CV

Experience

• Computational Epidemiologist, Biobot Analytics (2020–)
  • Developed mathematical model of waster epidemiology’s predictive value for COVID-19 activity
  • Established data-driven thresholds of COVID-19 risk based on SARS-CoV-2 wastewater concentrations
• Epidemiological Assistant (previously Postdoctoral Fellow), Harvard Chan School (2021–)
  • Discovered quantitative evidence of antibiotic resistance “spillover” between US states
  • Made first quantification of US nationwide racial/ethnic disparities in antibiotic use
  • Created comprehensive “landscape” of antibiotic use & resistance across 72 pathogen-drug combinations
  • Differentiated role of repeated, intensive antibiotic use versus “broad” use in selecting for resistance
  • Found evidence that market factors, not medical guidelines, drive trends in antibiotic prescribing
  • Demonstrated that use of azithromycin for respiratory infections affects resistance among N. gonorrhoeae
• Research Analyst, Institute for Public Research, CNA (2020–)
  • Implemented a Vaccine Vulnerability Index for DHS CISA
  • Executed an infectious disease threat assessment for the Greater Houston Region
  • Conceptualized portions of New York City Emergency Management’s Urban Risk Index
  • Supported COVID-19 after-action reviews for Virginia’s Departments of Health and Emergency Management
• COVID-19 Epidemiology Consultant (2020)
  • National Basketball Association
    • Built epidemiological model of COVID-19 transmission in a “bubble”
    • Advised on design of Orlando “bubble” system used for the 2020 playoffs
  • Epic Games
    • Built model of COVID-19 infection and absenteeism among employees
    • Advised on company’s strategic response to COVID-19 pandemic
• Scientific Director (later consultant), OpenBiome (2019–2021)
  • Acted as lead scientist for 70-person gut microbiota therapeutics nonprofit
  • Managed 2 dedicated research staff and multiple cross-departmental staff on internal research projects
  • Charted organization-wide 5-year research goals
  • Restructured 12-person research staff into thematic program areas
  • Planned and facilitated company-wide 2019 strategic planning process

Education

• Postdoctoral Fellowship, Harvard Chan School (2016–2018)
  • Advisor: Yonatan Grad
• PhD, Biological Engineering, MIT (2016)
  • Thesis: Quantitative modeling for microbial ecology and clinical trials (MIT Dspace)
  • Advisor: Eric Alm
• MPhil, Chemistry, University of Cambridge (2012)
  • Thesis: Coarse-grained models of chiral assemblies (pdf)
  • Advisor: David Wales
• MASt, Applied Mathematics & Theoretical Physics, University of Cambridge (2011)
• BA magna cum laude with Highest Honors, Physics, Williams College (2010)

Awards

• Kocaeli International Travel Award, Harvard Chan School (2017)
  • Funds one-week exchange program with Kocaeli University, Turkey
• NSF Graduate Research Fellowship (2013–2016)
• Presidential Fellow, MIT (2012–2013)
  • Fully funds first year of graduate student for 120 students
• Herchel Smith Fellowship, Williams College (2010–2012)
  • Fully funds 2 years of graduate study at the University of Cambridge
• Howard P. Stabler Prize in Physics, Williams College (2010)
• Barry M. Goldwater Scholarship (2009)

Publications

• SW Olesen, M Ikakaev, C Duvallet. Applications of wastewater-based epidemiology as a leading indicator for COVID-19. arXiv (submitted elsewhere). link

• J Chen, A Zaman, B Ramakrishna, SW Olesen. Stool banking for fecal microbiota transplantation: methods and operations at a large stool bank. Front Cell Infect Microbiol (2021). doi: 10.3389/fcimb.2021.622949

• M Santiago, SW Olesen. 16S rRNA sequencing of samples from universal stool bank donors. BMC Research Notes (2021). doi: 10.1186/s13104-021-05520-z

• A Zaman, T Qazi, P Pai, P Peters, S Nicolaysen, SW Olesen. Carriage rates of multidrug-resistant organisms among prospective stool donors. The Lancet Infectious Diseases (2021). doi: 10.1016/S1473-3099(21)00091-8

• SW Olesen. Fecal microbiota transplantation “donor effects” are not clinically relevant for Clostridioides difficile infection. Gastroenterology (2020). doi: 10.1053/j.gastro.2020.12.057 pubmed: 33387515

• D Bousbaine, P Bhagchandani, M London, M Mimee, SW Olesen, M Poyet, RW Cheloha, J Sidney, J Ling, A Gupta, TK Lu, A Sette, EJ Alm, D Mucida, AM Bilate, HL Ploegh. Antigen-specific induction of CD4+CD8αα+ intraepithelial T lymphocytes by Bacteroidetes species. bioRxiv (submitted elsewhere). doi: 10.1101/2020.08.05.236513

