Publications

2026

Brown TS, Nelson K, Kissler S, Martinez L, Horsburgh CR, White LF, Mathema B, Jacobson KR. Understanding and exploiting superspreading to disrupt Mycobacterium tuberculosis transmission. Lancet Infect Dis. 2026 Oct;26(10):e423-e432. doi: 10.1016/S1473-3099(26)00168-4. Epub 2026 May 14. PMID: 42134384.

Ghanem M, Srivastava R, Ektefaie Y, Hoppes D, Rosenfeld G, Yaniv Z, Grinev A, Xu AY, Yang E, Velásquez GE, Harrison L, Rosenthal A, Savic RM, Jacobson KR, Farhat MR. Tuberculosis Disease Severity Assessment Using Clinical Variables and Radiology Enabled by Artificial Intelligence. J Infect Dis. 2026 Sep 23;234(3):e600-e612. doi: 10.1093/infdis/jiag149. PMID: 41989328; PMCID: PMC13584190.

Kulkarni SG, Marin MG, Mann BC, Rawoot N, Goodwin S, Cesare N, Warren RM, Jacobson KR, Farhat MR. Within-host pathogen population diversity predicts treatment response in Tuberculosis. medRxiv [Preprint]. 2026 Jun 19:2026.06.16.26355818. doi: 10.64898/2026.06.16.26355818. PMID: 42369478; PMCID: PMC13308281.

Mann BC, Loubser J, Omar S, Glanz C, Ektefaie Y, Jacobson KR, Warren RM, Farhat MR. Systematic review and meta-analysis of protocols and sequencing yield for whole genome sequencing of Mycobacterium tuberculosis directly from sputum samples. Tuberculosis (Edinb). 2026 Mar;157:102743. doi: 10.1016/j.tube.2026.102743. Epub 2026 Jan 29. PMID: 41633150.

Murnane PM, Xia F, Afshar M, Brown JL, Chamie G, Cook RL, Couture MC, DiClemente RJ, Fatch R, Ferguson T, Francis JM, Haberer JE, Jacobson KR, Justice AC, Kapiga S, Kim TW, Krupitsky E, Marcus GM, Molina PE, Muyindike WR, Myers B, Page K, Phillips SA, Piano MR, Richards VL, So-Armah K, Stewart S, Sulkowski MS, Tien PC, Woolf-King S, Hahn JA. Exploring Phosphatidylethanol Cutoffs for Self-Reported Unhealthy Alcohol Use: An International Multi-Site Analysis. Alcohol Clin Exp Res (Hoboken). 2026 Jun;50(6):e70361. doi: 10.1111/acer.70361. PMID: 42345465; PMCID: PMC13296258.

Tabackman A, Karoly M, Jacobson KR, Horsburgh CR Jr, Linas B, Campbell J, Acuña-Villaorduña C, Sinha P. Optimizing Latent Tuberculosis Treatment Strategies Among Immigrants From High-Burden Settings. medRxiv [Preprint]. 2026 Aug 3:2026.07.13.26357974. doi: 10.64898/2026.07.13.26357974. PMID: 42523565; PMCID: PMC13405537.

2025

Tzelios CA, Malatesta S, Carney T, White LF, Weber SE, Thomson S, Theron D, Myers B, Parry CDH, Warren RM, Horsburgh CR, Farhat MR, Jacobson KR. Patient Determinants and Effects on Adherence of Adverse Drug Reactions to Tuberculosis Treatment: A Prospective Cohort Analysis. Clin Infect Dis. 2025 Aug 1;81(1):167-175. doi: 10.1093/cid/ciae642. PMID: 39973802; PMCID: PMC12314496.

Wijk M, Wasmann RE, Jacobson KR, Svensson EM, Denti P. A Pragmatic Approach to Handling Censored Data Below the Lower Limit of Quantification in Pharmacokinetic Modeling. CPT Pharmacometrics Syst Pharmacol. 2025 Jun;14(6):1042-1049. doi: 10.1002/psp4.70015. Epub 2025 Mar 11. PMID: 40067154; PMCID: PMC12167912.

