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Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues.

Meehan CJ, Goig GA, Kohl TA, Verboven L, Dippenaar A, Ezewudo M, Farhat MR, Guthrie JL, Laukens K, Miotto P, Ofori-Anyinam B, Dreyer V, Supply P, Suresh A, Utpatel C, van Soolingen D, Zhou Y, Ashton PM, Brites D, Cabibbe AM, de Jong BC, de Vos M, Menardo F, Gagneux S, Gao Q, Heupink TH, Liu Q, Loiseau C, Rigouts L, Rodwell TC, Tagliani E, Walker TM, Warren RM, Zhao Y, Zignol M, Schito M, Gardy J, Cirillo DM, Niemann S, Comas I, Van Rie A.

Nat Rev Microbiol. 2019 Sep;17(9):533-545. doi: 10.1038/s41579-019-0214-5. Review.


HIV incidence, pregnancy, and implementation outcomes from the Sakh'umndeni safer conception project in South Africa: a prospective cohort study.

Schwartz SR, Bassett J, Mutunga L, Yende N, Mudavanhu M, Phofa R, Sanne I, Van Rie A.

Lancet HIV. 2019 Jul;6(7):e438-e446. doi: 10.1016/S2352-3018(19)30144-4. Epub 2019 May 31.


Bedaquiline Microheteroresistance after Cessation of Tuberculosis Treatment.

de Vos M, Ley SD, Wiggins KB, Derendinger B, Dippenaar A, Grobbelaar M, Reuter A, Dolby T, Burns S, Schito M, Engelthaler DM, Metcalfe J, Theron G, van Rie A, Posey J, Warren R, Cox H.

N Engl J Med. 2019 May 30;380(22):2178-2180. doi: 10.1056/NEJMc1815121. No abstract available.


The impact of community- versus clinic-based adherence clubs on loss from care and viral suppression for antiretroviral therapy patients: Findings from a pragmatic randomized controlled trial in South Africa.

Hanrahan CF, Schwartz SR, Mudavanhu M, West NS, Mutunga L, Keyser V, Bassett J, Van Rie A.

PLoS Med. 2019 May 21;16(5):e1002808. doi: 10.1371/journal.pmed.1002808. eCollection 2019 May.


Pharmacokinetics of adjusted-dose 8-hourly lopinavir/ritonavir in HIV-infected children co-treated with rifampicin.

Rabie H, Rawizza H, Zuidewind P, Winckler J, Zar H, Van Rie A, Wiesner L, McIlleron H.

J Antimicrob Chemother. 2019 Aug 1;74(8):2347-2351. doi: 10.1093/jac/dkz171.


Integrating safer conception services into primary care: providers' perspectives.

Patwa MC, Bassett J, Holmes L, Mutunga L, Mudavanhu M, Makhomboti T, Van Rie A, Schwartz SR.

BMC Public Health. 2019 May 9;19(1):532. doi: 10.1186/s12889-019-6904-0.


Deciphering Within-Host Microevolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward.

Ley SD, de Vos M, Van Rie A, Warren RM.

Microbiol Mol Biol Rev. 2019 Mar 27;83(2). pii: e00062-18. doi: 10.1128/MMBR.00062-18. Print 2019 May 15. Review.


Infant feeding by South African mothers living with HIV: implications for future training of health care workers and the need for consistent counseling.

West NS, Schwartz SR, Yende N, Schwartz SJ, Parmley L, Gadarowski MB, Mutunga L, Bassett J, Van Rie A.

Int Breastfeed J. 2019 Feb 14;14:11. doi: 10.1186/s13006-019-0205-1. eCollection 2019.


Subfertility among HIV-affected couples in a safer conception cohort in South Africa.

Iyer JR, Van Rie A, Haberlen SA, Mudavanhu M, Mutunga L, Bassett J, Schwartz SR.

Am J Obstet Gynecol. 2019 Jul;221(1):48.e1-48.e18. doi: 10.1016/j.ajog.2019.02.040. Epub 2019 Feb 23.


