A5053475675- Antibiotic Resistance in Bacteria
- Bacterial Identification and Susceptibility Testing
- Antimicrobial Resistance in Staphylococcus
- Bacteriophages and microbial interactions
- Clostridium difficile and Clostridium perfringens research
- Vibrio bacteria research studies
- Genomics and Phylogenetic Studies
- Salmonella and Campylobacter epidemiology
- Enterobacteriaceae and Cronobacter Research
- Microbial infections and disease research
- Ocular Infections and Treatments
- Antibiotics Pharmacokinetics and Efficacy
- Bacterial Infections and Vaccines
- Infections and bacterial resistance
- Gastrointestinal motility and disorders
- Respiratory Support and Mechanisms
- Mycobacterium research and diagnosis
- Sepsis Diagnosis and Treatment
- Pneumonia and Respiratory Infections
- Microbial Metabolism and Applications
- Gut microbiota and health
- Bacterial Genetics and Biotechnology
- Antibiotic Use and Resistance
- Machine Learning in Healthcare
- Infective Endocarditis Diagnosis and Management
Minnesota Department of Health
2025
University of Pittsburgh
2017-2023
Genomics (United Kingdom)
2023
Dascena (United States)
2021
Carnegie Mellon University
2017
Multidrug-resistant bacteria pose a serious health threat, especially in hospitals. Horizontal gene transfer (HGT) of mobile genetic elements (MGEs) facilitates the spread antibiotic resistance, virulence, and environmental persistence genes between nosocomial pathogens. We screened genomes 2173 bacterial isolates from healthcare-associated infections single hospital over 18 months, identified identical nucleotide regions belonging to distinct genera. To further resolve these shared...
The carbapenem class of antibiotics is invaluable for the treatment selected multidrug-resistant Gram-negative pathogens. continued transmission carbapenem-resistant bacteria such as ST258 K. pneumoniae serious global public health concern, options these infections are limited. This genomic epidemiologic investigation traced natural history in a single care setting over nearly decade. We found that distinct subpopulations have caused both device-associated and ward-associated outbreaks, some...
Carbapenem-resistant Acinetobacter baumannii (CR
Patients with hematological malignancies or undergoing hematopoietic stem cell transplantation are vulnerable to colonization and infection multidrug-resistant organisms, including vancomycin-resistant Enterococcus faecium (VREfm). Over a 10-y period, we collected sequenced the genomes of 110 VREfm isolates from gastrointestinal blood cultures 24 pediatric patients chemotherapy for malignancy at St. Jude Children's Research Hospital. We used patient-specific reference identify variants that...
Pseudomonas aeruginosa infections can be difficult to treat and new therapeutics are needed. Bacteriophage therapy is a promising alternative traditional antibiotics, but large numbers of isolated characterized phages lacking. We collected 23 diverse P. isolates from people with cystic fibrosis (CF) clinical infections, used them screen isolate over dozen aeruginosa-targeting hospital wastewater. Phages were genome sequencing, comparative genomics, lytic activity screening against all...
The vast bacteriophage population harbors an immense reservoir of genetic information. Almost 2000 phage genomes have been sequenced from phages infecting hosts in the phylum Actinobacteria, and analysis these reveals substantial diversity, pervasive mosaicism, novel mechanisms for replication lysogeny. Here, we describe isolation genomic characterization 46 environmental samples at various geographic locations U.S. a single Arthrobacter sp. strain. These include representatives all three...
Hospitalized patients are at increased risk of becoming infected with antibiotic-resistant organisms. We used whole-genome sequencing to survey and compare over 3,000 clinical bacterial isolates collected from hospitalized a large medical center 2-year period.
Carbapenem-nonsusceptible Citrobacter spp. (CNSC) are increasingly recognized as health care-associated pathogens. Information regarding their clinical epidemiology, genetic diversity, and mechanisms of carbapenem resistance is lacking. We examined microbiology records adult patients at the University Pittsburgh Medical Center (UMPC) Presbyterian Hospital (PUH) from 2000 to 2018 for CNSC, defined by ertapenem nonsusceptibility. Over this time frame, proportion CNSC increased 4% 10% (P =...
Background: The frequent temporal recurrence of Clostridioides difficile infection (CDI) may be the result relapse with same strain or reinfection a different strain; role genetic evolution C. in is poorly understood. We used whole-genome sequencing (WGS) to determine frequency among CDI recurrences and changes diversity individual strains responsible for relapses over time. Methods: analyzed data from active population- laboratory-based surveillance Minnesota, USA. performed WGS on isolates...
Abstract Background Recurrent Clostridioides difficile infection (CDI) is typically defined as a positive C. toxin or assay in the 8 weeks following an incident CDI. However, detections outside of this timeframe could represent failure to clear initial and inside new CDI based on molecular analysis isolates. We performed whole genome sequencing consecutive isolates patients compare summarize isolate pairs Minnesota. Methods analyzed data from our active population- laboratory-based...
