Andrew Kasarskis
A5032714338- Antibiotic Resistance in Bacteria
- Bacterial Identification and Susceptibility Testing
- Antimicrobial Resistance in Staphylococcus
- Inflammatory Bowel Disease
- Clostridium difficile and Clostridium perfringens research
- Genomics and Rare Diseases
- Chronic Lymphocytic Leukemia Research
- Machine Learning in Healthcare
- Chronic Myeloid Leukemia Treatments
- Cancer Genomics and Diagnostics
- Helicobacter pylori-related gastroenterology studies
- Mycobacterium research and diagnosis
- IL-33, ST2, and ILC Pathways
- Antibiotics Pharmacokinetics and Efficacy
- Gut microbiota and health
- Circadian rhythm and melatonin
- Genetics, Bioinformatics, and Biomedical Research
- BRCA gene mutations in cancer
- Bioinformatics and Genomic Networks
- Cardiovascular Health and Risk Factors
- Sleep and Wakefulness Research
- Microscopic Colitis
- Tuberculosis Research and Epidemiology
- Genomics and Phylogenetic Studies
- Genetic Associations and Epidemiology
Icahn School of Medicine at Mount Sinai
2014-2025
Sema4 (United States)
2021-2022
Center for Information Technology
2020-2021
Mount Sinai Health System
2016-2020
Engineering Associates (United States)
2017
New York Proton Center
2017
Pediatrics and Genetics
2017
Pacific Biosciences (United States)
2010-2012
Rosetta Stone (United States)
2004-2011
Sage Bionetworks
2010
Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes in turn induce changes higher-order disease traits. Therefore, identifying the vary response DNA and also associate traits has potential provide functional information required only identify validate susceptibility genes affected by DNA, understand networks which such operate how these Toward end, we profiled more than 39,000 transcripts...
A large outbreak of diarrhea and the hemolytic-uremic syndrome caused by an unusual serotype Shiga-toxin-producing Escherichia coli (O104:H4) began in Germany May 2011. As July 22, a number cases E. have been reported--3167 without (16 deaths) 908 with (34 deaths)--indicating that this strain is notably more virulent than most strains. Preliminary genetic characterization suggested that, unlike these strains, it should be classified within enteroaggregative pathotype coli.We used...
Although cholera has been present in Latin America since 1991, it had not epidemic Haiti for at least 100 years. Recently, however, there a severe outbreak of Haiti.We used third-generation single-molecule real-time DNA sequencing to determine the genome sequences 2 clinical Vibrio cholerae isolates from current Haiti, 1 strain that caused and strains isolated South Asia 2002 2008. Using primary sequence data, we compared genomes these 5 set previously obtained partial genomic 23 diverse V....
Blighted Gotham Deaths caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in New York City (NYC) during the spring of 2020 have vastly exceeded those reported China and many other countries. What were early events that led to such a outbreak? Gonzalez-Reiche et al. sampled some patients seeking assistance February March at Mount Sinai Health System. Phylogenetic analysis virus sequences these people, who drawn from across NYC, showed had been independently introduced...
Escherichia colisequence type 131 (ST131) has emerged globally as the most predominant extraintestinal pathogenic lineage within this clinically important species, and its association with fluoroquinolone extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of lineage, antimicrobial elements it, remain unclearly defined. This study largest worldwide collection (n= 215) sequenced ST131E. coliisolates to date demonstrates that clonal...
The recent widespread emergence of carbapenem resistance in Enterobacteriaceae is a major public health concern, as carbapenems are therapy last resort against this family common bacterial pathogens. Resistance genes can mobilize via various mechanisms, including conjugation and transposition; however, the importance mobility short-term evolution, such within nosocomial outbreaks, unknown. Using combination short- long-read whole-genome sequencing 281 blaKPC-positive isolates from single...
Liver cytochrome P450s (P450s) play critical roles in drug metabolism, toxicology, and metabolic processes. Despite rapid progress the understanding of these enzymes, a systematic investigation full spectrum functionality individual P450s, interrelationship or networks connecting them, genetic control each gene/enzyme is lacking. To this end, we genotyped, expression-profiled, measured P450 activities 466 human liver samples applied systems biology approach via integration genetics, gene...
