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3. Testing novel strategies for patients hospitalised with HIV-associated disseminated tuberculosis (NewStrat-TB): protocol for a randomised controlled trial

Author

Namale, Phiona E., Boloko, Linda, Vermeulen, Marcia, Haigh, Kate A., Bagula, Fortuna, Maseko, Alexis, Sossen, Bianca, Lee-Jones, Scott, Msomi, Yoliswa, McIlleron, Helen, Mnguni, Ayanda Trevor, Crede, Thomas, Szymanski, Patryk, Naude, Jonathan, Ebrahim, Sakeena, Vallie, Yakoob, Moosa, Muhammed Shiraz, Bandeker, Ismail, Hoosain, Shakeel, Nicol, Mark P., Samodien, Nazlee, Centner, Chad, Dowling, Wentzel, Denti, Paolo, Gumedze, Freedom, Little, Francesca, Parker, Arifa, Price, Brendon, Schietekat, Denzil, Simmons, Bryony, Hill, Andrew, Wilkinson, Robert J., Oliphant, Ida, Hlungulu, Siphokazi, Apolisi, Ivy, Toleni, Monica, Asare, Zimkhitha, Mpalali, Mkanyiseli Kenneth, Boshoff, Erica, Prinsloo, Denise, Lakay, Francisco, Bekiswa, Abulele, Jackson, Amanda, Barnes, Ashleigh, Johnson, Ryan, Wasserman, Sean, Maartens, Gary, Barr, David, Schutz, Charlotte, and Meintjes, Graeme

Published
2024
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4. Diagnostic yield as an important metric for the evaluation of novel tuberculosis tests: rationale and guidance for future research

Author

Broger, Tobias, Marx, Florian M, Theron, Grant, Marais, Ben J, Nicol, Mark P, Kerkhoff, Andrew D, Nathavitharana, Ruvandhi, Huerga, Helena, Gupta-Wright, Ankur, Kohli, Mikashmi, Nichols, Brooke E, Muyoyeta, Monde, Meintjes, Graeme, Ruhwald, Morten, Peeling, Rosanna W, Pai, Nitika Pant, Pollock, Nira R, Pai, Madhukar, Cattamanchi, Adithya, Dowdy, David W, Dewan, Puneet, and Denkinger, Claudia M

Published
2024
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6. Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease

Author

Abotsi, Regina E., Dube, Felix S., Rehman, Andrea M., Claassen-Weitz, Shantelle, Xia, Yao, Simms, Victoria, Mwaikono, Kilaza S., Gardner-Lubbe, Sugnet, McHugh, Grace, Ngwira, Lucky G., Kwambana-Adams, Brenda, Heyderman, Robert S., Odland, Jon Ø., Ferrand, Rashida A., and Nicol, Mark P.

Published
2023
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7. Diagnostic Accuracy of a Novel Tuberculosis Point-of-Care Urine Lipoarabinomannan Assay for People Living with HIV: A Meta-Analysis of Individual In- and Outpatient Data

Author

Broger, Tobias, primary, Nicol, Mark P., additional, Székely, Rita, additional, Bjerrum, Stephanie, additional, Sossen, Bianca, additional, Schutz, Charlotte, additional, Opintan, Japheth A., additional, Johansen, Isik S., additional, Mitarai, Satoshi, additional, Chikamatsu, Kinuyo, additional, Kerkhoff, Andrew D., additional, Macé, Aurélien, additional, Ongarello, Stefano, additional, Meintjes, Graeme, additional, Denkinger, Claudia M., additional, and Schumacher, Samuel G., additional

Published
2023
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8. Diagnosis of childhood febrile illness using a multi-class blood RNA molecular signature

