A5064024002- Antibiotic Resistance in Bacteria
- Malaria Research and Control
- Bacterial Identification and Susceptibility Testing
- Mosquito-borne diseases and control
- Data Analysis with R
- Mycobacterium research and diagnosis
- Antibiotic Use and Resistance
- Antimicrobial Resistance in Staphylococcus
- Pneumonia and Respiratory Infections
- Evolution and Genetic Dynamics
- Scientific Computing and Data Management
- Clostridium difficile and Clostridium perfringens research
- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Insect symbiosis and bacterial influences
- Machine Learning and Data Classification
- Machine Learning in Healthcare
- Bacteriophages and microbial interactions
- Invertebrate Immune Response Mechanisms
- Parasite Biology and Host Interactions
- Antibiotics Pharmacokinetics and Efficacy
- Tuberculosis Research and Epidemiology
- Computational Physics and Python Applications
- Plant Pathogenic Bacteria Studies
- Genetics, Bioinformatics, and Biomedical Research
Los Alamos National Laboratory
2024-2025
Duke University
2021-2024
Duke Institute for Health Innovation
2022-2024
University of Michigan–Ann Arbor
2017-2023
Abstract The human infectious reservoir of Plasmodium falciparum is governed by transmission efficiency during vector-human contact and mosquito biting preferences. Understanding bias in a natural setting can help target interventions to interrupt transmission. In 15-month cohort western Kenya, we detected P. indoor-resting Anopheles blood samples qPCR matched bloodmeals participants using short-tandem repeat genotyping. Using risk factor analyses discrete choice models, assessed behavior...
Machine learning (ML) for classification and prediction based on a set of features is used to make decisions in healthcare, economics, criminal justice more. However, implementing an ML pipeline including preprocessing, model selection, evaluation can be time-consuming, confusing, difficult. Here, we present mikropml (prononced "meek-ROPE em el"), easy-to-use R package that implements pipelines using regression, support vector machines, decision trees, random forest, or gradient-boosted...
Integrating whole-genome sequencing and interfacility patient-transfer data reveals transmission pathways of a multidrug-resistant organism.
Abstract Background Carbapenem-resistant Enterobacterales (CRE) harboring blaKPC have been endemic in Chicago-area healthcare networks for more than a decade. During 2016–2019, series of regional point-prevalence surveys identified increasing prevalence blaNDM-containing CRE multiple long-term acute care hospitals (LTACHs) and ventilator-capable skilled nursing facilities (vSNFs). We performed genomic epidemiology investigation blaNDM-producing to understand their emergence spread. Methods...
The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These are not representative viral evolution can therefore alter the results downstream sequence analyses if included. We previously published software Hypermut, which detects hypermutation events relative to a reference. Two versions this method available as webtool. Neither these methods consider multistate characters or gaps alignment. Here, we present an updated,...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an antibiotic resistance threat of the highest priority. Given limited treatment options for this multidrug-resistant organism (MDRO), there urgent need targeted strategies to prevent transmission.
Abstract Background Hepatitis C virus (HCV) has high genetic diversity and is classified into 8 genotypes >90 subtypes, with some endemic to specific world regions. This could compromise direct-acting antiviral efficacy global HCV elimination. Methods We characterized subtypes “rare” in the United Kingdom (non-1a/1b/2b/3a/4d) by means of whole-genome sequencing via a national surveillance program. Genetic analyses determine genotype samples unresolved were undertaken comparison...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical-priority antibiotic resistance threat that has emerged over the past several decades, spread across globe, and accumulated to last-line agents. While CRKP infections are associated with high mortality, only subset of patients acquiring extraintestinal colonization will develop clinical infection. Here, we sought ascertain relative importance patient characteristics genetic background in determining risk Machine learning models...
Molecular epidemiologic studies of malaria parasites and other pathogens commonly employ amplicon deep sequencing (AmpSeq) marker genes derived from dried blood spots (DBS) to answer public health questions related topics such as transmission drug resistance. As these methods are increasingly employed inform direct action, it is important rigorously evaluate the risk false positive negative haplotypes clinically-relevant sample types. We performed a control experiment evaluating haplotype...
While variant identification pipelines are becoming increasingly standardized, less attention has been paid to the pre-processing of variants prior their use in bacterial genome-wide association studies (bGWAS). Three nuances that impact downstream genetic associations include separation at multiallelic sites, overlapping genes, and referencing relative ancestral alleles. Here we demonstrate importance these steps on diverse genomic datasets present prewas, an R package, standardizes...
Patients entering nursing facilities (NFs) are frequently colonized with antibiotic-resistant organisms (AROs). To understand the determinants of ARO colonization on NF admission, we applied whole-genome sequencing to track spread 4 species across regional NFs and evaluated patient-level characteristics transfer acute care hospitals (ACHs) as risk factors for colonization.Patients from 6 (n = 584) were surveyed methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant...
