Patrick Cudahy, MD, MSc
Assistant Professor of Medicine (Infectious Diseases)Cards
Appointments
Additional Titles
Affiliated Faculty, Yale Institute for Global Health
About
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Titles
Assistant Professor of Medicine (Infectious Diseases)
Affiliated Faculty, Yale Institute for Global Health
Biography
Dr. Cudahy is an assistant professor in infectious diseases with a research interest in HIV and tuberculosis co-infection. He currently conducts research in South Africa focusing on improving treatment outcomes in people co-infected with tuberculosis and HIV by investigating biomarkers of treatment response and analysis of within-host tuberculosis strain diversity. Dr. Cudahy is board certified in Internal Medicine and Infectious Diseases.
Appointments
Infectious Diseases
Assistant ProfessorPrimary
Other Departments & Organizations
- All Institutions
- Infectious Diseases
- Internal Medicine
- Janeway Society
- Yale Institute for Global Health
- Yale Medicine
- Yale New Haven Health System
Education & Training
- MSc
- The London School of Hygiene & Tropical Medicine, Epidemiology (2023)
- Fellowship
- Yale New Haven Hospital (2019)
- Fellowship
- Yale University (2017)
- Internship and Residency
- Stanford University (2013)
- MD
- Medical College of Wisconsin (2010)
- BA
- University of California at Berkeley, Molecular and Cell Biology (2005)
Research
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Overview
Medical Research Interests
Public Health Interests
ORCID
0000-0003-4462-9567- View Lab Website
Cohen Lab
Research at a Glance
Yale Co-Authors
Publications Timeline
Research Interests
Ted Cohen, DPH, MD, MPH
Joshua Warren, PhD
Daniel Weinberger, PhD
Elizabeth Corbett
Kenneth Gunasekera
Sheela Shenoi, MD, MPH, FIDSA
Mycobacterium tuberculosis
Tuberculosis, Multidrug-Resistant
Tuberculosis
HIV
Biomarkers
Mycobacterium kansasii
Publications
2025
Distribution and transmission of M. tuberculosis in a high-HIV prevalence city in Malawi: A genomic and spatial analysis
Chitwood M, Corbett E, Ndhlovu V, Sobkowiak B, Colijn C, Andrews J, Burke R, Cudahy P, Dodd P, Imai-Eaton J, Engelthaler D, Folkerts M, Feasey H, Lan Y, Lewis J, McNichol J, Menzies N, Chipungu G, Nliwasa M, Weinberger D, Warren J, Salomon J, MacPherson P, Cohen T. Distribution and transmission of M. tuberculosis in a high-HIV prevalence city in Malawi: A genomic and spatial analysis. PLOS Global Public Health 2025, 5: e0004040. PMID: 40173177, PMCID: PMC11964229, DOI: 10.1371/journal.pgph.0004040.Peer-Reviewed Original ResearchCitationsAltmetricConceptsHigh HIV prevalence citiesTime of tuberculosisPoor health outcomesCity-wide interventionsTransmission of M. tuberculosisHealth outcomesTargeted interventionsHighest tuberculosis burdenTargeted screeningGeneral populationGeographic concentrationSurveillance dataCommunity characteristicsTuberculosis burdenLocal tacticsBlantyreWhole-genome sequencingInfectious tuberculosisCulture-positive tuberculosis casesInterventionMalawiSustained impactTreated individualsCityEvidence of local transmissionA new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission
Sobkowiak B, Cudahy P, Chitwood M, Clark T, Colijn C, Grandjean L, Walter K, Crudu V, Cohen T. A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission. Genome Medicine 2025, 17: 8. PMID: 39871355, PMCID: PMC11771024, DOI: 10.1186/s13073-025-01430-y.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsShort-read WGS dataWhole-genome sequencingStrain sequencesWGS dataMultiple strainsStrain proportionsMycobacterium tuberculosis populationMixed infectionGenome sequenceBioinformatics pipelineClustering allele frequenciesDownstream analysisAllele frequenciesEvidence of mixed infectionSequenceTuberculosis populationStrainIsolatesIn vitroTransmission clustersMixed samplesAllelesInfectionMycobacterium tuberculosis infectionPathogens
2024
Phylogeographic Analysis of Mycobacterium kansasii Isolates from Patients with M. kansasii Lung Disease in Industrialized City, Taiwan - Volume 30, Number 8—August 2024 - Emerging Infectious Diseases journal - CDC