Author

Habgood-Coote, Dominic, Wilson, Clare, Shimizu, Chisato, Barendregt, Anouk M., Philipsen, Ria, Galassini, Rachel, Calle, Irene Rivero, Workman, Lesley, Agyeman, Philipp K.A., Ferwerda, Gerben, Anderson, Suzanne T., van den Berg, J. Merlijn, Emonts, Marieke, Carrol, Enitan D., Fink, Colin G., de Groot, Ronald, Hibberd, Martin L., Kanegaye, John, Nicol, Mark P., Paulus, Stéphane, Pollard, Andrew J., Salas, Antonio, Secka, Fatou, Schlapbach, Luregn J., Tremoulet, Adriana H., Walther, Michael, Zenz, Werner, Van der Flier, Michiel, Zar, Heather J., Kuijpers, Taco, Burns, Jane C., Martinón-Torres, Federico, Wright, Victoria J., Coin, Lachlan J.M., Cunnington, Aubrey J., Herberg, Jethro A., Levin, Michael, and Kaforou, Myrsini

Published
2023
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9. Diagnostic sensitivity of SILVAMP TB-LAM (FujiLAM) point-of-care urine assay for extra-pulmonary tuberculosis in people living with HIV

Author

Kerkhoff, Andrew D, Sossen, Bianca, Schutz, Charlotte, Reipold, Elena Ivanova, Trollip, Andre, Moreau, Emmanuel, Schumacher, Samuel G, Burton, Rosie, Ward, Amy, Nicol, Mark P, Meintjes, Graeme, Denkinger, Claudia M, and Broger, Tobias

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, Clinical Research, Tuberculosis, Rare Diseases, HIV/AIDS, Lung, Orphan Drug, Infection, Good Health and Well Being, Humans, HIV Infections, Mycobacterium tuberculosis, Point-of-Care Systems, Sensitivity and Specificity, Tuberculosis, Pulmonary, Medical and Health Sciences, Respiratory System, Cardiovascular medicine and haematology
Abstract

FujiLAM point-of-care rapid urine test for TB detects a large proportion of pulmonary and traditionally difficult-to-diagnose extra-pulmonary forms of TB in hospitalised patients with advanced HIV http://bit.ly/36Dl0Eo

Published
2020

10. Lung function trajectories in South African children with pulmonary tuberculosis (TB) compared to those with non-TB lower respiratory tract infection: A prospective study

Author

Gray, Diane M, primary, Githinji, Leah, additional, Brittain, Kirsty, additional, Franckling-Smith, Zoe, additional, Bateman, Lindy, additional, Prins, Margaretha, additional, Baard, Cynthia B, additional, McFarlane, David, additional, Nicol, Mark P, additional, Workman, Lesley, additional, and Zar, Heather J, additional

Published
2024
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12. Testing Novel Strategies for Patients Hospitalized with HIV-associated Disseminated Tuberculosis (NewStrat-TB): Protocol for a Randomised Controlled Trial

Author

Namale, Phiona E, primary, Boloko, Linda, additional, Vermeulen, Marcia, additional, Haigh, Kate A, additional, Bagula, Fortuna, additional, Maseko, Alexis, additional, Sossen, Bianca, additional, Lee-Jones, Scott, additional, Msomi, Yoliswa, additional, Mclleron, Helen, additional, Mnguni, Ayanda T, additional, Crede, Thomas, additional, Szymanski, Patryk, additional, Naude, Jonathan, additional, Ebrahim, Sakeena, additional, Vallie, Yakoob, additional, Moosa, Muhammed S, additional, Bandeker, Ismail, additional, Hoosain, Shakeel, additional, Nicol, Mark P, additional, Samodien, Nazlee, additional, Centner, Chad, additional, Dowling, Wentzel, additional, Denti, Paolo, additional, Gumedze, Freedom, additional, Little, Francesca, additional, Parker, Arifa, additional, Price, Brendon, additional, Schietekat, Denzil, additional, Simmons, Bryony, additional, Hill, Andrew, additional, Wilkinson, Robert, additional, Oliphant, Ida, additional, Hlungulu, Siphokazi, additional, Apolisi, Ivy, additional, Toleni, Monica, additional, Asare, Zimkhitha, additional, Mpalali, Mkanyiseli K, additional, Boshoff, Erica, additional, Prinsloo, Denise, additional, Lakay, Francisco, additional, Bekiswa, Abulele, additional, Jackson, Amanda, additional, Barnes, Ashleigh, additional, Johnson, Ryan, additional, Wasserman, Sean, additional, Maartens, Gary, additional, Barr, David, additional, Schutz, Charlotte, additional, and Meintjes, Graeme, additional

