A5025904777- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Clostridium difficile and Clostridium perfringens research
- Burkholderia infections and melioidosis
- Gut microbiota and health
- Helicobacter pylori-related gastroenterology studies
- Biomedical Text Mining and Ontologies
- Antibiotic Resistance in Bacteria
- Bacterial Identification and Susceptibility Testing
- Antimicrobial Resistance in Staphylococcus
- PARP inhibition in cancer therapy
- Advancements in Semiconductor Devices and Circuit Design
- Mycobacterium research and diagnosis
- Diphtheria, Corynebacterium, and Tetanus
- Nosocomial Infections in ICU
- Gene expression and cancer classification
- Urinary Tract Infections Management
- Environmental DNA in Biodiversity Studies
- Identification and Quantification in Food
- Botulinum Toxin and Related Neurological Disorders
- Legume Nitrogen Fixing Symbiosis
- Respiratory and Cough-Related Research
- COVID-19 and healthcare impacts
- RNA and protein synthesis mechanisms
- COVID-19 Clinical Research Studies
Northern Arizona University
2016-2024
The global dissemination of Klebsiella pneumoniae and carbapenemase (KPC) has been largely attributed to a few high-risk sequence types (STs) (ST258, ST11, ST512) associated with human disease. ST101 is an emerging clone that identified in different parts the world potential become global, persistent public health threat. Recent research suggests lineage 11% increase mortality rate comparison non-ST101 infections. In this study, we generated high-quality, near-finished genome assembly...
ABSTRACT Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive identify strict core genome that is specific target pathogen. As additional genomes analyzed, size reduced and there erosion target-specific regions due commonality with related species, potentially resulting in false positives and/or negatives. IMPORTANCE A comparative analysis 1,130...
Nosocomial acquisition of Clostridium difficile is well documented, yet recent studies have highlighted the importance community acquired infections and identified associated reservoirs for this pathogen. Multiple implicated companion pets farm animals as possible sources C. in humans. To explore potential role pet dogs human we systematically collected canine fecal samples (n = 197) Flagstaff, AZ. Additionally, nineteen were at a local veterinary clinic from diarrheic dogs. We used these...
Clostridioides difficile is a pathogen often associated with hospital-acquired infection or antimicrobial-induced disease; however, increasing evidence indicates infections can result from community environmental sources. Most genomic sequencing of C. has focused on clinical strains, although growing that spores are widespread in soil and water the environment. In this study, we sequenced 38 genomes collected isolates Flagstaff (AZ, USA) Slovenia an effort targeted towards surveillance...
New therapeutics are urgently needed in the fight against COVID-19. Repurposing drugs that either already approved for human use or advanced stages of approval process can facilitate more rapid advances toward this goal.
is a diverse pathogen, causing range of disease in humans, from self-limiting diarrhea to urinary tract infections (UTIs). Uropathogenic
Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and pathogen evolved towards commensal relationship host. In current study, used whole-genome sequencing to monitor this long-term symbiotic better understand B. persistence in P314's sputum despite intensive initial therapeutic regimens. We collected sequenced 118 isolates from airways over >16-year period, also sampled...
Diverse members of the genus Clostridium produce botulinum neurotoxins (BoNTs), which cause a flaccid paralysis known as botulism. While multiple species clostridia BoNTs, majority human botulism cases have been attributed to groups I and II. Recent comparative genomic studies demonstrated diversity within these BoNT-producing species. This report introduces multiplex PCR assay for differentiating C. group I, sporogenes, two major subgroups Coding region sequences unique each four...
Although infections caused by Clostridioides difficile have historically been attributed to hospital acquisition, growing evidence supports the role of community acquisition in C. infection (CDI). Symptoms CDI can range from mild, self-resolving diarrhoea toxic megacolon, pseudomembranous colitis, and death. In this study, we sampled clinical, environmental, canine reservoirs Flagstaff, Arizona, USA, understand distribution transmission pathogen a One Health framework; Flagstaff is...
