A5051933336- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- Vaccine Coverage and Hesitancy
- Viral gastroenteritis research and epidemiology
- Bacteriophages and microbial interactions
- Reproductive tract infections research
- Urinary Tract Infections Management
- Genomics and Phylogenetic Studies
- COVID-19 epidemiological studies
- COVID-19 Clinical Research Studies
- Vibrio bacteria research studies
- vaccines and immunoinformatics approaches
- Viral Infections and Outbreaks Research
- Antibiotic Resistance in Bacteria
- Trypanosoma species research and implications
- Burkholderia infections and melioidosis
- Rabies epidemiology and control
- Pelvic floor disorders treatments
- Genetics, Bioinformatics, and Biomedical Research
- Animal Virus Infections Studies
- Insect symbiosis and bacterial influences
- Infections and bacterial resistance
- Insect-Plant Interactions and Control
- Bacterial Infections and Vaccines
- Environmental DNA in Biodiversity Studies
Leidos (United States)
2017-2024
Naval Medical Research Command
2017-2024
United States Army Medical Research and Development Command
2024
Virginia Commonwealth University
2010-2013
Multi-drug resistance is increasing at alarming rates. The efficacy of phage therapy, treating bacterial infections with bacteriophages alone or in combination traditional antibiotics, has been demonstrated emergency cases the United States and other countries, however remains to be approved for wide-spread use US. One limiting factor a lack guidelines assessing genomic safety candidates. We present characterization workflow used by our team generate data submitting phages Federal Drug...
Abstract In 2016, a 68-year-old patient with disseminated multidrug-resistant Acinetobacter baumannii infection was successfully treated using lytic bacteriophages. Here we report the genomes of nine phages used for treatment and three strains A. isolated prior to during treatment. The in initial are related, T4-like myophages. Analysis 19 isolates collected before phage shows that resistance appeared two days following start We generate complete genomic sequences (TP1, TP2 TP3) treatment,...
It has been known for decades that some insect-infecting trypanosomatids can survive in culture without heme supplementation while others cannot, and this capability is associated with the presence of a betaproteobacterial endosymbiont flagellate's cytoplasm. However, specific mechanisms involved process remained obscure. In work, we sequence phylogenetically analyze pathway genes from symbionts their hosts, as well number synthesis-deficient Kinetoplastida. Our results show enzymes...
It has been long known that insect-infecting trypanosomatid flagellates from the genera Angomonas and Strigomonas harbor bacterial endosymbionts (Candidatus Kinetoplastibacterium or TPE [trypanosomatid proteobacterial endosymbiont]) supplement host metabolism. Based on previous analyses of other endosymbiont genomes lineages, a stereotypical path genome evolution in such bacteria over duration their association with eukaryotic characterized. In this work, we sequence analyze five TPEs,...
Human and animal infections with bacteria of the genus Sarcina (family Clostridiaceae) are associated gastric dilation emphysematous gastritis. However, potential roles sarcinae as commensals or pathogens remain unclear. Here, we investigate a lethal disease unknown etiology that affects sanctuary chimpanzees (Pan troglodytes verus) in Sierra Leone. The disease, which have named "epizootic neurologic gastroenteric syndrome" (ENGS), is characterized by gastrointestinal signs results death...
Introduction We sought to determine pre-infection correlates of protection against SARS-CoV-2 post-vaccine inzfections (PVI) acquired during the first Omicron wave in United States. Methods Serum and saliva samples from 176 vaccinated adults were collected October December 2021, immediately before wave, assessed for Spike-specific IgG IgA binding antibodies (bAb). Sera also bAb using commercial assays, neutralization activity several variants. PVI duration severity, as well risk...
Background: Marine recruits training at Parris Island experienced an unexpectedly high rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, despite preventive measures including a supervised, 2-week, pre-entry quarantine. We characterize SARS-CoV-2 transmission in this cohort. Methods: Between May and November 2020, we monitored 2,469 unvaccinated, mostly male, prospectively during basic training. If participants tested negative for by quantitative polymerase chain...
Abstract The vagina is an interactive interface between the host and environment. Its surface covered by a protective epithelium colonized bacteria other microorganisms. ectocervix nonsterile, whereas endocervix upper genital tract are assumed to be sterile in healthy women. Therefore, cervix serves pivotal role as gatekeeper protect from microbial invasion subsequent reproductive pathology. Microorganisms that cross this barrier can cause preterm labor, pelvic inflammatory disease,...
The world's most consequential pathogens occur in regions with the fewest diagnostic resources, leaving true burden of these diseases largely under-represented. During a prospective observational study sepsis Takeo Province Cambodia, we enrolled 200 patients over an 18-month period. By coupling traditional methods such as culture, serology, and PCR to Next Generation Sequencing (NGS) advanced statistical analyses, successfully identified pathogenic cause 46.5% our cohort. In all, detected 25...