Published
2024
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14. Effect of Xpert MTB/RIF on clinical outcomes in routine care settings: individual patient data meta-analysis

Author

Di Tanna, Gian Luca, Khaki, Ali Raza, Theron, Grant, McCarthy, Kerrigan, Cox, Helen, Mupfumi, Lucy, Trajman, Anete, Zijenah, Lynn Sodai, Mason, Peter, Bandason, Tsitsi, Durovni, Betina, Bara, Wilbert, Hoelscher, Michael, Clowes, Petra, Mangu, Chacha, Chanda, Duncan, Pym, Alexander, Mwaba, Peter, Cobelens, Frank, Nicol, Mark P, Dheda, Keertan, Churchyard, Gavin, Fielding, Katherine, and Metcalfe, John Z

Subjects
Epidemiology, Health Services and Systems, Public Health, Health Sciences, Rare Diseases, Clinical Research, Clinical Trials and Supportive Activities, Comparative Effectiveness Research, Tuberculosis, HIV/AIDS, Infectious Diseases, Infection, Good Health and Well Being, Adult, Antitubercular Agents, Brazil, Cause of Death, Female, HIV Infections, Humans, Male, Middle Aged, Mortality, Mycobacterium tuberculosis, Nucleic Acid Amplification Techniques, Odds Ratio, Outcome Assessment, Health Care, Proportional Hazards Models, South Africa, Sputum, Tanzania, Time-to-Treatment, Tuberculosis, Pulmonary, Zambia, Zimbabwe, Microbiology, Public Health and Health Services, Health services and systems, Public health
Abstract

BackgroundXpert MTB/RIF, the most widely used automated nucleic acid amplification test for tuberculosis, is available in more than 130 countries. Although diagnostic accuracy is well documented, anticipated improvements in patient outcomes have not been clearly identified. We performed an individual patient data meta-analysis to examine improvements in patient outcomes associated with Xpert MTB/RIF.MethodsWe searched PubMed, Embase, ClinicalTrials.gov, and the Pan African Clinical Trials Registry from inception to Feb 1, 2018, for randomised controlled trials (RCTs) comparing the use of Xpert MTB/RIF with sputum smear microscopy as tests for tuberculosis diagnosis in adults (aged 18 years or older). We excluded studies of patients with extrapulmonary tuberculosis, and studies in which mortality was not assessed. We used a two-stage approach for our primary analysis and a one-stage approach for the sensitivity analysis. To assess the primary outcome of cumulative 6-month all-cause mortality, we first performed logistic regression models (random effects for cluster randomised trials, with robust SEs for multicentre studies) for each trial, and then pooled the odds ratio (OR) estimates by a fixed-effects (inverse variance) or random-effects (Der Simonian Laird) meta-analysis. We adjusted for age and gender, and stratified by HIV status and previous tuberculosis-treatment history. The study protocol has been registered with PROSPERO, number CRD42014013394.FindingsOur search identified 387 studies, of which five RCTs were eligible for analysis. 8567 adult clinic attendees (4490 [63·5%] of 7074 participants for whom data were available were HIV-positive) were tested for tuberculosis with Xpert MTB/RIF (Xpert group) versus sputum smear microscopy (sputum smear group), across five low-income and middle-income countries (South Africa, Brazil, Zimbabwe, Zambia, and Tanzania). The primary outcome (reported in three studies) occurred in 182 (4·5%) of 4050 patients in the Xpert group and 217 (5·3%) of 4093 patients in the smear group (pooled adjusted OR 0·88, 95% CI 0·68-1·14 [p=0·34]; for HIV-positive individuals OR 0·83, 0·65-1·05 [p=0·12]). Kaplan-Meier estimates showed a lower rate of death (12·73 per 100 person-years in the Xpert group vs 16·38 per 100 person-years in the sputum smear group) for HIV-positive patients (hazard ratio 0·76, 95% CI 0·60-0·97; p=0·03). The risk of bias was assessed as reasonable and the statistical heterogeneity across studies was low (I2

Published
2019

15. Integrating environmental health and genomics research in Africa: challenges and opportunities identified during a Human Heredity and Health in Africa (H3Africa) Consortium workshop.

