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Cynthia Monaco, M.D., Ph.D.

Contact Information

Phone Numbers

Appointment: (585) 275-0526

URMFGA member of the University of Rochester Medical Faculty Group

groupAn Accountable Health Partner

assignmentAccepting New Patients

Research Labs

Patient Care Setting

Infectious Diseases


Professional Background

Dr. Monaco received her MD and PhD degrees at University of Texas Southwestern Medical Center in Dallas, and her Internal Medicine Residency and Infectious Diseases Fellowship at Washington University in St. Louis. She continued there as faculty in the Department of Medicine at Washington University from 2015 to 2017. She then joined the faculty of the Division of Infectious Diseases at the University of Rochester Medical Center in 2017, where she continues to pursue microbiome research and sees inpatient ID consults.


Dr. Monaco's research involves elucidating components of the bacterial and viral microbiome in healthy and disease states using next-generation sequencing. She has shown that severe immunodeficiency in AIDS correlated with an expanded enteric virome and altered bacterial microbiome in a sub-Saharan cohort. She additionally is collaborating with colleagues at other institutions to study the lung microbiome in transplant recipients.



  • Infectious Disease - American Board of Internal Medicine
  • Internal Medicine - American Board of Internal Medicine


MD, PhD | University of Texas Southwestern Medical School at

Post-doctoral Training & Residency

7/1/2011 - 6/23/2015
Fellowship in Infectious Disease at Barnes Jewish Hospital

6/22/2010 - 6/22/2011
Residency in Internal Medicine at Barnes Jewish Hospital

6/22/2009 - 6/22/2010
Internship in Internal Medicine at Barnes Jewish Hospital

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Journal Articles

Monaco CL, Kwon DS. "Next-generation Sequencing of the DNA Virome from Fecal Samples." Bio-protocol.. 2017 Mar 5; 7(5)

Monaco CL, Gootenberg DB, Zhao G, Handley SA, Ghebremichael MS, Lim ES, Lankowski A, Baldridge MT, Wilen CB, Flagg M, Norman JM, Keller BC, Luévano JM, Wang D, Boum Y, Martin JN, Hunt PW, Bangsberg DR, Siedner MJ, Kwon DS, Virgin HW. "Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome." Cell host & microbe.. 2016 Mar 9; 19(3):311-22.

Handley SA, Desai C, Zhao G, Droit L, Monaco CL, Schroeder AC, Nkolola JP, Norman ME, Miller AD, Wang D, Barouch DH, Virgin HW. "SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination." Cell host & microbe.. 2016 Mar 9; 19(3):323-35.

Books & Chapters

Chapter Title: Infection in the Non-HIV Immunocompromised Host
Book Title: The Washington Manual Infectious Disease Subspecialty Consult
Author List: Johnson, Cynthia; Santos, Carlos
Edited By: Kirmani, N; Woeltje, K; Babcock, HM
Published By: Washington University Press 2013