• SW Olesen. Power calculations for detecting differences in efficacy of fecal microbiota donors. Contemporary Clinical Trials Communications (2020). doi: 10.1016/j.conctc.2020.100674 pubmed: 33241161

• SW Olesen, A Zaman, M Osman, B Ramakrishna. Modelling donor screening strategies to reduce the risk of SARS-CoV-2 via fecal microbiota transplantation. Open Forum Infect Dis (2020). doi: 10.1093/ofid/ofaa499 pubmed: 33235890

• SW Olesen, M Lipsitch, YH Grad. The role of “spillover” in antibiotic resistance. PNAS (2020). doi: 10.1073/pnas.2013694117 pubmed: 33139558

• L Mamoon, SW Olesen. Fecal microbiota transplants annually and their positive clinical impact. Clin Transl Gastroenterol (2020). doi: 10.14309/ctg.0000000000000247 pubmed: 33259159

• C Zellmer, MRA Sater, MH Huntley, M Osman, SW Olesen B Ramakrishna. Shiga toxin-producing E. coli transmission via fecal microbiota transplant. Clin Infect Dis (2020). doi: 10.1093/cid/ciaa1486 pubmed: 33159210

• SW Olesen, Y Gerardin. Re-evaluating the evidence for fecal microbiota transplantation “super-donors” in inflammatory bowel disease. Journal of Crohn’s and Colitis (2020). doi: 10.1093/ecco-jcc/jjaa170 pubmed: 32808030

• AM Tsou, SW Olesen (co-first), EJ Alm, SB Snapper. 16S rRNA sequencing analysis: the devil is in the details. Gut Microbes (2020). doi: 10.1080/19490976.2020.1747336 pubmed: 32329652

• SW Olesen, P Panchal, J Chen, S Budree, M Osman. Global disparities and underserved populations in fecal microbiota transplantation research. Lancet Gastro Hepatol (2020). doi: 10.1016/S2468-1253(19)30452-2 pubmed: 32061326

• S Ryu, BJ Cowling, P Wu, SW Olesen, C Fraser, DS Sun, M Lipsitch, YH Grad. Case-based surveillance of antimicrobial resistance with full susceptibility profiles. JAC Antimicrob Resist (2019). doi: 10.1093/jacamr/dlz070 pubmed: 32280945

• BJ Sutherland, SW Olesen, H Kusumaatmaja, JWR Morgan, DJ Wales. Morphological analysis of chiral rod clusters from a coarse-grained single-site chiral potential. Soft Matter (2019). doi: 10.1039/C9SM01343A pubmed: 31589219

• E Goldstein, SW Olesen, Z Karaca, CA Steiner, C Viboud, M Lipsitch. Levels of outpatient prescribing for four major antibiotic classes and rates of septicemia hospitalization in adults in different US states – a statistical analysis. BMC Public Health 19: 1139 (2019). doi: 10.1186/s12889-019-7431-8 pubmed: 31426780

• SW Olesen, D MacFadden, YH Grad. Cumulative probability of receiving an antibiotic prescription over time. NEJM 380(19): 1872–1873 (2019). doi: 10.1056/NEJMc1816699 pubmed: 31067381

• RM Klevens, E Caten, SW Olesen, A DeMaria, S Troppy, YH Grad. Outpatient Antibiotic Prescribing in Massachusetts, 2011–2015. Open Forum Infectious Diseases 6(5): ofz169 (2019). doi: 10.1093/ofid/ofz169 pubmed: 31065563

• JI Miller, S Techtmann, J Fortney, N Mahmoudi, D Joyner, J Liu, SW Olesen, E Alm, A Fernandez, P Gardinali, N GaraJayeva, FS Askerov, TC Hazen. Oil hydrocarbon degradation by Caspian Sea microbial communities. Front Microbiol (2019). doi: 10.3389/fmicb.2019.00995 pubmed: 31143165

• SW Olesen, M Lipsitch, YH Grad. Response to comment on “The distribution of antibiotic use and its association with antibiotic resistance”. eLife 8:e47124 (2019). doi: 10.7554/eLife.47124 pubmed: 31050649

• DR MacFadden, M Lipsitch, SW Olesen, Y Grad. Multidrug-resistant Neisseria gonorrhoeae: implications for future treatment strategies. The Lancet Infectious Diseases (2018). doi: 10.1016/S1473-3099(18)30274-3 pubmed: 29856349

• SW Olesen, ML Barnett, DR MacFadden, JS Brownstein, S Hernandez-Diaz, M Lipsitch, YH Grad. The distribution of antibiotic use and its association with antibiotic resistance. eLife 7:e39435 (2018). doi: 10.7554/eLife.39435 pubmed: 30560781