A Patient-Centered Multicomponent Strategy for Accelerated Linkage to Care Following Community-Wide HIV Testing in Rural Uganda and Kenya.

Ayieko J, Petersen ML, Charlebois ED, Brown LB, Clark TD, Kwarisiima D, Kamya MR, Cohen CR, Bukusi EA, Havlir DV, Van Rie A.

J Acquir Immune Defic Syndr. 2019 Apr 1;80(4):414-422. doi: 10.1097/QAI.0000000000001939.


Health system barriers to implementation of TB preventive strategies in South African primary care facilities.

Van Ginderdeuren E, Bassett J, Hanrahan C, Mutunga L, Van Rie A.

PLoS One. 2019 Feb 14;14(2):e0212035. doi: 10.1371/journal.pone.0212035. eCollection 2019.


Incidence rate of sexually transmitted infections among HIV infected patients on long-term ART in an urban and a rural clinic in Uganda.

Okoboi S, Castelnuovo B, Moore DM, Musaazi J, Kambugu A, Birungi J, Nanfuka M, Van Rie A.

BMC Public Health. 2019 Jan 18;19(1):87. doi: 10.1186/s12889-019-6417-x.


A patient-centered multi-component strategy for accelerated linkage to care following community-wide HIV testing in rural Uganda and Kenya.

Ayieko J, Petersen ML, Charlebois ED, Brown LB, Clark TD, Kwarisiima D, Kamya MR, Cohen CR, Bukusi EA, Havlir DV, Van Rie A.

J Acquir Immune Defic Syndr. 2018 Dec 20. doi: 10.1097/QAI.0000000000001939. [Epub ahead of print]


Diagnostic strategies for childhood tuberculosis in the context of primary care in a high burden setting: the value of alternative sampling methods.

Hanrahan CF, Dansey H, Mutunga L, France H, Omar SV, Ismail N, Bassett J, Van Rie A.

Paediatr Int Child Health. 2019 May;39(2):88-94. doi: 10.1080/20469047.2018.1533321. Epub 2018 Oct 31.


Evaluation of the intensified tuberculosis case finding guidelines for children living with HIV.

Sawry S, Moultrie H, Van Rie A.

Int J Tuberc Lung Dis. 2018 Nov 1;22(11):1322-1328. doi: 10.5588/ijtld.17.0825.


Risky sexual behavior among patients on long-term antiretroviral therapy: a prospective cohort study in urban and rural Uganda.

Okoboi S, Castelnuovo B, Moore DM, Musaazi J, Kambugu A, Birungi J, Kaleebu P, Nanfuka M, Kamya MR, Van Rie A.

AIDS Res Ther. 2018 Oct 19;15(1):15. doi: 10.1186/s12981-018-0203-1.


Mental health in South African adolescents living with HIV.

West N, Schwartz S, Mudavanhu M, Hanrahan C, France H, Nel J, Mutunga L, Bernhardt S, Bassett J, Van Rie A.

AIDS Care. 2019 Jan;31(1):117-124. doi: 10.1080/09540121.2018.1533222. Epub 2018 Oct 10.


The unmet needs and health priorities of the urban poor: Generating the evidence base for urban community health worker programmes in South Africa.

Van Rie A, West NS, Schwartz SR, Mutanga L, Hanrahan CF, Ncayiyana J, Bassett J.

S Afr Med J. 2018 Aug 28;108(9):734-740. doi: 10.7196/SAMJ.2018.v108i9.13054.


"Hurdles on the path to 90-90-90 and beyond": Qualitative analysis of barriers to engagement in HIV care among individuals in rural East Africa in the context of test-and-treat.

Ayieko J, Brown L, Anthierens S, Van Rie A, Getahun M, Charlebois ED, Petersen ML, Clark TD, Kamya MR, Cohen CR, Bukusi EA, Havlir DV, Camlin CS.

PLoS One. 2018 Aug 30;13(8):e0202990. doi: 10.1371/journal.pone.0202990. eCollection 2018.


The potential use of rifabutin for treatment of patients diagnosed with rifampicin-resistant tuberculosis.

