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Scientific innovation to combat the spread of microbial pathogens
Scientific innovation to combat the spread of microbial pathogens
I draw from my professional experiences in government public health, academia, private industry, and the military
to create and strengthen strategies to identify, track, and intervene against the spread of infectious diseases.
Peer-Reviewed Publications
Hyperlink to Google Scholar profile Peer-Reviewed Publications
2026
Pathogen genomics training: Mapping global needs, gaps, and opportunities
Alice Matimba, Kristy Lee Garson, Nidia Trovao, Siddiqah George, Yiqun Toni Li, Daniel Evans, Jorge Batista da Rocha, James Otieno, Jolynne Mokaya, Tracey Calvert-Joshua, Heather Blankenship, and Nicola Mulder
Under peer review
Outbreak of Neisseria gonorrhoeae ST16676 among disseminated infections in Minnesota, USA, 2025
Daniel Evans, Allison LaPointe, Christine Peel, Khalid Bo-Subait, Elizabeth Dufort, Jenell Stewart, John Kaiyalethe, Bradley Craft, Matthew Plumb, Bonnie Weber, Laura Bohnker-Voels, Kelly Pung, Alyssa Mondelli, Jacob Garfin, Sarah Namugenyi, Paula Snippes-Vagnone, M. Elizabeth Gyllstrom, Kathryn Como-Sabetti, and Ruth Lynfield
Preprint on medRxiv; under peer review
https://www.medrxiv.org/content/10.64898/2026.01.09.26343522v1
Hybrid genomes of three multidrug-resistant Salmonella enterica serovar Newport (REPJJP01) isolates from exotic captive felids in North Dakota, USA
Brianna Stenger, Daniel Evans, and Kelli Maddock
Under peer review
Expanded genomic surveillance and characterization of human respiratory syncytial virus infections in Minnesota, USA, 2023-2025
Daniel Evans, Henry Kunerth, Erica Mumm, Matthew Plumb, Laura Bohnker-Voels, Sarah Bistodeau, Scott Cunningham, Jordan Davis, Kathryn Como-Sabetti, Sarah Namugenyi, Xiong Wang, Ruth Lynfield, Anna Strain, and Sarah Vetter
Preprint on medRxiv; under peer review
https://www.medrxiv.org/content/10.1101/2025.10.10.25337732v1
2025
Spots, stripes, and strains: a case report of multidrug-resistant Salmonella Newport in exotic felids
Brianna Stenger, Daniel Evans, Sarah Gefroh, Alyssa Bruer, Heidi Pecoraro, and Kelli Maddock
ASM Case Reports, 2025
https://doi.org/10.1128/asmcr.00098-25
Insights on recurrent and sequential Clostridioides difficile infections from genomic surveillance in Minnesota, USA, 2019-2021
Daniel Evans, Bree Friedman, Kelly Pung, Bonnie Weber, Matthew Plumb, Jacob Garfin, Christine Lees, Stacy Holzbauer, Ruth Lynfield, and Xiong Wang
Journal of Infectious Diseases, 2025
https://doi.org/10.1093/infdis/jiaf505
Genomic investigation of disseminated gonococcal infections, Minnesota, USA, 2024
Daniel Evans, Hannah Friedlander, Khalid Bo-Subait, John Kaiyalethe, Bradley Craft, Matthew Plumb, Bonnie Weber, Laura Bohnker-Voels, Kelly Pung, Alyssa Mondelli, Jacob Garfin, Jennifer Zipprich, Paula Snippes-Vagnone, Kathryn Como-Sabetti, and Ruth Lynfield
Emerging Infectious Diseases, 2025
https://doi.org/10.3201/eid3110.250785
2024
Establishment of prospective genomic surveillance of respiratory syncytial virus in Minnesota, USA
Daniel Evans, Henry Kunerth, Erica Mumm, Sarah Namugenyi, Matthew Plumb, Sarah Bistodeau, Scott Cunningham, Katherine Como-Sabetti, Ruth Lynfield, and Xiong Wang
Emerging Infectious Diseases
https://doi.org/10.3201/eid3011.241000
2023
Empirically derived sequence similarity thresholds to study the genomic epidemiology of plasmids shared among healthcare-associated bacterial pathogens
Daniel Evans, Alexander Sundermann, Marissa Griffith, Vatsala Srinivasa, Mustapha Mustapha, Jieshi Chen, Artur Dubrawski, Vaughn Cooper, Lee Harrison, and Daria Van Tyne
eBioMedicine
https://doi.org/10.1016/j.ebiom.2023.104681
Optimal discharge of patients from intensive care via a data-driven policy learning framework
Fernando Lejarza, Jacob Calvert, Misty Attwood, Daniel Evans, and Qingqing Mao
Operations Research for Healthcare
https://doi.org/10.1016/j.orhc.2023.100400
2022
Enterococci enhance Clostridioides difficile pathogenesis
Alexander Smith, Matthew Jenior, Orlaith Keenan, ... , Daniel Evans, ... et al.