• C Tedijanto, SW Olesen, YH Grad, M Lipsitch. Estimating the proportion of bystander selection for antibiotic resistance among potentially pathogenic bacterial flora. PNAS (2018). doi: 10.1073/pnas.1810840115 pubmed: 30559213

• SW Olesen, YH Grad. Racial/ethnic disparities in antimicrobial drug use, United States, 2014-2015. Emerging Infectious Diseases 24(11): 2126-2128 (2018). doi: 10.3201/eid2411.180762 pubmed: 30334733

• K Arora-Williams, SW Olesen, BP Scandella, K Delwiche, SJ Spencer, EM Myers, S Abraham, A Sooklal, SP Preheim. Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake. Microbiome (2018). doi: 10.1186/s40168-018-0556-7 pubmed: 30227897

• SW Olesen, EA Torrone, JR Papp, RD Kirkcaldy, M Lipsitch, YH Grad. Azithromycin susceptibility in Neisseria gonorrhoeae and seasonal macrolide use. Journal of Infectious Diseases (2018). doi: 10.1093/infdis/jiy551 pubmed: 30239814

• SW Olesen, ML Barnett, DR MacFadden, M Lipsitch, YH Grad. Trends in outpatient antibiotic prescribing practice among US older adults, 2011–2015: observational study. BMJ (2018). doi: 10.1136/bmj.k3155 pubmed: 30054353

• N Wilck, MG Matus, SM Kearney, SW Olesen, K Forslund, H Bartolomaeus, S Haase, A Mahler, A Balogh, L Marko, O Vvedenskaya, FH Kleiner, D Tsvetkov, L Klug, PI Costea, S Sunagawa, L Maier, N Rakova, V Schatz, P Neubert, C Fratzer, A Krannich, M Gollasch, DA Grohme, BF Corte-Real, RG Gerlach, M Basic, A Typas, C Wu, JM Titze, J Jantsch, M Boschmann, R Dechend, M Kleinewietfeld, S Kempa, P Bork, RA Linker, EJ Alm, DN Muller. Salt-responsive gut commensal modules TH17 axis and disease. Nature (2017). doi: 10.1038/nature24628 pubmed: 29143823

• SW Olesen, ML Leier, EJ Alm, SA Kahn. Searching for superstool: maximizing the therapeutic potential of FMT. Nature Reviews Gastroenterology & Hepatology 15, 387–388 (2018). doi: 10.1038/s41575-018-0019-4 pubmed: 29703976

• SW Olesen, C Duvallet, EJ Alm. dbOTU3: A new implementation of distribution-based OTU calling. PLOS ONE 12(5): e0176335 (2017). doi: 10.1371/journal.pone.0176335 pubmed: 28472072

• SW Olesen*, T Gurry* (co-first), EJ Alm. Designing fecal microbiota transplant trials that account for stool donor heterogeneity. Statistical Methods in Medical Research 27(10), 2906–2917 (2017). doi: 10.1177/0962280216688502 pubmed: 28178876

• SW Olesen, EJ Alm. Dysbiosis is not an answer. Nature Microbiology 1: 16228 (2016). doi: 10.1038/nmicrobiol.2016.228 pubmed: 27886190

• SP Preheim*, SW Olesen* (co-first), A Materna, C Varadharajan, M Blackburn, J Friedman, J Rodriguez, H Hemond, EJ Alm. Surveys, simulations, and single-cell assays relate function and phylogeny in a lake ecosystem. Nature Microbiology 1: 16130 (2016). doi: 10.1038/nmicrobiol.2016.130 pubmed: 27562262

• Olesen SW, Vora S, Techtmann SM, Fortney JL, Bastidas-Oyanedel JR, Rodriguez J, Hazen TC, Alm EJ. A novel analysis method for paired-sample microbial ecology experiments. PLOS ONE 11: e0154804 (2016). doi: 10.1371/journal.pone.0154804 pubmed: 27152415

• Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA, Jr, Preheim SP, Sanders MS, Yang J, Mueller MA, Brooks S, Watson DB, Zhang P, He Z, Dubinsky EA, Adams PD, Arkin AP, Fields MW, Zhou J, Alm EJ, Hazen TC. Natural bacterial communities serve as quantitative geochemical biosensors. mBio 6, e00326-15 (2015). doi: 10.1128/mBio.00326-15 pubmed: 25968645

• SW Olesen, SN Fejer, D Chakrabarti, and DJ Wales. A left-handed building block self-assembles into right-and left-handed helices. RSC Advances, 3, 12905-12908 (2013). doi: 10.1039/C3RA41813H