Author

Joubert, Bonnie R, Berhane, Kiros, Chevrier, Jonathan, Collman, Gwen, Eskenazi, Brenda, Fobil, Julius, Hoyo, Cathrine, John, Chandy C, Kumie, Abera, Nicol, Mark, Ramsay, Michèle, Smith, Joshua, Steyn, Adrie, Tshala-Katumbay, Desire, and McAllister, Kimberly

Subjects
Africa, G x E, H3Africa, environmental health, gene-environment interactions, global environmental health, workshop, Genetics, Prevention, Pediatric Research Initiative, Human Genome, Biotechnology, Aetiology, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being
Abstract

Individuals with African ancestry have extensive genomic diversity but have been underrepresented in genomic research. There is also extensive global diversity in the exposome (the totality of human environmental exposures from conception onwards) which should be considered for integrative genomic and environmental health research in Africa. To address current research gaps, we organized a workshop on environmental health research in Africa in conjunction with the H3Africa Consortium and the African Society of Human Genetics meetings in Kigali, Rwanda. The workshop was open to all researchers with an interest in environmental health in Africa and involved presentations from experts within and outside of the Consortium. This workshop highlighted innovative research occurring on the African continent related to environmental health and the interplay between the environment and the human genome. Stories of success, challenges, and collaborative opportunities were discussed through presentations, breakout sessions, poster presentations, and a panel discussion. The workshop informed participants about environmental risk factors that can be incorporated into current or future epidemiology studies and addressed research design considerations, biospecimen collection and storage, biomarkers for measuring chemical exposures, laboratory strategies, and statistical methodologies. Inclusion of environmental exposure measurements with genomic data, including but not limited to H3Africa projects, can offer a strong platform for building gene-environment (G x E) research in Africa. Opportunities to leverage existing resources and add environmental exposure data for ongoing and planned studies were discussed. Future directions include expanding the measurement of both genomic and exposomic risk factors and incorporating sophisticated statistical approaches for analyzing high dimensional G x E data. A better understanding of how environmental and genomic factors interact with nutrition and infection is also needed. Considering that the environment represents many modifiable risk factors, these research findings can inform intervention and prevention efforts towards improving global health.

Published
2019

16. Variation in the observed effect of Xpert MTB/RIF testing for tuberculosis on mortality: A systematic review and analysis of trial design considerations

Author

Ochodo, Eleanor A, Kalema, Nelson, Schumacher, Samuel, Steingart, Karen, Young, Taryn, Mallett, Susan, Deeks, Jon, Cobelens, Frank, Bossuyt, Patrick M, Nicol, Mark P, and Cattamanchi, Adithya

Subjects
Health Services and Systems, Health Sciences, Infectious Diseases, Rare Diseases, Tuberculosis, Clinical Trials and Supportive Activities, Emerging Infectious Diseases, Biodefense, Clinical Research, Infection, Good Health and Well Being, Diagnostic trials, Impact studies, Tuberculosis diagnosis, methodology, Xpert MTB/RIF, Impact, Pragmatic trials, diagnostic trials, Methodology, Systematic review, Biomedical and clinical sciences, Health sciences
Abstract