Whitfield MG, Warren RM, Mathys V, Scott L, De Vos E, Stevens W, Streicher EM, Groenen G, Sirgel FA, Van Rie A.

J Antimicrob Chemother. 2018 Oct 1;73(10):2667-2674. doi: 10.1093/jac/dky248.


Effect of a Patient-Centered Phone Call by a Clinical Officer at Time of HIV Testing on Linkage to Care in Rural Kenya.

Ayieko J, Petersen ML, van Rie A, Wafula E, Opudo W, Clark TD, Kamya MR, Balzer LB, Cohen CR, Bukusi EA, Charlebois ED, Havlir DV.

Open Forum Infect Dis. 2018 May 29;5(6):ofy126. doi: 10.1093/ofid/ofy126. eCollection 2018 Jun 1.


Diagnostic Accuracy of Clinical and Microbiological Signs in Patients With Skin Lesions Resembling Buruli Ulcer in an Endemic Region.

Eddyani M, Sopoh GE, Ayelo G, Brun LVC, Roux JJ, Barogui Y, Affolabi D, Faber WR, Boelaert M, Van Rie A, Portaels F, de Jong BC.

Clin Infect Dis. 2018 Aug 31;67(6):827-834. doi: 10.1093/cid/ciy197.


Innovative approach to the design and evaluation of treatment adherence interventions for drug-resistant TB.

Alegria-Flores K, Weiner BJ, Wiesen CA, Lich KLH, Van Rie A, Paul JE, Tovar MA.

Int J Tuberc Lung Dis. 2017 Nov 1;21(11):1160-1166. doi: 10.5588/ijtld.17.0296.


Defining the research agenda to measure and reduce tuberculosis stigmas.

Macintyre K, Bakker MI, Bergson S, Bhavaraju R, Bond V, Chikovore J, Colvin C, Craig GM, Cremers AL, Daftary A, Engel N, France NF, Jaramillo E, Kimerling M, Kipp A, Krishnaratne S, Mergenthaler C, Ngicho M, Redwood L, Rood EJJ, Sommerland N, Stangl A, van Rie A, van Brakel W, Wouters E, Zwerling A, Mitchell EMH.

Int J Tuberc Lung Dis. 2017 Nov 1;21(11):87-96. doi: 10.5588/ijtld.17.0151.


Evidence-based interventions to reduce tuberculosis stigma: a systematic review.

Sommerland N, Wouters E, Mitchell EMH, Ngicho M, Redwood L, Masquillier C, van Hoorn R, van den Hof S, Van Rie A.

Int J Tuberc Lung Dis. 2017 Nov 1;21(11):81-86. doi: 10.5588/ijtld.16.0788. Review.


A proposed novel framework for monitoring and evaluation of the cascade of HIV-associated TB care at the health facility level.

Hanrahan CF, Van Rie A.

J Int AIDS Soc. 2017 Apr 20;20(1):21375. doi: 10.7448/IAS.20.01.21375.


Client uptake of safer conception strategies: implementation outcomes from the Sakh'umndeni Safer Conception Clinic in South Africa.

Schwartz SR, Bassett J, Holmes CB, Yende N, Phofa R, Sanne I, Van Rie A.

J Int AIDS Soc. 2017 Mar 8;20(Suppl 1):21291. doi: 10.7448/IAS.20.2.21291.


The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis.

Dheda K, Gumbo T, Maartens G, Dooley KE, McNerney R, Murray M, Furin J, Nardell EA, London L, Lessem E, Theron G, van Helden P, Niemann S, Merker M, Dowdy D, Van Rie A, Siu GK, Pasipanodya JG, Rodrigues C, Clark TG, Sirgel FA, Esmail A, Lin HH, Atre SR, Schaaf HS, Chang KC, Lange C, Nahid P, Udwadia ZF, Horsburgh CR Jr, Churchyard GJ, Menzies D, Hesseling AC, Nuermberger E, McIlleron H, Fennelly KP, Goemaere E, Jaramillo E, Low M, Jara CM, Padayatchi N, Warren RM.