2024

Campbell JI, Lavache D, Garing A, Sabharwal V, Haberer JE, Dubois M, Jenkins HE, Brooks MB, Joseph NT, Kissler K, Horsburgh CR, Jacobson KR. Evaluation of the Tuberculosis Infection Care Cascade Among Pregnant Individuals in a Low-Tuberculosis-Burden Setting. Open Forum Infect Dis. 2024 Aug 28;11(9):ofae494. doi: 10.1093/ofid/ofae494. PMID: 39238842; PMCID: PMC11376066.

Kulkarni S, Weber SE, Buys C, Lambrechts T, Myers B, Drainoni ML, Jacobson KR, Theron D, Carney T. Patient and provider perceptions of the relationship between alcohol use and TB and readiness for treatment: a qualitative study in South Africa. BMC Public Health. 2024 Aug 14;24(1):2216. doi: 10.1186/s12889-024-19570-y. PMID: 39143513; PMCID: PMC11325746.

Marin MG, Quinones-Olvera N, Wippel C, Behruznia M, Jeffrey BM, Harris M, Mann BC, Rosenthal A, Jacobson KR, Warren RM, Li H, Meehan CJ, Farhat MR. Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species. Bioinformatics. 2025 May 6;41(5):btaf219. doi: 10.1093/bioinformatics/btaf219. PMID: 40341387; PMCID: PMC12119186.

Murnane PM, Afshar M, Chamie G, Cook RL, Ferguson T, Haque LY, Jacobson KR, Justice AC, Kim TW, Khalili M, Krupitsky E, McGinnis KA, Molina P, Muyindike WR, Myers B, Richards VL, So-Armah K, Stewart S, Sulkowski MS, Tien PC, Hahn JA. Using Phosphatidylethanol as an Adjunct to Self-Reported Alcohol Use Improves Identification of Liver Fibrosis Risk. Am J Gastroenterol. 2024 Oct 31;120(7):1567-1575. doi: 10.14309/ajg.0000000000003178. PMID: 39480054; PMCID: PMC12041314.

Overbeck V, Malatesta S, Carney T, Myers B, Parry CDH, Horsburgh CR, Theron D, White LF, Warren RM, Jacobson KR, Bouton TC. Understanding the impact of pandemics on long-term medication adherence: directly observed therapy in a tuberculosis treatment cohort pre- and post-COVID-19 lockdowns. BMC Infect Dis. 2024 Oct 14;24(1):1154. doi: 10.1186/s12879-024-09994-7. PMID: 39396938; PMCID: PMC11475609.

Savinkina A, Muyindike W, Hahn JA, Emenyonu NI, Fatch R, Ngabirano C, Adong J, Jacobson KR, Linas BP. Strategies for isoniazid preventive therapy in HIV-positive patients who consume alcohol. Int J Tuberc Lung Dis. 2024 Jul 1;28(7):335-342. doi: 10.5588/ijtld.23.0303. PMID: 38961548; PMCID: PMC11875055.

Shapiro AN, Scott L, Moultrie H, Jacobson KR, Bor J, Conradie F, da Silva P, Mlisana K, Jenkins HE, Stevens WS. Risk factors for and timing of presumptive recurrent TB. Int J Tuberc Lung Dis. 2024 Nov 1;28(11):527-533. doi: 10.5588/ijtld.24.0019. PMID: 39468024.

Wijk M, Gausi K, Malatesta S, Weber SE, Court R, Myers B, Carney T, Parry CDH, Horsburgh CR, White LF, Wiesner L, Warren RM, Uren C, McIlleron H, Kloprogge F, Denti P, Jacobson KR. The impact of alcohol and illicit substance use on the pharmacokinetics of first-line TB drugs. J Antimicrob Chemother. 2024 Aug 1;79(8):2022-2030. doi: 10.1093/jac/dkae206. PMID: 38985541; PMCID: PMC11290884.

2023

Acuña-Villaorduña C, Jacobson KR, Horsburgh CR, Canning M, Sinha P. Initial experience with BPaL-based regimens to treat multidrug-resistant TB. Int J Tuberc Lung Dis. 2023 Aug 1;27(8):649-650. doi: 10.5588/ijtld.23.0185. PMID: 37491751; PMCID: PMC10365559.