Background: Most studies evaluating the effect of Xpert MTB/RIF testing for tuberculosis (TB) concluded that it did not reduce overall mortality compared to usual care. We conducted a systematic review to assess whether key study design and execution features contributed to earlier identification of patients with TB and decreased pre-treatment loss to follow-up, thereby reducing the potential impact of Xpert MTB/RIF testing. Methods: We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, and Scopus for literature published from 1 st January 2009 to February 2019. We included all primary intervention studies that had evaluated the effect of Xpert MTB/RIF on mortality compared to usual care in participants with presumptive pulmonary TB. We critically reviewed features of included studies across: Study setting and context, Study population, Participant recruitment and enrolment, Study procedures, and Study follow-up. Results: We included seven randomised and one non-randomised study.  All included studies demonstrated relative reductions in overall mortality in the Xpert MTB/RIF arm ranging from 6% to 40%. However, mortality reduction was reported to be statistically significant in two studies. Study features that could explain the lack of observed effect on mortality included: the higher quality of care at study sites; inclusion of patients with a higher pre-test probability of TB leading to higher than expected empirical rates; performance of additional diagnostic testing not done in usual care leading to increased TB diagnosis or empiric treatment initiation; the recruitment of participants likely to return for follow-up; and involvement of study staff in ensuring adherence with care and follow-up. Conclusion: Most studies of Xpert MTB/RIF were designed and conducted in a manner that resulted in more patients being diagnosed and treated for TB, minimising the potential difference in mortality Xpert MTB/RIF testing could have achieved compared to usual care.

Published
2019

17. Investigating resistance in clinical Mycobacterium tuberculosis complex isolates with genomic and phenotypic antimicrobial susceptibility testing: a multicentre observational study

Author

Finci, Iris, Albertini, Audrey, Merker, Matthias, Andres, Sönke, Bablishvili, Nino, Barilar, Ivan, Cáceres, Tatiana, Crudu, Valeriu, Gotuzzo, Eduardo, Hapeela, Nchimunya, Hoffmann, Harald, Hoogland, Christine, Kohl, Thomas A, Kranzer, Katharina, Mantsoki, Anna, Maurer, Florian P, Nicol, Mark P, Noroc, Ecaterina, Plesnik, Sara, Rodwell, Timothy, Ruhwald, Morten, Savidge, Theresa, Salfinger, Max, Streicher, Elizabeth, Tukvadze, Nestani, Warren, Robin, Zemanay, Widaad, Zurek, Anna, Niemann, Stefan, and Denkinger, Claudia M

Published
2022
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19. Global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in children younger than 5 years in 2019: a systematic analysis

Author

Abram, Michael, Aerssens, Jeroen, Alafaci, Annette, Balmaseda, Angel, Bandeira, Teresa, Barr, Ian, Batinović, Ena, Beutels, Philippe, Bhiman, Jinal, Blyth, Christopher C, Bont, Louis, Bressler, Sara S, Cohen, Cheryl, Cohen, Rachel, Costa, Anna-Maria, Crow, Rowena, Daley, Andrew, Dang, Duc-Anh, Demont, Clarisse, Desnoyers, Christine, Díez-Domingo, Javier, Divarathna, Maduja, du Plessis, Mignon, Edgoose, Madeleine, Ferolla, Fausto Martín, Fischer, Thea K, Gebremedhin, Amanuel, Giaquinto, Carlo, Gillet, Yves, Hernandez, Roger, Horvat, Come, Javouhey, Etienne, Karseladze, Irakli, Kubale, John, Kumar, Rakesh, Lina, Bruno, Lucion, Florencia, MacGinty, Rae, Martinon-Torres, Federico, McMinn, Alissa, Meijer, Adam, Milić, Petra, Morel, Adrian, Mulholland, Kim, Mungun, Tuya, Murunga, Nickson, Newbern, Claire, Nicol, Mark P, Odoom, John Kofi, Openshaw, Peter, Ploin, Dominique, Polack, Fernando P, Pollard, Andrew J, Prasad, Namrata, Puig-Barberà, Joan, Reiche, Janine, Reyes, Noelia, Rizkalla, Bishoy, Satao, Shilpa, Shi, Ting, Sistla, Sujatha, Snape, Matthew, Song, Yanran, Soto, Giselle, Tavakoli, Forough, Toizumi, Michiko, Tsedenbal, Naranzul, van den Berge, Maarten, Vernhes, Charlotte, von Mollendorf, Claire, Walaza, Sibongile, Walker, Gregory, Li, You, Wang, Xin, Blau, Dianna M, Caballero, Mauricio T, Feikin, Daniel R, Gill, Christopher J, Madhi, Shabir A, Omer, Saad B, Simões, Eric A F, Campbell, Harry, Pariente, Ana Bermejo, Bardach, Darmaa, Bassat, Quique, Casalegno, Jean-Sebastien, Chakhunashvili, Giorgi, Crawford, Nigel, Danilenko, Daria, Do, Lien Anh Ha, Echavarria, Marcela, Gentile, Angela, Gordon, Aubree, Heikkinen, Terho, Huang, Q Sue, Jullien, Sophie, Krishnan, Anand, Lopez, Eduardo Luis, Markić, Joško, Mira-Iglesias, Ainara, Moore, Hannah C, Moyes, Jocelyn, Mwananyanda, Lawrence, Nokes, D James, Noordeen, Faseeha, Obodai, Evangeline, Palani, Nandhini, Romero, Candice, Salimi, Vahid, Satav, Ashish, Seo, Euri, Shchomak, Zakhar, Singleton, Rosalyn, Stolyarov, Kirill, Stoszek, Sonia K, von Gottberg, Anne, Wurzel, Danielle, Yoshida, Lay-Myint, Yung, Chee Fu, Zar, Heather J, and Nair, Harish