We summarize a genomic investigation of 4-fold increase in disseminated gonococcal infections (DGI) Minnesota, USA, 2024. detected the emergence strain Neisseria gonorrhoeae rarely observed sequence type, which carries porB1a allele previously associated with disease and lacks genetic island.
Healthcare-associated bacterial pathogens frequently carry plasmids that contribute to antibiotic resistance and virulence. The horizontal transfer of in healthcare settings has been previously documented, but genomic epidemiologic methods study this phenomenon remain underdeveloped. objectives were apply whole-genome sequencing systematically resolve track carried by nosocomial a single hospital, identify links indicated likely plasmid transfer.We performed an observational circulating...
Clostridium perfringens type D strains cause enterotoxemia and enteritis in livestock via epsilon toxin production. In strain CN3718, CodY was previously shown to increase the level of production repress sporulation. C. A producing enterotoxin (CPE) human food poisoning antibiotic-associated diarrhea. Sporulation is critical for since spores contribute transmission resistance harsh environment sporulation essential CPE Therefore, current study asked whether also regulates SM101, a derivative...
Enterococcus faecalis are hospital-associated opportunistic pathogens and also causative agents of post-operative endophthalmitis. Patients with enterococcal endophthalmitis often have poor visual outcomes, despite appropriate antibiotic therapy. Here we investigated the genomic phenotypic characteristics E. isolates collected from 13 patients treated at University Pittsburgh Medical Center Eye over 19 years. Comparative analysis indicated that were infected belonging to diverse multi-locus...
ABSTRACT Clostridium perfringens can produce up to three different sialidases, including NanI, its major exosialidase. The current study first showed that human intestinal strains of C. grow by utilizing either glucose or sialic acids, such as N -acetylneuraminic acid (Neu5Ac), which are the end products sialidase activity. For enteropathogenic strain F4969, it was then determined culture supernatant activity and expression exosialidase genes, particularly nanI , influenced presence Neu5Ac...
Background A high number of patients who are hospitalized with COVID-19 develop acute respiratory distress syndrome (ARDS). Objective In response to the need for clinical decision support tools help manage next pandemic during early stages (ie, when limited labeled data present), we developed machine learning algorithms that use semisupervised (SSL) techniques predict ARDS development in general and populations based on data. Methods SSL were applied 29,127 encounters admitted 7 US hospitals...
We describe 2 human cases of infection with a new Neisseria species (putatively N. brasiliensis), 1 which involved bacteremia. Genomic analyses found that both isolates were distinct strains the same species, closely related to iguanae, and contained capsule synthesis operon similar meningitidis.
Background:Enterobacter spp. are opportunistic pathogens that cause nosocomial infections. Bacteriophages could be used to treat antibiotic-resistant Enterobacter Materials and Methods: We 10 genetically diverse clinical isolates identify lytic bacteriophages in hospital municipal wastewater. Comparative genomics was performed on host bacterial isolated phages. Activity of each phage against all determined. also tested activity paired from two patients who developed ceftazidime-avibactam...
ABSTRACT Multidrug-resistant bacterial pathogens pose a serious public health threat, especially in hospital settings. Horizontal gene transfer (HGT) of mobile genetic elements (MGEs) contributes to this threat by facilitating the rapid spread genes conferring antibiotic resistance, enhanced virulence, and environmental persistence between nosocomial pathogens. Despite recent advances microbial genomics, studies HGT settings remain limited scope. The objective study was identify track...
Summary Background Healthcare-associated bacterial pathogens frequently carry plasmids that contribute to antibiotic resistance and virulence. The horizontal transfer of in healthcare settings has been previously documented, but genomic epidemiologic methods study this phenomenon remain underdeveloped. objectives were develop a method systematically resolve track circulating single hospital, identify links indicated likely plasmid transfer. Methods We derived empirical thresholds sequence...
Abstract Background Carbapenem non-susceptible Citrobacter sp. (CNSC) are becoming increasingly recognized as healthcare-associated (HA) pathogens, but data on clinical and molecular epidemiology, species diversity mechanisms of carbapenem resistance lacking. Methods We reviewed patients at University Pittsburgh Medical Center with CNSC positive cultures from 2000 to 2018. The among a subset isolates all UPMC sites was confirmed by 16S rRNA typing, the presence carbapenemase enzymes in same...
Abstract Carbapenem-resistant Acinetobacter baumannii (CR Ab ) are a major cause of healthcare-associated infections. CR typically multidrug-resistant and infection is difficult to treat. Despite the urgent threat that pose, few systematic studies clinical molecular epidemiology have been conducted. The Study Network as Carbapenem-Resistant Pathogen (SNAP) designed investigate characteristics contemporary population structure circulating in US hospital systems using whole genome sequencing...