Tobias Cudahy P, Liu P, Warren J, Sobkowiak B, Yang C, Ioerger T, Wu C, Lu P, Wang J, Chang H, Huang H, Cohen T, Lin H. Phylogeographic Analysis of Mycobacterium kansasii Isolates from Patients with M. kansasii Lung Disease in Industrialized City, Taiwan - Volume 30, Number 8—August 2024 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2024, 30: 1562-1570. PMID: 39043390, PMCID: PMC11286038, DOI: 10.3201/eid3008.240021.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsM. kansasii lung diseaseM. kansasii pulmonary diseasePulmonary diseaseM. kansasii isolatesSputum mycobacterial cultureWhole-genome sequencingEvaluate risk factorsPhylogeographic analysisAge of participantsGenetic relatednessEnvironmental acquisitionLung diseaseMycobacterial cultureOdds ratioRisk factorsM. kansasiiPatientsDiseasePlantsEnvironmental transmissionIsolatesPark plantingsCDCRiskDistribution and transmission of M. tuberculosis in a high-HIV prevalence city in Malawi: a genomic and spatial analysis
Distribution and transmission of M. tuberculosis in a high-HIV prevalence city in Malawi: a genomic and spatial analysis Melanie H. Chitwood, Elizabeth L. Corbett, Victor Ndhlovu, Benjamin Sobkowiak, Caroline Colijn, Jason R. Andrews, Rachael M. Burke, Patrick G.T. Cudahy, Peter J. Dodd, Jeffrey W. Imai-Eaton, David M. Engelthaler, Megan Folkerts, Helena Feasey, Yu Lan, Jen Lewis, Nicolas A Menzies, Geoffrey Chipungu, Marriott Nliwasa, Daniel M. Weinberger, Joshua L. Warren, Joshua A. Salomon, Peter MacPherson, Ted Cohen medRxiv 2024.05.17.24307525; doi: https://doi.org/10.1101/2024.05.17.24307525Peer-Reviewed Original Research In Press
2023
Urine and sputum tuberculosis tests: defining the trade-offs in endemic HIV and tuberculosis settings
Wilson D, Cudahy P, Drain P. Urine and sputum tuberculosis tests: defining the trade-offs in endemic HIV and tuberculosis settings. The Lancet Global Health 2023, 11: e809-e810. PMID: 37202010, DOI: 10.1016/s2214-109x(23)00215-2.Commentaries, Editorials and LettersCitationsAltmetricMeSH Keywords and Concepts
2022
A doctor at a PHC clinic: A ‘must-have’ or ‘nice-to-have’?
Kerry T, Cudahy P, Holst H, Ramsunder A, McGrath N. A doctor at a PHC clinic: A ‘must-have’ or ‘nice-to-have’? South African Medical Journal 2022, 113: 24-30. PMID: 36537544, DOI: 10.7196/samj.2023.v113i1.16700.Peer-Reviewed Original ResearchCitationsMeSH Keywords and ConceptsConceptsNon-communicable diseasesPHC clinicsClinic doctorsNurse cliniciansMedical conditionsPatient consultationsCommon non-communicable diseasesPrimary healthcare clinicsMedical servicesComplex clinical conditionsMedical doctorsNational Health InsuranceRenal diseaseClinic levelClinical conditionsChild healthClinic teamHealthcare clinicsClinical complexityMedical consultationClinicMental illnessPatientsCommunicable diseasesDoctor consultationsWhole-Genome Sequencing Has the Potential To Improve Treatment for Rifampicin-Resistant Tuberculosis in High-Burden Settings: a Retrospective Cohort Study
Cox H, Goig GA, Salaam-Dreyer Z, Dippenaar A, Reuter A, Mohr-Holland E, Daniels J, Cudahy PGT, Nicol MP, Borrell S, Reinhard M, Doetsch A, Beisel C, Gagneux S, Warren RM, Furin J. Whole-Genome Sequencing Has the Potential To Improve Treatment for Rifampicin-Resistant Tuberculosis in High-Burden Settings: a Retrospective Cohort Study. Journal Of Clinical Microbiology 2022, 60: e02362-21. PMID: 35170980, PMCID: PMC8925891, DOI: 10.1128/jcm.02362-21.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsDrug susceptibility testingRifampicin-resistant tuberculosisShort regimenMDR/RR-TB patientsMDR/RR-TBRR-TB patientsRetrospective cohort studyMore effective treatment regimensHigh-burden settingsRoutine drug susceptibility testingTB drug resistanceEffective treatment regimensWhole-genome sequencingTolerable regimensCohort studyRetrospective cohortRR-TBRegimen changeTreatment regimensTreatment recommendationsPatient outcomesTreatment individualizationClinical dataIndividualized treatmentIneffective drugsPhylogeography and transmission of M. tuberculosis in Moldova: A prospective genomic analysis
Yang C, Sobkowiak B, Naidu V, Codreanu A, Ciobanu N, Gunasekera KS, Chitwood MH, Alexandru S, Bivol S, Russi M, Havumaki J, Cudahy P, Fosburgh H, Allender CJ, Centner H, Engelthaler DM, Menzies NA, Warren JL, Crudu V, Colijn C, Cohen T. Phylogeography and transmission of M. tuberculosis in Moldova: A prospective genomic analysis. PLOS Medicine 2022, 19: e1003933. PMID: 35192619, PMCID: PMC8903246, DOI: 10.1371/journal.pmed.1003933.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsMultidrug-resistant tuberculosisDrug-resistant M. tuberculosisM. tuberculosis strainsPutative transmission clustersM. tuberculosisTransmission clustersMultidrug-resistant M. tuberculosis strainsTuberculosis strainsMultiple M. tuberculosis strainsCulture-positive TB casesLocal transmissionMDR-TB epidemicDrug-susceptible tuberculosisDrug resistance mutationsDrug resistance profilesUrgency of interventionTB casesDemographic dataNew casesTuberculosisInadequate treatmentNatural historyResistance mutationsBeijing lineageMycobacterium tuberculosis