Published
2022
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20. A citywide, clonal outbreak of Pseudomonas aeruginosa

Author

Opperman, Christoffel J., Moodley, Clinton, Lennard, Katie, Smith, Mariette, Ncayiyana, Jabulani, Vulindlu, Mjikisile, Gafoor, Musarrat, Govender, Nevashan, Ismail, Husna, Bamford, Colleen, McCarthy, Kerrigan M., Nicol, Mark P., and Centner, Chad M.

Published
2022
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24. The Nasopharyngeal Microbiome in South African Children with Lower Respiratory Tract Infection: A Nested Case-Control Study of the Drakenstein Child Health Study

Author

Claassen-Weitz, Shantelle, primary, Xia, Yao, additional, Workman, Lesley, additional, Hannan, Luke, additional, Gardner-Lubbe, Sugnet, additional, Mwaikono, Kilaza Samson, additional, Harris Mounaud, Stephanie, additional, Nierman, William C., additional, Africa, Samantha, additional, Patel, Fadheela, additional, Dube, Felix, additional, Allen, Veronica, additional, Ah Tow Edries, Lemese, additional, Zar, Heather, additional, and Nicol, Mark P., additional

Published
2024
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25. Microbiological Diagnosis of Tuberculosis Disease in Children – A Prospective Study of Microbiological Yield in Low- and Middle- Income Countries

Author

Olbrich, Laura, primary, Franckling-Smith, Zoe, additional, Larsson, Leyla, additional, Sabi, Issa, additional, Ntinginya, Nyanda Elias, additional, Khosa, Celso, additional, Banze, Denise, additional, Nliwasa, Marriott, additional, Corbett, Elizabeth, additional, Semphere, Robina, additional, Verghese, Valsan Philip, additional, Michael, Joy Sarojini, additional, Ninan, Marilyn, additional, Saathoff, Elmar, additional, McHugh, Timothy D., additional, Razid, Alia, additional, Graham, Stephen M., additional, Song, Rinn, additional, Nabeta, Pamela, additional, Trollip, Andre, additional, Nicol, Mark P., additional, Hoelscher, Michael, additional, Geldmacher, Christof, additional, Heinrich, Norbert, additional, Zar, Heather, additional, and Consortium, RaPaed-AIDA-TB, additional

Published
2024
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32. Global burden of respiratory infections associated with seasonal influenza in children under 5 years in 2018: a systematic review and modelling study