Plasmodium falciparum is the deadliest human malaria parasite, and infections consisting of concurrent, multiple strains are common in regions high endemicity. During transitions within between parasite’s mosquito hosts, these subject to population bottlenecks, distinct parasite may have differential fitness various environments encountered.
Abstract Measuring vector–human contact in a natural setting can inform precise targeting of interventions to interrupt transmission vector‐borne diseases. One approach is directly match human DNA vector bloodmeals the individuals who were bitten using genotype panels discriminative short tandem repeats (STRs). Existing methods for matching STR profiles people preclude ability most incomplete and multisource individuals. We developed bistro, an R package that implements three pre‐existing as...
Increasing evidence of regional pathogen transmission networks highlights the importance investigating dissemination multidrug-resistant organisms (MDROs) across a region to identify where is occurring and how pathogens move regions. We developed framework for MDRO dynamics using whole-genome sequencing data created regentrans , an easy-to-use, open source R package that implements these methods ( https://github.com/Snitkin-Lab-Umich/regentrans ). Using dataset over 400 carbapenem-resistant...
Carbapenem-resistant
Molecular epidemiologic studies of malaria parasites commonly employ amplicon deep sequencing (AmpSeq) marker genes derived from dried blood spots (DBS) to answer public health questions related topics such as transmission and drug resistance. As these methods are increasingly employed inform direct action, it is important rigorously evaluate the risk false positive negative haplotypes clinically-relevant sample types. We performed a control experiment evaluating haplotype recovery AmpSeq 5 (
We are bioinformatics trainees at the University of Michigan who started a local chapter Girls Who Code to provide fun and supportive environment for high school women learn power coding. Our goal was cover basic coding topics data science concepts through live hands-on practice. However, we could not find resource that exactly met our needs. Therefore, over past three years, have developed curriculum instructional format using Jupyter notebooks effectively teach introductory Python science....
Inspired by well-established material and pedagogy provided The Carpentries (Wilson, 2016), we developed a two-day workshop curriculum that teaches introductory R programming for managing, analyzing, plotting reporting data using packages from the tidyverse (Wickham et al., 2019), Unix shell, version control with git, GitHub. While official Software Carpentry is comprehensive, found it contains too much content workshop. We also felt independent nature of lessons left learners confused about...
Abstract Summary The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These are not representative viral evolution can therefore alter the results downstream sequence analyses if included. We previously published software Hypermut, which detects hypermutation events relative to a reference. Two versions this method available as webtool. Neither these methods consider multistate characters or gaps alignment. Here, we...
Abstract The human infectious reservoir of Plasmodium falciparum malaria parasites is governed by the efficiency parasite transmission during vector contact as well mosquito biting preferences. Understanding bias in a natural setting can help inform precise targeting interventions to efficiently interrupt transmission. In 15-month longitudinal cohort study high western Kenya, we investigated and factors associated with differential matching DNA single- multi-source Anopheles bloodmeals...
<title>Abstract</title> <bold>Background:</bold> Much effort and resources have been invested to control malaria transmission in Sub-Saharan Africa, but it remains a major public health problem. For the disease be transmitted from one person another, female <italic>Anopheles</italic> vector must survive 10-14 days following an infective bite for <italic>Plasmodium</italic>gametocytes develop into infectious sporozoites which can next during bloodmeal. The goal of this investigation was...
Abstract Background Significant effort and resources have been invested to control malaria transmission in sub-Saharan Africa, but it remains a major public health problem. For the parasite be transmitted, female Anopheles vector must survive 10–14 days following an infective bite allow Plasmodium gametocytes develop into infectious sporozoites. The goal of this study was assess factors associated with wild-caught survival infection host-seeking indoor resting. Methods conducted between...
Abstract There is an urgent need to improve our understanding of how new antibiotic resistant organisms emerge and spread. A high-priority resistance threat the ST258 lineage carbapenem-resistant Klebsiella pneumoniae . Here, we studied last-line drug colistin among by tracking its evolution across 21 U.S. hospitals over course a year. Phylogenetic analysis supported significant fitness cost being associated with resistance, as emergence was common but variants were rarely transmitted....
Abstract We assessed susceptibility patterns to newer antimicrobial agents among clinical carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates from patients in long-term acute-care hospitals (LTACHs) 2014 2015. Meropenem-vaborbactam and imipenem-relebactam nonsusceptibility were observed 9.9% 9.1% of isolates, respectively. Nonsusceptibility ceftazidime-avibactam (1.1%) plazomicin (0.8%) uncommon.
We assessed risk factors for colistin resistance among carbapenem-resistant Klebsiella pneumoniae (CRKP) from 375 patients in long-term acute care hospitals. Recent or polymyxin B exposure was associated with increased odds of (adjusted ratio = 1.11 per day exposure, 95% confidence interval 1.03-1.19, P .007).