2021
Potential contribution of HIV during first-line tuberculosis treatment to subsequent rifampicin-monoresistant tuberculosis and acquired tuberculosis drug resistance in South Africa: a retrospective molecular epidemiology study
Cox H, Salaam-Dreyer Z, Goig GA, Nicol MP, Menardo F, Dippenaar A, Mohr-Holland E, Daniels J, Cudahy PGT, Borrell S, Reinhard M, Doetsch A, Beisel C, Reuter A, Furin J, Gagneux S, Warren RM. Potential contribution of HIV during first-line tuberculosis treatment to subsequent rifampicin-monoresistant tuberculosis and acquired tuberculosis drug resistance in South Africa: a retrospective molecular epidemiology study. The Lancet Microbe 2021, 2: e584-e593. PMID: 34766068, PMCID: PMC8563432, DOI: 10.1016/s2666-5247(21)00144-0.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsFirst-line tuberculosis treatmentPrevious tuberculosis treatmentRifampicin-resistant tuberculosisRifampicin-monoresistant tuberculosisTuberculosis treatmentHIV positivityCohort studyLarge-scale prospective cohort studyResistance acquisitionPrevious treatmentRetrospective cohort studyProspective cohort studyTuberculosis drug resistancePatient-level dataLogistic regression analysisWhole-genome sequencingMolecular epidemiology studiesProspective databaseMDR tuberculosisRetrospective cohortFemale sexHigh burdenPatientsHIVEpidemiology studiesRifampicin-Monoresistant Tuberculosis Is Not the Same as Multidrug-Resistant Tuberculosis: a Descriptive Study from Khayelitsha, South Africa
Salaam-Dreyer Z, Streicher EM, Sirgel FA, Menardo F, Borrell S, Reinhard M, Doetsch A, Cudahy PGT, Mohr-Holland E, Daniels J, Dippenaar A, Nicol MP, Gagneux S, Warren RM, Cox H. Rifampicin-Monoresistant Tuberculosis Is Not the Same as Multidrug-Resistant Tuberculosis: a Descriptive Study from Khayelitsha, South Africa. Antimicrobial Agents And Chemotherapy 2021, 65: 10.1128/aac.00364-21. PMID: 34460307, PMCID: PMC8522772, DOI: 10.1128/aac.00364-21.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsMultidrug-resistant TBRMR-TBRR-TBPatient-level clinical dataPhenotypic drug susceptibility testingRifampicin-monoresistant tuberculosisRR-TB patientsMultidrug-resistant tuberculosisHIV-positive individualsRifampin-resistant tuberculosisDrug susceptibility testingRifampin monoresistanceHIV infectionMDR isolatesTB drugsRisk factorsClinical dataSusceptibility testingSubset of isolatesTuberculosisDescriptive studyMycobacterium tuberculosisAvailable WGS dataSignificant differencesPatients
Academic Achievements & Community Involvement
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Activities
activity American Journal of Tropical Medicine & Hygiene
2023 - PresentJournal ServiceRevieweractivity Chest
2023 - PresentJournal ServiceReviewer
Teaching & Mentoring
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Teaching
Didactic EMD 567: Tackling the Big Three: Malaria, TB, and HIV in Resource-Limited Settings
LecturerLecture SettingDetails10/1/2022 - PresentForGraduate3 Average Instructional Hours Per YearMalaria, tuberculosis, and HIV account for more than five million deaths worldwide each year. This course provides a deep foundation for understanding these pathogens and explores the public health issues that surround these infectious diseases in resource-limited settings. Emphasis is placed on issues in Africa, but contrasts for each disease are provided in the broader developing world. The course is divided into three sections, each focusing in depth on the individual infectious disease as well as discussions of interactions among the three diseases. The sections consist of three to four lectures each on the biology, individual consequences, and community/public health impact of each infectious disease. Discussion of ongoing, field-based research projects involving the diseases is led by relevant faculty (research into practice). The course culminates with a critical discussion of major public health programmatic efforts to tackle these diseases, such as those of PEPFAR, the Bill & Melinda Gates Foundation, the Global Fund, and the Stop TB Partnership.