Antimicrobial resistance (AMR) in the nosocomial pathogen, Acinetobacter baumannii, is becoming a serious public health threat. While some mechanisms of AMR have been reported, understanding novel critical for identifying emerging resistance. One first steps performing genotype/phenotype association studies. However, studies complicated by plastic nature A. baumannii pan-genome. In this study, we compared antibiograms 12 antimicrobials associated with multiple drug families 84 isolates, many...
Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and northern Australia that causes the disease, melioidosis. Although global genomic diversity of clinical B. isolates has been investigated, there limited understanding its across small geographic scales, especially in soil. In this study, we obtained 288 from single soil sample (~100g; intensive site 2, INT2) collected at depth 30cm Ubon Ratchathani Province, Thailand. We sequenced genomes 169 these represent...
Clostridioides difficile is a ubiquitous, diarrhoeagenic pathogen often associated with healthcare-acquired infections that can cause range of symptoms from mild, self-limiting disease to toxic megacolon and death. Since the early 2000s, large proportion C. cases have been attributed ribotype 027 (RT027) lineage, which sequence type 1 (ST1) in multilocus typing scheme. The spread ST1 has attributed, part, resistance fluoroquinolones used treat unrelated infections, creates conditions ideal...
As the size of reference sequence databases and high-throughput sequencing datasets continue to grow, it is becoming computationally infeasible use traditional alignment large genome for taxonomic classification metagenomic reads. Exact matching approaches can rapidly assign taxonomy summarize composition microbial communities, but they sacrifice accuracy lead false positives. Full tools provide higher confidence assignments sequences from genomes that diverge sequences; however, full are...
Abstract High-throughput comparative genomics has changed our view of bacterial evolution and relatedness. Many genomic comparisons, especially those regarding the accessory genome that is variably conserved across strains in a species, are performed using assembled genomes. For completed genomes, an assumption made entire was incorporated into assembly, while for draft assemblies, often constructed from short sequence reads, assembly approximation genome. To understand potential effects...
Background Burkholderia pseudomallei , causative agent of melioidosis, is a One Health concern as it acquired directly from soil and water causes disease in humans agricultural wild animals. We examined B . goats at single farm the Northern Territory Australia where >30 melioidosis over nine years. Methodology/Principal findings cultured 45 isolates 35 sampled around goat enclosures to isolate detect evaluate characteristics associated with its occurrence; 33 were obtained 1993–1994 116...
Abstract Clostridioides difficile is a ubiquitous, diarrheagenic pathogen often associated with healthcare-acquired infections that can cause range of symptoms from mild, self-limiting disease to toxic megacolon and death. Since the early 2000s, large proportion C. cases have been attributed ribotype 027 (RT027) lineage, which sequence type 1 (ST1) in multilocus typing (MLST) scheme. The spread ST1 has attributed, part, resistance fluoroquinolones used treat un-related infections, creates...
Abstract Antimicrobial resistance (AMR) in the nosocomial pathogen, Acinetobacter baumannii , is becoming a serious public health threat. While some mechanisms of AMR have been reported, understanding novel critical for identifying emerging resistance. One first steps performing genotype/phenotype association studies. However, studies complicated by plastic nature A. pan-genome. In this study, we compared antibiograms 12 antimicrobials associated with multiple drug families 84 isolates, many...
Abstract Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and pathogen evolved towards commensal relationship host. In current study, used whole-genome sequencing to monitor this chronic infection better understand B. persistence in P314’s sputum despite intense repeated therapeutic regimens. We collected sequenced 118 isolates from airways over >16-year period, also...
ABSTRACT By late 2020, the coronavirus disease (COVID-19) pandemic, caused by SARS-CoV-2 has tens of millions infections and over 1 million deaths worldwide. A protective vaccine more effective therapeutics are urgently needed. We evaluated a new PARP inhibitor, stenoparib, which was recently advanced to Stage II clinical trials for treatment ovarian cancer, activity against human respiratory coronaviruses, including SARS-CoV-2, in vitro . Stenoparib exhibits dose-dependent suppression...