Background COVID-19 has infected millions of people worldwide and is responsible for several hundred thousand fatalities. The pandemic necessitated thoughtful resource allocation early identification high-risk patients. However, effective methods to meet these needs are lacking. Objective aims this study were analyze the electronic health records (EHRs) patients who tested positive admitted hospitals in Mount Sinai Health System New York City; develop machine learning models making...
To identify factors that regulate gut microbiota density and the impact of varied on health, we assayed this fundamental ecosystem property in fecal samples across mammals, human disease, therapeutic interventions. Physiologic features host (carrying capacity) fitness shape density. Therapeutic manipulation mice altered metabolic immune homeostasis. In humans, was reduced Crohn’s ulcerative colitis, ileal pouch-anal anastomosis. The recurrent Clostridium difficile infection had lower were...
Tyrosine kinase domain mutations are a common cause of acquired clinical resistance to tyrosine inhibitors (TKI) used treat cancer, including the FLT3 inhibitor quizartinib. Mutation "gatekeeper" residues, which control access an allosteric pocket adjacent ATP-binding site, has been frequently implicated in TKI resistance. The molecular underpinnings gatekeeper mutation-mediated incompletely understood. We report first cocrystal structure with quizartinib, demonstrates that quizartinib...
Ceftazidime-avibactam is an antibiotic with activity against serine beta-lactamases, including Klebsiella pneumoniae carbapenemase (KPC). Recently, reports have emerged of KPC-producing isolates resistant to this antibiotic, a report wild-type KPC-3 producing sequence type 258 that was ceftazidime-avibactam. We describe detailed analysis isolate, in the context two other closely related isolates, recovered from same patient. Both encoded nonfunctional OmpK35, whereas we demonstrate novel...
The global emergence of Klebsiella pneumoniae carbapenemase-producing K. (KPC-Kp) multilocus sequence type ST258 is widely recognized. Less known about the molecular and epidemiological details non-ST258 in setting an outbreak mediated by endemic plasmid. We describe interplay blaKPC plasmids strains their relationship to location acquisition a U.S. health care institution. Whole-genome sequencing (WGS) analysis was applied KPC-Kp clinical isolates collected from single institution over 5...
ABSTRACT NDM-producing Klebsiella pneumoniae strains represent major clinical and infection control challenges, particularly in resource-limited settings with high rates of antimicrobial resistance. Determining whether transmission occurs at a gene, plasmid, or bacterial strain level within hospital and/or the community has implications for monitoring controlling spread. Whole-genome sequencing (WGS) is highest-resolution typing method available epidemiology. We sequenced...
Whole exome/genome sequencing (WES/WGS) is increasingly offered to ostensibly healthy individuals. Understanding the motivations and concerns of research participants seeking out personal WGS their preferences regarding return-of-results data sharing will help optimize protocols for WES/WGS. Baseline interviews including both qualitative quantitative components were conducted with (n=35) in HealthSeq project, a longitudinal cohort study individuals receiving results. Data recorded during...
Whole exome and genome sequencing (WES/WGS) is now routinely offered as a clinical test by growing number of laboratories. As part the design process each laboratory must determine performance characteristics platform, informatics pipeline. This report documents one such characterization WES/WGS.Whole whole was performed on multiple technical replicates five reference samples using Illumina HiSeq 2000/2500. The data processed with GATK-based analysis pipeline to evaluate: intra-run,...
The dissemination of carbapenem resistance in Escherichia coli has major implications for the management common infections. bla KPC, encoding a transmissible carbapenemase (KPC), historically largely been associated with Klebsiella pneumoniae, predominant plasmid (pKpQIL), and specific transposable element (Tn4401, ~10 kb). Here we characterize genetic features KPC emergence global E. coli, 2008-2013, using both long- short-read whole-genome sequencing. Amongst 43/45 successfully sequenced...