Lancet Respir Med. 2017 Mar 15. pii: S2213-2600(17)30079-6. doi: 10.1016/S2213-2600(17)30079-6. [Epub ahead of print] Review.


The relationship between entomological indicators of Aedes aegypti abundance and dengue virus infection.

Cromwell EA, Stoddard ST, Barker CM, Van Rie A, Messer WB, Meshnick SR, Morrison AC, Scott TW.

PLoS Negl Trop Dis. 2017 Mar 23;11(3):e0005429. doi: 10.1371/journal.pntd.0005429. eCollection 2017 Mar.


Acceptability and Preferences among Men and Women for Male Involvement in Antenatal Care.

Yende N, Van Rie A, West NS, Bassett J, Schwartz SR.

J Pregnancy. 2017;2017:4758017. doi: 10.1155/2017/4758017. Epub 2017 Jan 24.


Implications of Failure to Routinely Diagnose Resistance to Second-Line Drugs in Patients With Rifampicin-Resistant Tuberculosis on Xpert MTB/RIF: A Multisite Observational Study.

Jacobson KR, Barnard M, Kleinman MB, Streicher EM, Ragan EJ, White LF, Shapira O, Dolby T, Simpson J, Scott L, Stevens W, van Helden PD, Van Rie A, Warren RM.

Clin Infect Dis. 2017 Jun 1;64(11):1502-1508. doi: 10.1093/cid/cix128. Erratum in: Clin Infect Dis. 2017 Oct 15;65(8):1431-1433.


Early Antiretroviral Therapy Initiation and Mortality Among Infants Diagnosed With HIV in the First 12 Weeks of Life: Experiences From Kinshasa, DR Congo and Blantyre, Malawi.

Sheahan A, Feinstein L, Dube Q, Edmonds A, Chirambo CM, Smith E, Behets F, Heyderman R, Van Rie A.

Pediatr Infect Dis J. 2017 Jul;36(7):654-658. doi: 10.1097/INF.0000000000001539.


The contributions of Steve Lawn to the science, advocacy and policy of HIV-associated TB.

Van Rie A, Cohen T.

Int J Tuberc Lung Dis. 2016 Dec;20(12):1563-1564. No abstract available.


Prevalence of latent tuberculosis infection and predictive factors in an urban informal settlement in Johannesburg, South Africa: a cross-sectional study.

Ncayiyana JR, Bassett J, West N, Westreich D, Musenge E, Emch M, Pettifor A, Hanrahan CF, Schwartz SR, Sanne I, van Rie A.

BMC Infect Dis. 2016 Nov 8;16(1):661.


Performance of HIV Rapid Tests Among Breastfeeding, Malawian Infants.

Smith ER, Sheahan AD, Heyderman RS, Miller WC, Wheeler S, Hudgens M, Nelson JA, Dube Q, Van Rie A.

Pediatr Infect Dis J. 2017 Apr;36(4):405-411. doi: 10.1097/INF.0000000000001384.


Timing of HIV Seroreversion Among HIV-Exposed, Breastfed Infants in Malawi: Type of HIV Rapid Test Matters.

Smith ER, Hudgens M, Sheahan AD, Miller WC, Wheeler S, Nelson JAE, Dube Q, Van Rie A.

Matern Child Health J. 2017 Feb;21(2):248-252. doi: 10.1007/s10995-016-2152-4.


Prevalence of pyrazinamide resistance across the spectrum of drug resistant phenotypes of Mycobacterium tuberculosis.

Whitfield MG, Streicher EM, Dolby T, Simpson JA, Sampson SL, Van Helden PD, Van Rie A, Warren RM.

Tuberculosis (Edinb). 2016 Jul;99:128-30. doi: 10.1016/ Epub 2016 May 30.


Bioavailability of two licensed paediatric rifampicin suspensions: implications for quality control programmes.

McIlleron H, Hundt H, Smythe W, Bekker A, Winckler J, van der Laan L, Smith P, Zar HJ, Hesseling AC, Maartens G, Wiesner L, van Rie A.