• D Bingemann, MR Allen, SW Olesen. Single molecules reveal the dynamics of heterogeneities in a polymer at the glass transition. Journal of Chemical Physics, 134, 024513 (2011). doi: 10.1063/1.3516516 pubmed: 21241126

Talks & posters

• Invited talk: “Improving safety and scale: the role of stool banks in C. difficile treatment and in research”. Fred Hutch Microbiome Symposium (Apr 2020)

• Invited talk: “Regulating fecal microbiota transplantation”. RAND Boston (Jan 2020)

• Invited talk: “Data-driven approaches to antimicrobial resistance policy”. NIAID, NIH (Dec 2019)

• Invited talk: “Fecal microbiota transplantation: the role of the donor in treating C. difficile and other diseases”. Rochester Institute of Technology, School of Life Sciences (Nov 2019)

• Invited talk: “Bugs and drugs: How (and how much) does changing antibiotic use change antibiotic resistance?”. Kolokotrones Seminar, Harvard Chan School of Public Health (Nov 2019)

• Oral abstract: “Azithromycin susceptibility in Neisseria gonorrhoeae and seasonal macrolide use”. STD Prevention Conference, DC (Sep 2018)

• Invited talk: “What’s causing azithromycin nonsusceptibility in Neisseria gonorrhoeae?”. Massachusetts Department of Public Health (Apr 2018)

• Talk: “Ecological association between unequal antibiotic consumption and antibiotic resistance”. Epidemics (Dec 2017)

• Oral abstract: “Antibiotic consumption and antibiotic resistance across organisms, drugs, and consumer groups.”. ID Week (Oct 2017)

• Invited talk: “Discovering hidden ecological relationships between bacteria using modeling and statistics.”. Williams College, Department of Statistics (Oct 2016)

• Poster: “Dynamics of high-salt-induced gut microbiome alterations in mice”. N Wilck, DN Muller, SW Olesen, MG Matus, S Kearney, EJ Alm. Keystone C1 (Gut Microbiota Modulation of Host Physiology) (Mar 2015)

• Poster: “A high-salt diet in mice increases the prevalence of a commensal gut microbe linked to other unhealthy diets”. SW Olesen, MG Matus, A Perrotta, M Smith, EJ Alm. Keystone D1 (Exploiting and Understanding Chemical Biotransformations in the Human Microbiome) (Apr 2014)

Teaching

• Translational Microbiome Research for Child Health - Microbiome sequencing. Aga Khan University. (Apr 2021)

• Data Wrangling. CNA Data Science Academy. (Mar 2021)

• “Adventures in the Microbiome”. Keynote for Cornell Microbiome Hackathon. Invited by Ilana Brito. (Apr 2019)

• “OpenBiome”. Lecture for MIT class 7.343 (Microbiome and Drug Delivery). Invited by Miguel Jimenez. (Apr 2019)

• “Distribution-based clustering”. Lecture for MIT class 1.871 (Computational Ecology). Invited by Otto Cordero. (Oct 2016)

• “Who’s there?: Practical bacterial phylogenetics”. Lecture for Williams College class BIOL 319 (Integrative Bioinformatics, Genomics and Proteomics). Invited by Lois Banta. (Oct 2016)

• “Bayesian statistics”. Lecture for MIT class 20.560 (Statistics for Biological Engineering Graduate Students). Course co-organizer. (Jan 2016)

• “Cooperative binding”. Lecture for MIT class 20.111 (Thermodynamics of biomolecular systems). Invited by Eric Alm. (Apr 2014)

• Supervisor. Emmanuel College & Department of Physics, University of Cambridge. (2012–2013)

• Teaching assistant. Department of Physics, Williams College. (2007–2010)

Service, leadership, and community

• President, Postdoctoral Association (PDA), Harvard Chan School (2018)
  • Led a consolidation of PDA council for >15 officers to 4
  • Initiated a Training Evaluation Initiative to create a common administrator-trainee language for negotiations
• Member, Dean’s Advisory Committee on Diversity and Inclusion, Harvard Chan School (2016–2018)
• Communication Fellow, MIT Biological Engineering Communication Lab (2013–2016)
  • Co-founding Fellow and mentor to junior Fellows
  • Coached >100 undergraduate, graduate, and postdoc clients
  • Co-led creation of the CommKit: online, content-specific communication guide
• Diversity Co-Chair, Graduate Student Board, MIT Biological Engineering (2013–2016)
  • Developed new programming for events exploring student diversity
  • Co-designed and conducted first departmental diversity climate survey
• Discussion leader & participant, MIT Science Policy Initiative (2012–2016)
  • Team member for visits to executive agencies and Congressional offices
  • Engaged in 30-hour Science Policy Bootcamp