Bacterial vaginosis affects 15 to 50% of women reproductive age, and recurrence is common after treatment with an antibiotic agent. The high incidence suggests the need for new treatments prevent recurrent bacterial vaginosis.
ABSTRACT Background Serological tests are crucial tools for assessments of SARS-CoV-2 exposure, infection and potential immunity. Their appropriate use interpretation require accurate assay performance data. Method We conducted an evaluation 10 lateral flow assays (LFAs) two ELISAs to detect anti-SARS-CoV-2 antibodies. The specimen set comprised 128 plasma or serum samples from 79 symptomatic RT-PCR-positive individuals; 108 pre-COVID-19 negative controls; 52 recent individuals who underwent...
Abstract We identified a novel SARS-CoV-2 variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California. Named B.1.427/B.1.429 to denote its 2 lineages, the emerged around May 2020 and increased 0% >50% sequenced cases September 1, January 29, 2021, exhibiting an 18.6-24% increase transmissibility relative wild-type circulating strains. The carries 3 mutations spike protein, including L452R substitution. Our analyses revealed 2-fold...
Abstract Given the limited availability of serological testing to date, seroprevalence SARS-CoV-2-specific antibodies in different populations has remained unclear. Here, we report very low SARS-CoV-2 two San Francisco Bay Area populations. Seroreactivity was 0.26% 387 hospitalized patients admitted for non-respiratory indications and 0.1% 1,000 blood donors early April 2020. We additionally describe longitudinal dynamics immunoglobulin-G (IgG), immunoglobulin-M (IgM), vitro neutralizing...
Abstract We evaluated the performance of Abbott BinaxNOW rapid antigen test for coronavirus disease 2019 (Binax-CoV2) to detect virus among persons, regardless symptoms, at a public plaza site ongoing community transmission. Titration with cultured severe acute respiratory syndrome 2 yielded human observable threshold between 1.6 × 104-4.3 104 viral RNA copies (cycle [Ct], 30.3–28.8). Among 878 subjects tested, 3% (26 878) were positive by reverse-transcription polymerase chain reaction,...
ABSTRACT An outbreak of novel betacoronavirus, SARS-CoV-2 (formerly named 2019-nCoV), began in Wuhan, China December 2019 and the COVID-19 disease associated with infection has since spread rapidly to multiple countries. Here we report development DETECTR, a rapid (∼30 min), low-cost, accurate CRISPR-Cas12 based lateral flow assay for detection from respiratory swab RNA extracts. We validated this method using contrived reference samples clinical infected US patients demonstrated comparable...
Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) is an agnostic method for broad-based diagnosis central nervous system (CNS) infections. Here we analyzed the 7-year performance clinical CSF mNGS testing 4,828 samples from June 2016 to April 2023 performed by University California, San Francisco (UCSF) microbiology laboratory. Overall, detected 797 organisms 697 (14.4%) samples, consisting 363 (45.5%) DNA viruses, 211 (26.4%) RNA 132 (16.6%) bacteria, 68 (8.5%)...