Clinical Internal Medicine Morning Report
LecturerLecture SettingDetails3/1/2024 - PresentForHouse Staff2 Average Instructional Hours Per YearThe purpose of morning report is to teach residents how to think. This includes an emphasis on clinical reasoning, test characteristics, and cognitive bias. Some reports focus on diagnostic challenges, others focus on management decisions. Morning Report is run by the chief residents and attended by the program director, Mark Siegel, as well as a few core faculty members or invited consultants. Interns and residents volunteer to present a recent or current patient from their service. The presenter is expected to share the history, physical exam, and primary data including labs and imaging for the patient. We emphasize personal review of primary data (including chest X-rays, CT scans, ultrasound, and EKGs) to enhance housestaff interpretive skills. Then, as a group, we focus on summarizing the case into a succinct syndrome around which we build our differential diagnosis. Residents are expected to share their opinion about the "most likely" diagnosis and their estimation of pre-test probability of that diagnosis. The conversation is resident-run, with faculty interjecting only when they feel they have a pearl or tip to add. At the end, the presenter shares the hospital course of the patient and takes an active role in discussion some teaching points related to the case.
Didactic MD 1075: Attacks and Defenses
LecturerLecture SettingDetails11/1/2023 - PresentForGraduate4 Average Instructional Hours Per YearAttacks and Defenses introduces principles of immunity, tissue injury and repair and medical microbiology. These principles are integrated with the clinical fields of clinical immunology and allergy, infectious diseases, dermatology and rheumatology. Students are introduced to the prevention, diagnosis, and management of infectious, allergic, autoimmune and immune deficiency related diseases. Selected examples of immune based neoplastic therapy especially with respect to melanoma. Medical microbiology and infectious disease are taught during the entire course. Principles of immunobiology are taught concurrently with clinical immunology, followed by rheumatology and then dermatology. Understanding disease in underserved and diverse populations is a critical component of the course.
Didactic PA 2050: Clinical Medicine I
LecturerLecture SettingDetails11/1/2024 - PresentForGraduate2 Average Instructional Hours Per YearClinical Yale Affiliated Hospitals Program
LecturerLecture SettingDetails7/1/2024 - PresentForHouse Staff4 Average Instructional Hours Per YearFull-time faculty of the Department of Internal Medicine at Yale provide a series of lectures (including residency noon conferences, subspecialty presentations, ward rounds, and grand rounds) at the nine other affiliated hospitals. These lectures comprise a major proportion of the education of the residents at the affiliated institutions.
Mentoring
Isaac Chan
Postdoc2024 - 2026
Clinical Care
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Overview
Patrick Cudahy, MD, is an infectious diseases specialist focusing on the treatment and research of HIV and tuberculosis co-infection. He explores biomarkers of treatment response and studies the diversity of tuberculosis strains within patients. His work is particularly engaged in South Africa, where he aims to tackle the high mortality rates associated with tuberculosis, fueled by a significant prevalence of HIV.
As an assistant professor of medicine (infectious diseases) at Yale School of Medicine, Dr. Cudahy investigates ways to enhance understanding of the epidemiology of these co-infections.
He received his medical degree from the Medical College of Wisconsin, followed by an internship and residency in internal medicine at Stanford University and a fellowship in infectious diseases at Yale University.
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