Esmail H, Coussens AK, Thienemann F, Sossen B, Mukasa SL, Warwick J, Goliath RT, Davies NO, Douglass E, Jackson A, Lakay F, Streicher E, Munro JE, Barrios MH, Heinsohn T, Macpherson L, Sheerin D, Aziz S, Serole K, Daroowala R, Taliep A, Ahlers P, Malherbe ST, Bowden R, Warren R, Walzl G, Via LE, Bahlo M, Jacobson KR, Horsburgh CR Jr, Salgame P, Alland D, Barry CE 3rd, Flynn JL, Ellner JJ, Wilkinson RJ. High resolution imaging and five-year tuberculosis contact outcomes. medRxiv [Preprint]. 2023 Jul 3:2023.07.03.23292111. doi: 10.1101/2023.07.03.23292111. PMID: 37461515; PMCID: PMC10350144.

Hahn JA, Ngabirano C, Fatch R, Emenyonu NI, Cheng DM, Adong J, Tumwegamire A, Terrault NA, Linas BP, Jacobson KR, Muyindike WR. Safety and tolerability of isoniazid preventive therapy for tuberculosis for persons with HIV with and without alcohol use. AIDS. 2023 Aug 1;37(10):1535-1543. doi: 10.1097/QAD.0000000000003613. Epub 2023 May 29. PMID: 37260251; PMCID: PMC10355800.

Mann BC, Jacobson KR, Ghebrekristos Y, Warren RM, Farhat MR. Assessment and validation of enrichment and target capture approaches to improve Mycobacterium tuberculosis WGS from direct patient samples. J Clin Microbiol. 2023 Oct 24;61(10):e0038223. doi: 10.1128/jcm.00382-23. Epub 2023 Sep 20. PMID: 37728909; PMCID: PMC10595060.

Myers B, Carney T, Rooney J, Malatesta S, Ragan EJ, White LF, Natcheva H, Bouton TC, Weber SE, Farhat M, McIlleron H, Theron D, Parry CDH, Horsburgh CR, Warren RM, Jacobson KR. Smoked drug use in patients with TB is associated with higher bacterial burden. Int J Tuberc Lung Dis. 2023 Jun 1;27(6):444-450. doi: 10.5588/ijtld.22.0650. PMID: 37231597; PMCID: PMC10407961.

Petros BA, Turcinovic J, Welch NL, White LF, Kolaczyk ED, Bauer MR, Cleary M, Dobbins ST, Doucette-Stamm L, Gore M, Nair P, Nguyen TG, Rose S, Taylor BP, Tsang D, Wendlandt E, Hope M, Platt JT, Jacobson KR, Bouton T, Yune S, Auclair JR, Landaverde L, Klapperich CM, Hamer DH, Hanage WP, MacInnis BL, Sabeti PC, Connor JH, Springer M. Early Introduction and Rise of the Omicron Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variant in Highly Vaccinated University Populations. Clin Infect Dis. 2023 Feb 8;76(3):e400-e408. doi: 10.1093/cid/ciac413. PMID: 35616119; PMCID: PMC9213864.

Scott LE, Shapiro AN, Da Silva MP, Tsoka J, Jacobson KR, Emch M, Moultrie H, Jenkins HE, Moore D, Van Rie A, Stevens WS. Integrating Molecular Diagnostics and GIS Mapping: A Multidisciplinary Approach to Understanding Tuberculosis Disease Dynamics in South Africa Using Xpert MTB/RIF. Diagnostics (Basel). 2023 Oct 10;13(20):3163. doi: 10.3390/diagnostics13203163. PMID: 37891984; PMCID: PMC10606157.

Shapiro AN, Scott L, Moultrie H, Jacobson KR, Bor J, Fofana AM, Dor G, Ndjeka NO, da Silva P, Mlisana K, Jenkins HE, Stevens WS. Tuberculosis testing patterns in South Africa to identify groups that would benefit from increased investigation. Sci Rep. 2023 Nov 27;13(1):20875. doi: 10.1038/s41598-023-47148-y. PMID: 38012266; PMCID: PMC10682361.