Nature
https://doi.org/10.1038/s41586-022-05438-x
Genomic diversity of hospital-acquired infections revealed through prospective whole-genome sequencing-based surveillance
Mustapha Mustapha, Vatsala Srinivasa, Marissa Griffith, Shu-Ting Cho, Daniel Evans, Kady Waggle, Chinelo Ezeonwuka, Daniel Snyder, Jane Marsh, Lee Harrison, Vaughn Cooper, and Daria Van Tyne
mSystems
https://doi.org/10.1128/msystems.01384-21
Genomic characterization of lytic bacteriophages targeting genetically diverse Pseudomonas aeruginosa clinical isolates
Hayley Nordstrom, Daniel Evans, Amanda Finney, Kevin Westbrook, Paula Zamora, Casey Hofstaedter, Mohamed Yassin, Akansha Pradhan, Alina Iovleva, Robert Ernst, Jennifer Bomberger, Ryan Shields, Yohei Doi, and Daria Van Tyne
iScience
https://doi.org/10.1016/j.isci.2022.104372
Carbapenem-resistant Acinetobacter baumannii in US hospitals: diversification of circulating lineages and antimicrobial resistance
Alina Iovleva, Mustapha Mustapha, Marissa Griffith, Lauren Komarow, Courtney Luterbach, Daniel Evans, Eric Cober, Sandra Richter, Kirsten Rydell, Cesar Arias, Jesse Jacob, Robert Salata, Michael Satlin, Darren Wong, Robert Bonomo, David Van Duin, Vaughn Cooper, Daria Van Tyne, and Yohei Doi
mBio
https://doi.org/10.1128/mbio.02759-21
2021
Isolation and characterization of lytic bacteriophages targeting diverse Enterobacter spp. clinical isolates
Amanda Finney, Jalyne Perry, Daniel Evans, Kevin Westbrook, Christi McElheny, Alina Iovleva, Yohei Doi, Ryan K Shields, and Daria Van Tyne
PHAGE: Therapy, Applications, and Research
https://doi.org/10.1089/phage.2021.0011
Semisupervised deep learning techniques for predicting acute respiratory distress syndrome from time-series clinical data: Model development and validation study
Carson Lam, Chak Foon Tso, Abigail Green-Saxena, Emily Pellegrini, Zohora Iqbal, Daniel Evans, Jana Hoffman, Jacob Calvert, Qingqing Mao, and Ritankar Das
JMIR Formative Research
https://doi.org/10.2196/28028
Genomic and phenotypic diversity of Enterococcus faecalis isolated from endophthalmitis
Gayatri Shankar Chilambi, Hayley R Nordstrom, Daniel Evans, Regis Kowalski, Deepinder Dhaliwal, Vishal Jhanji, Robert Shanks, and Daria Van Tyne
PLoS One
https://doi.org/10.1371/journal.pone.0250084
2020
Clinical and genomic epidemiology of carbapenem-nonsusceptible Citrobacter spp. at a tertiary health care center over 2 decades
Ahmed Babiker, Daniel Evans, Marissa Griffith, Christi McElheny, Mohamed Hassan, Lloyd G Clarke, Roberta Mettus, Lee Harrison, Yohei Doi, Ryan Shields, and Daria Van Tyne
Journal of Clinical Microbiology
https://doi.org/10.1128/jcm.00275-20
Evolution of vancomycin-resistant Enterococcus faecium during colonization and infection in immunocompromised pediatric patients
Gayatri Chilambi, Hayley Nordstrom, Daniel Evans, Jose Ferrolino, Randall Hayden, Gabriela Marón, Anh Vo, Michael Gilmore, Joshua Wolf, Jason Rosch, and Daria Van Tyne
Proceedings of the National Academy of Sciences
https://doi.org/10.1073/pnas.1917130117
Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital
Daniel Evans, Marissa Griffith, Alexander Sundermann, Kathleen Shutt, Melissa Saul, Mustapha Mustapha, Jane Marsh, Vaughn Cooper, Lee H Harrison, and Daria Van Tyne
eLife
https://doi.org/10.7554/eLife.53886
Two cases of newly characterized Neisseria species, Brazil
Mustapha Mustapha, Ana Paula Lemos, Marissa Griffith, Daniel Evans, Ramon Marx, Elizabeth Coltro, Christian Siebra, Loeci Timm, Hamilton Ribeiro, Alessandro Monteiro, A. William Pasculle, Jane Marsh, Daria Van Tyne, Lee H Harrison, and Claudio T Sacchi
Emerging Infectious Diseases
https://doi.org/10.3201/eid2602.190191
2019
Evolution of outbreak-causing carbapenem-resistant Klebsiella pneumoniae ST258 at a tertiary care hospital over 8 years
Jane Marsh, Mustapha Mustapha, Marissa Griffith, Daniel Evans, Chinelo Ezeonwuka, A. William Pasculle, Kathleen Shutt, Alexander Sundermann, Ashley Ayres, Ryan Shields, Ahmed Babiker, Vaughn Cooper, Daria Van Tyne, and Lee Harrison
MBio
https://doi.org/10.1128/mbio.01945-19