Abstract Background The frequency of asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is unclear and may be influenced by how symptoms are evaluated. In this study, we sought to determine the SARS-CoV-2 in a prospective cohort health care workers (HCWs). Methods A HCWs, confirmed negative for exposure upon enrollment, were evaluated infection monthly analysis antibodies as well referral polymerase chain reaction testing whenever they exhibited disease 2019...
Next-generation sequencing (NGS) offers unparalleled resolution for untargeted organism detection and characterization. However, the majority of NGS analysis programs require users to be proficient in programming command-line interfaces. EDGE bioinformatics was developed offer scientists with little no expertise a point-and-click platform analyzing data rapid reproducible manner. (Empowering Development Genomics Expertise) v1.0 released January 2017, is an intuitive web-based engineered...
In 2018/2019, two large Guillain–Barré Syndrome (GBS) outbreaks took place in Peru. Here, we report a comprehensive analysis of biological samples from GBS patients the 2019 outbreak. We applied metagenomic, microbiologic, and serological analyses to different collected patients. Further phenotypic genomic characterization was conducted on Campylobacter jejuni isolates samples. Microbiologic metagenomic revealed several with multiple co-infections, yet no common infectious agents were found...
Abstract The vagina is an interactive interface between the host and environment. Its surface covered by a protective epithelium colonized bacteria other microorganisms. ectocervix nonsterile, whereas endocervix upper genital tract are assumed to be sterile in healthy women. Therefore, cervix serves pivotal role as gatekeeper protect from microbial invasion subsequent reproductive pathology. Microorganisms that cross this barrier can cause preterm labor, pelvic inflammatory disease,...
Abstract Background Antibiotic resistance is rising at disturbing rates and contributes to the deaths of millions people yearly. resistant infections disproportionately affect those with immunocompromising conditions, chronic colonization, frequent antibiotic use such as transplant patients or cystic fibrosis. However, clinicians lack diagnostic tools confidently diagnose treat infections, leading widespread empiric broad spectrum antimicrobials, often for prolonged duration. Case...
The emergence of SARS-CoV-2 variants complicates efforts to control the COVID-19 pandemic. Increasing genomic surveillance is imperative for early detection emerging variants, trace movement and monitor effectiveness countermeasures. Additionally, determining amount viable virus present in clinical samples helpful better understand impact these have on viral shedding. In this study, we analyzed nasal swab collected between March 2020 November 2021 from a cohort United States (U.S.) military...
Abstract We sought to determine pre-infection correlates of protection against SARS-CoV-2 post-vaccine infections (PVI) acquired during the first Omicron wave in United States. Serum and saliva samples from 176 vaccinated adults were collected October December 2021, immediately before wave, assessed for Spike-specific IgG IgA binding antibodies (bAb). Sera also bAb using commercial assays, neutralization activity several variants. PVI duration severity, as well risk precautionary behaviors,...
Infection with either
Melioidosis is a potentially severe disease caused by the gram-negative soil-dwelling bacterium called Burkholderia pseudomallei . The true breadth of distribution this tropical pathogen starting to emerge with environmental and clinical isolates frequently characterized in new countries regions. Even so, isolates, cases, genetic data from continent Africa remain scant. We previously confirmed presence B. environment Ghana, unmasking area endemicity for pathogen. Here, we describe...
Early in the pandemic, March of 2020, an outbreak COVID-19 occurred aboard aircraft carrier USS Theodore Roosevelt (CVN-71), during deployment Western Pacific. Out crew 4,779 personnel, 1,331 service members were suspected or confirmed to be infected with SARS-CoV-2. The demographic, epidemiologic, and laboratory findings from subsequent investigations have characterized as widespread transmission virus relatively mild symptoms asymptomatic infection among mostly young healthy adults. At...
Epidemics of emerging and re-emerging infectious diseases are a danger to civilian military populations worldwide. Health security mitigation disease threats is priority the US Government Department Defense (DoD). Next generation sequencing (NGS) Bioinformatics (BI) enhances traditional biosurveillance by providing additional data understand transmission, identify resistance virulence factors, make predictions, update risk assessments. As more laboratories adopt NGS BI technologies they...
Functional genome annotation is the process of labelling functional genomic regions with descriptive information. Manual curation can produce higher quality annotations than fully automated methods. efforts are time-consuming and complex; however, software help reduce these drawbacks.We created Annotation Studio (MAS) to improve efficiency manual prokaryotic viral genomes. MAS allows users upload unannotated genomes, provides an interface edit annotations, tracks history progress, saves data...
The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the disparity between developed and developing countries for infectious disease surveillance sequencing of pathogen genomes. majority SARS-CoV-2 sequences published are from Europe, North America, Asia. Between April 2020 January 2022, 795 SARS-CoV-2-positive nares swabs individuals in U.S. Navy installation Camp Lemonnier, Djibouti, were collected, sequenced, analyzed. In this study,...