2022

Bouton TC, Atarere J, Turcinovic J, Seitz S, Sher-Jan C, Gilbert M, White L, Zhou Z, Hossain MM, Overbeck V, Doucette-Stamm L, Platt J, Landsberg HE, Hamer DH, Klapperich C, Jacobson KR, Connor JH. Viral Dynamics of Omicron and Delta Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants With Implications for Timing of Release from Isolation: A Longitudinal Cohort Study. Clin Infect Dis. 2023 Feb 8;76(3):e227-e233. doi: 10.1093/cid/ciac510. PMID: 35737948; PMCID: PMC9278204.

Carney T, Rooney JA, Niemand N, Myers B, Theron D, Wood R, White LF, Meade CS, Chegou NN, Ragan E, Walzl G, Horsburgh R, Warren RM, Jacobson KR. Transmission Of Tuberculosis Among illicit drug use Linkages (TOTAL): A cross-sectional observational study protocol using respondent driven sampling. PLoS One. 2022 Feb 15;17(2):e0262440. doi: 10.1371/journal.pone.0262440. PMID: 35167586; PMCID: PMC8846525.

Malatesta S, Weir IR, Weber SE, Bouton TC, Carney T, Theron D, Myers B, Horsburgh CR, Warren RM, Jacobson KR, White LF. Methods for handling missing data in serially sampled sputum specimens for mycobacterial culture conversion calculation. BMC Med Res Methodol. 2022 Nov 19;22(1):297. doi: 10.1186/s12874-022-01782-8. PMID: 36402979; PMCID: PMC9675206.

Runels T, Ragan EJ, Ventura AS, Winter MR, White LF, Horsburgh CR, Samet JH, Saitz R, Jacobson KR. Testing and treatment for latent tuberculosis infection in people living with HIV and substance dependence: a prospective cohort study. BMJ Open. 2022 Mar 10;12(3):e058751. doi: 10.1136/bmjopen-2021-058751. PMID: 35273063; PMCID: PMC8915380.

Sy KTL, Leavitt SV, de Vos M, Dolby T, Bor J, Horsburgh CR Jr, Warren RM, Streicher EM, Jenkins HE, Jacobson KR. Spatial heterogeneity of extensively drug resistant-tuberculosis in Western Cape Province, South Africa. Sci Rep. 2022 Jun 27;12(1):10844. doi: 10.1038/s41598-022-14581-4. PMID: 35760977; PMCID: PMC9237070.

Turcinovic J, Schaeffer B, Taylor BP, Bouton TC, Odom-Mabey AR, Weber SE, Lodi S, Ragan EJ, Connor JH, Jacobson KR, Hanage WP. Understanding Early Pandemic Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in a Medical Center by Incorporating Public Sequencing Databases to Mitigate Bias. J Infect Dis. 2022 Nov 11;226(10):1704-1711. doi: 10.1093/infdis/jiac348. PMID: 35993116; PMCID: PMC9452097.

Wigger GW, Bouton TC, Jacobson KR, Auld SC, Yeligar SM, Staitieh BS. The Impact of Alcohol Use Disorder on Tuberculosis: A Review of the Epidemiology and Potential Immunologic Mechanisms. Front Immunol. 2022 Mar 31;13:864817. doi: 10.3389/fimmu.2022.864817. PMID: 35432348; PMCID: PMC9009367.

2021

Barocas JA, Savinkina A, Lodi S, Epstein RL, Bouton TC, Sperring H, Hsu HE, Jacobson KR, Schechter-Perkins EM, Linas BP, White LF. Projected Long-Term Impact of the Coronavirus Disease 2019 (COVID-19) Pandemic on Hepatitis C Outcomes in the United States: A Modeling Study. Clin Infect Dis. 2022 Aug 24;75(1):e1112-e1119. doi: 10.1093/cid/ciab779. PMID: 34499124; PMCID: PMC8522427.

Bouton TC, Lodi S, Turcinovic J, Schaeffer B, Weber SE, Quinn E, Korn C, Steiner J, Schechter-Perkins EM, Duffy E, Ragan EJ, Taylor BP, Miller N, Davidoff R, Hanage WP, Connor J, Pierre C, Jacobson KR. Coronavirus Disease 2019 Vaccine Impact on Rates of Severe Acute Respiratory Syndrome Coronavirus 2 Cases and Postvaccination Strain Sequences Among Health Care Workers at an Urban Academic Medical Center: A Prospective Cohort Study. Open Forum Infect Dis. 2021 Sep 17;8(10):ofab465. doi: 10.1093/ofid/ofab465. PMID: 34646910; PMCID: PMC8500299.