NanR regulates nanI sialidase expression by Clostridium perfringens F4969, a human enteropathogenic strain
Jihong Li, Daniel Evans, John Freedman, and Bruce A McClane
Infection and Immunity
https://doi.org/10.1128/iai.00241-17
2017
Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages
Karen Klyczek, J. Alfred Bonilla, Deborah Jacobs-Sera, ..., Daniel Evans, ... et al.
PLoS One
https://doi.org/10.1371/journal.pone.0180517
CodY promotes sporulation and enterotoxin production by Clostridium perfringens type A strain SM101
Jihong Li, John C Freedman, Daniel Evans, and Bruce A McClane
Infection and Immunity
https://doi.org/10.1128/iai.00855-16
Scientific Presentations
Scientific Presentations
2026
Genomic epidemiology in civilian public health and military force health protection
Invited lecture at the United States Army Medical Research Institute of Infectious Diseases (USAMRIID)
Fort Detrick, MD
Genomic epidemiology: "State of the states"
Presentation at the OAMD Leads biannual conference
Atlanta, GA
Genomic surveillance of respiratory syncytial virus (RSV) in Minnesota: Insights from "season 2"
Presentation to the Massachusetts Consortium on Pathogen Readiness (MassCPR)
Remote
Antimicrobial resistance surveillance in wastewater
Panelist at the Global Emerging Infections Surveillance (GEIS) Next-Generation Sequencing Summit
Silver Spring, MD
Genomic influenza surveillance: Considerations and experiences at the state level
Webinar jointly presented by the Association of Public Health Laboratories (APHL) and the Council of State and Territorial Epidemiologists (CSTE)
Remote
Connecting bioinformatics to epidemiology
Presented at the Association of Public Health Laboratories (APHL) Bioinformatics Leadership Program summit
Bethesda, MD
Genomic surveillance of influenza viruses: "Know before you go"
Presented at the Association of Public Health Laboratories (APHL) Annual Conference
Portland, OR (remote)
Essential principles of pathogen genomic surveillance: Methods, strategies, and workforce development
Presented at AMD Academy 2025
Atlanta, GA
Building trust and capacity through evidence-based communication
Presented at AMD Academy 2025
Atlanta, GA
Next steps for next-generation sequencing: Genomic epidemiology
Presented at ID Lab Con 2025
Pasadena, CA
2024
Genomic epidemiology of respiratory syncytial virus: Statewide surveillance with global impact
Presented at the Minnesota Inter-laboratory Microbiology Association (MIMA) semi-annual meeting
Minneapolis, MN
Genomic epidemiology: Laboratorian and epidemiologist communication strategies
Presented at the AMD Days Conference
Decatur, GA
Concise and effective communication in advanced molecular detection
Presented at the Council of State and Territorial Epidemiologists (CTSE) annual conference
Pittsburgh, PA
Genomic surveillance and characterization of respiratory syncytial virus in Minnesota
Presented at the Council of State and Territorial Epidemiologists (CTSE) annual conference
Pittsburgh, PA
From infantry to infection control: A military reservist's perspective on public health
Invited speaker for MDH Speaks public outreach event, run by the Minnesota Department of Health
St. Paul, MN
The Applied Genomic Epidemiology Community of Practice
Presented at the AMD Leads conference
Atlanta, GA
2023
Adaptable wastewater biosurveillance for emerging disease threats
Presented at the Global Emerging Infectious Surveillance (GEIS) Next-Generation Sequencing Summit,
Washington, DC
Training and workforce development through the Antimicrobial Resistance Surveillance Task Force
Presented at the Council of State and Territorial Epidemiologists (CTSE) annual conference
Salt Lake City, UT
Empirical methods in genomic epidemiology to improve the surveillance of plasmids exchanged among healthcare-associated bacteria
Presented at the Council of State and Territorial Epidemiologists (CTSE) annual conference
Salt Lake City, UTCo-authored presentation at the Association of Professionals in Infection Control and Epidemiology (APIC) annual conference
Orlando, FL
2022
Genomics methods to track the spread of plasmids among healthcare-associated bacterial pathogens.