Int J Tuberc Lung Dis. 2016 Jul;20(7):915-9. doi: 10.5588/ijtld.15.0833.


Can we translate findings on inequality in tuberculosis mortality into policy?

Van Rie A, Taylor R.

Int J Tuberc Lung Dis. 2016 May;20(5):569-70. doi: 10.5588/ijtld.16.0224. No abstract available.


Air Pollution and Pulmonary Tuberculosis: A Nested Case-Control Study among Members of a Northern California Health Plan.

Smith GS, Van Den Eeden SK, Garcia C, Shan J, Baxter R, Herring AH, Richardson DB, Van Rie A, Emch M, Gammon MD.

Environ Health Perspect. 2016 Jun;124(6):761-8. doi: 10.1289/ehp.1408166. Epub 2016 Feb 9.


Xpert(®) MTB/RIF for smear-negative presumptive TB: impact on case notification in DR Congo.

Mbonze NB, Tabala M, Wenzi LK, Bakoko B, Brouwer M, Creswell J, Van Rie A, Behets F, Yotebieng M.

Int J Tuberc Lung Dis. 2016 Feb;20(2):240-6. doi: 10.5588/ijtld.15.0177.


Multivariable analysis to determine if HIV-1 Tat dicysteine motif is associated with neurodevelopmental delay in HIV-infected children in Malawi.

Dara J, Dow A, Cromwell E, Sturdevant CB, Mallewa M, Swanstrom R, Van Rie A, Prasad VR.

Behav Brain Funct. 2015 Dec 17;11:38. doi: 10.1186/s12993-015-0083-7.


MDR tuberculosis control: time to change the dogma?

Van Rie A, Warren RM.

Lancet Respir Med. 2015 Dec;3(12):907-9. doi: 10.1016/S2213-2600(15)00477-4. Epub 2015 Nov 18. No abstract available.


CHAPAS-3 fills the gap.

Moultrie H, Van Rie A.

Lancet Infect Dis. 2016 Feb;16(2):133-4. doi: 10.1016/S1473-3099(15)00346-1. Epub 2015 Oct 5. No abstract available.


Impact of combination antiretroviral therapy initiation on adherence to antituberculosis treatment.

Knight M, van Zyl RL, Sanne I, Bassett J, van Rie A.

South Afr J HIV Med. 2015 Oct 8;16(1):346. doi: 10.4102/sajhivmed.v16i1.346. eCollection 2015.


Acceptability and preferences for safer conception HIV prevention strategies: a qualitative study.

Schwartz SR, West N, Phofa R, Yende N, Sanne I, Bassett J, Van Rie A.

Int J STD AIDS. 2016 Oct;27(11):984-92. doi: 10.1177/0956462415604091. Epub 2015 Sep 18.


Mycobacterium tuberculosis pncA Polymorphisms That Do Not Confer Pyrazinamide Resistance at a Breakpoint Concentration of 100 Micrograms per Milliliter in MGIT.

Whitfield MG, Warren RM, Streicher EM, Sampson SL, Sirgel FA, van Helden PD, Mercante A, Willby M, Hughes K, Birkness K, Morlock G, van Rie A, Posey JE.

J Clin Microbiol. 2015 Nov;53(11):3633-5. doi: 10.1128/JCM.01001-15. Epub 2015 Aug 19.


A Global Perspective on Pyrazinamide Resistance: Systematic Review and Meta-Analysis.

Whitfield MG, Soeters HM, Warren RM, York T, Sampson SL, Streicher EM, van Helden PD, van Rie A.

PLoS One. 2015 Jul 28;10(7):e0133869. doi: 10.1371/journal.pone.0133869. eCollection 2015. Review.


Should countries implement Xpert MTB/RIF when empirical treatment precludes a clinical effect?

Van Rie A.

Lancet Respir Med. 2015 Aug;3(8):591-3. doi: 10.1016/S2213-2600(15)00231-3. Epub 2015 Jul 22. No abstract available.


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