Hahn JA, Murnane PM, Vittinghoff E, Muyindike WR, Emenyonu NI, Fatch R, Chamie G, Haberer JE, Francis JM, Kapiga S, Jacobson K, Myers B, Couture MC, DiClemente RJ, Brown JL, So-Armah K, Sulkowski M, Marcus GM, Woolf-King S, Cook RL, Richards VL, Molina P, Ferguson T, Welsh D, Piano MR, Phillips SA, Stewart S, Afshar M, Page K, McGinnis K, Fiellin DA, Justice AC, Bryant K, Saitz R. Factors associated with phosphatidylethanol (PEth) sensitivity for detecting unhealthy alcohol use: An individual patient data meta-analysis. Alcohol Clin Exp Res. 2021 Jun;45(6):1166-1187. doi: 10.1111/acer.14611. Epub 2021 May 7. PMID: 33837975; PMCID: PMC8254773.

Leavitt SV, Jacobson KR, Ragan EJ, Bor J, Hughes J, Bouton TC, Dolby T, Warren RM, Jenkins HE. Decentralized Care for Rifampin-Resistant Tuberculosis, Western Cape, South Africa. Emerg Infect Dis. 2021;27(3):728-739. doi: 10.3201/eid2703.203204. PMID: 33622466; PMCID: PMC7920662.

Myers B, Carney T, Rooney J, Malatesta S, White LF, Parry CDH, Bouton TC, Ragan EJ, Horsburgh CR Jr, Warren RM, Jacobson KR. Alcohol and Tobacco Use in a Tuberculosis Treatment Cohort during South Africa’s COVID-19 Sales Bans: A Case Series. Int J Environ Res Public Health. 2021 May 19;18(10):5449. doi: 10.3390/ijerph18105449. PMID: 34069737; PMCID: PMC8161406.

Ragan EJ, Gill CJ, Banos M, Bouton TC, Rooney J, Horsburgh CR, Warren RM, Myers B, Jacobson KR. Directly Observed Therapy to Measure Adherence to Tuberculosis Medication in Observational Research: Protocol for a Prospective Cohort Study. JMIR Res Protoc. 2021 Jun 16;10(6):e24510. doi: 10.2196/24510. PMID: 34132642; PMCID: PMC8277341.

Ragan EJ, McCallum C, Marathe J, Cole M, Hofman M, Henderson AJ, Flack T, Miller NS, Burks EJ, Zhao GQ, Denis R, Lin NH, Jacobson KR, Andry CD, Pelton SI, Duffy ER, Bhadelia N. Pandemic Response Requires Research Samples: A U.S. Safety-Net Hospital’s Experience and Call for National Action. Ann Intern Med. 2021 Dec;174(12):1727-1732. doi: 10.7326/M21-2857. Epub 2021 Nov 2. PMID: 34724402; PMCID: PMC11234338.

2020

Ragan EJ, Kleinman MB, Sweigart B, Gnatienko N, Parry CD, Horsburgh CR, LaValley MP, Myers B, Jacobson KR. The impact of alcohol use on tuberculosis treatment outcomes: a systematic review and meta-analysis. Int J Tuberc Lung Dis. 2020 Jan 1;24(1):73-82. doi: 10.5588/ijtld.19.0080. PMID: 32005309; PMCID: PMC7491444.

2019

van der Heijden YF, Hughes J, Dowdy DW, Streicher E, Chihota V, Jacobson KR, Warren R, Theron G. Overcoming limitations of tuberculosis information systems: researcher and clinician perspectives. Public Health Action. 2019 Sep 21;9(3):120-127. doi: 10.5588/pha.19.0014. PMID: 31803584; PMCID: PMC6827492.

2018

Myers B, Bouton TC, Ragan EJ, White LF, McIlleron H, Theron D, Parry CDH, Horsburgh CR, Warren RM, Jacobson KR. Impact of alcohol consumption on tuberculosis treatment outcomes: a prospective longitudinal cohort study protocol. BMC Infect Dis. 2018 Sep 29;18(1):488. doi: 10.1186/s12879-018-3396-y. PMID: 30268101; PMCID: PMC6162918.