Presented at the annual meeting of the Allegheny Branch of American Society for Microbiology (AB-ASM)
Morgantown, WV
2021
Genomic epidemiology of horizontal plasmid transfer among healthcare-associated bacterial pathogens in a tertiary hospital
Master's thesis defense at University of Pittsburgh School of Public Health
Pittsburgh, PA
2019
Comprehensive analysis of horizontal gene transfer among multidrug resistant bacterial pathogens in a single hospital
Presented at the Infectious Diseases and Microbiology Research Day, University of Pittsburgh School of Public Health
Pittsburgh, PA
Tracking horizontal gene transfer in clinical settings
Continuing education training seminar at the University of Pittsburgh School of Medicine
Pittsburgh, PA
2014
Characterization and molecular phylogeny of novel Arthrobacter bacteriophages reveals high diversity and unusually small genomes
Presented at the SEA-PHAGES annual research conference
Ashburn, VA
Other Accepted Scientific Abstracts
Other Accepted Scientific Abstracts
2025
Insights from the integration of statewide genomic and clinical surveillance of RSV in Minnesota, USA, July 2023 to April 2024
International Respiratory Syncytial Virus (RSV) Symposium
Iguazu Falls, Brazil
Highlighting epidemiological and genomic RSV surveillance program in Minnesota: Detection of a K68N variant cluster
International Respiratory Syncytial Virus (RSV) Symposium
Iguazu Falls, Brazil
2024
One Health approach to Salmonella infections
Council of State and Territorial Epidemiologists (CTSE) annual conference
Pittsburgh, PA
SNP-ing COVID-19's wings: A genomic epidemiology approach and investigative response to a COVID-19 cluster in Minnesota
Co-authorship of a presentation at the Council of State and Territorial Epidemiologists (CTSE) annual conference
Pittsburgh, PA
2022
Optimal intensive care unit patient discharge via a data-driven policy learning framework
American Medical Informatics Association (AMIA) Clinical Informatics Conference
Houston, TX
Early prediction of ventilator-associated pneumonia in intensive care unit patients using an intelligible machine learning algorithm
American Thoracic Society annual conference
San Francisco, CA
2020
Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital
American Society for Microbiology (ASM) Microbe conference
Remote
Clinical and microbial genomic features of enterococcal endophthalmitis infections
Annual Meeting of the Association for Research in Vision and Ophthalmology (ARVO)
Remote
2019
Comprehensive analysis of horizontal gene transfer among multidrug-resistant bacterial pathogens in a single hospital
Rust Belt Microbiome conference
Pittsburgh, PAInfectious Diseases and Microbiology Research Day
Pittsburgh, PA
Isolation and characterization of bacteriophages that target multidrug-resistant bacterial strains
Pittsburgh Bacterial Meeting
Pittsburgh, PA
Evolutionary dynamics of vancomycin-resistant Enterococcus faecium during gastrointestinal tract colonization and bloodstream infection in pediatric patients
Rust Belt Microbiome conference
Pittsburgh, PA
Clinical and molecular epidemiology of carbapenem non-susceptible Citrobacter spp.
IDWeek annual conference
Washington DC
2018
Back to the future: Screening hospital wastewater for phages that target multidrug-resistant bacteria
University of Pittsburgh Annual Science Conference
Pittsburgh, PA
2017
Synthesis of a bifacially binding Janus nucleobase oligomer on a chiral gamma-PNA backbone
Sigma Xi Annual Meeting
Raleigh, NC
2016
The effects of NanI sialidase production on host cell attachment and toxin expression of Clostridium perfringens Type C
Sigma Xi Annual Meeting
Atlanta, GA
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