Author

Nair, Harish, Campbell, Harry, Wang, Xin, Li, You, Chung, Alexandria, Rahi, Manveer, Abbas, Qalab, Ali, Asad, Bhutta, Zulfiqar A, Saeed, Bushra, Soofi, Sajid B, Yousafzai, Mohammad Tahir, Zaidi, Anita K, Amu, Alberta, Awini, Elizabeth, Azziz-Baumgartner, Eduardo, Baggett, Henry C, Chaves, Sandra S, Shang, Nong, Schrag, Stephanie J, Widdowson, Marc-Alain, Tempia, Stefano, Bassat, Quique, Lanaspa, Miguel, Acácio, Sozinho, Brooks, W Abdullah, Driscoll, Amanda, Knoll, Maria Deloria, O'Brien, Katherine L, Prosperi, Christine, Baqui, Abdullah H, Mullany, Luke, Byass, Peter, Cohen, Cheryl, von Gottberg, Anne, Hellferscee, Orienka, Treurnicht, Florette K, Walaza, Sibongile, Goswami, Doli, Rahman, Mustafizur, Connor, Nicholas E, El Arifeen, Shams, Echavarria, Marcela, Marcone, Débora N, Reyes, Noelia, Gutierrez, Andrea, Rodriguez, Ivan, Lopez, Olga, Ortiz, David, Gonzalez, Nathaly, Gentile, Angela, del Valle Juarez, Maria, Gordon, Aubree, Cutland, Clare, Groome, Michelle, Madhi, Shabir A, Nunes, Marta C, Nzenze, Susan, Heikkinen, Terho, Hirve, Siddhivinayak, Juvekar, Sanjay, Halasa, Natasha, Jara, Jorge H, Bernart, Chris, Katz, Mark A, Gofer, Ilan, Avni, Yonat Shemer, Khuri-Bulos, Najwa, Faori, Samir, Shehabi, Asem, Krishnan, Anand, Kumar, Rakesh, Amarchand, Ritvik, Contreras, Carmen L, de Leon, Oscar, Lopez, Maria R, McCracken, John P, Maldonado, Herberth, Samayoa, Antonio P, Gomez, Ana B, Lucero, Marilla G, Nillos, Leilani T, Lupisan, Socorro P, Nohynek, Hanna, Mira-Iglesias, Ainara, Puig-Barberà, Joan, Díez-Domingo, Javier, Gessner, Bradford D, Njanpop-Lafourcade, Berthe-Marie, Moïsi, Jennifer C, Tall, Haoua, Munywoki, Patrick K, Ngama, Mwanjuma, Nokes, D James, Omer, Saad B, Clark, Dayna R, Ourohiré, Millogo, Ali, Sié, Pascal, Zabré, Cheik, Bagagnan H, Caballero, Mauricio T, Libster, Romina, Polack, Fernando P, Rasmussen, Zeba A, Thomas, Elizabeth D, Baker, Julia M, Rath, Barbara A, Obermeier, Patrick E, Hassanuzzaman, MD., Islam, Maksuda, Islam, Mohammad S, Saha, Samir K, Panigrahi, Pinaki, Bose, Anuradha, Isaac, Rita, Murdoch, David, Nanda, Pritish, Qazi, Shamim A, Hessong, Danielle, Simőes, Eric AF, Sotomayor, Viviana, Thamthitiwat, Somsak, Chittaganpitch, Malinee, Dawood, Halima, Kyobutungi, Catherine, Wamukoya, Marylene, Ziraba, Abdhalah K, Yoshida, Lay-Myint, Yoshihara, Keisuke, Dand, Duc-Anh, Le, Minh-Nhat, Nicol, Mark P, Zar, Heather J, Broor, Shobha, Chadha, Mandeep, Madrid, Lola, Gresh, Lionel, Balmaseda, Angel, Kuan, Guillermina, Wairagkar, Niteen, Tapia, Milagritos D, Knobler, Stacey L, Barahona, Alfredo, Ferguson, Ericka, Schweiger, Brunhilde, Abdullah Brooks, W, Fasce, Rodrigo A, and Simões, Eric AF

Published
2020
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33. Diagnostic accuracy of 3 urine lipoarabinomannan tuberculosis assays in HIV-negative outpatients

Author

Broger, Tobias, Nicol, Mark P., Sigal, George B., Gotuzzo, Eduardo, Zimmer, Alexandra J., Surtie, Shireen, Caceres- Nakiche, Tatiana, Mantsoki, Anna, Reipold, Elena Ivanova, Szekely, Rita, Tsionsky, Michael, van Heerden, Judith, Plisova, Tatiana, Chikamatsu, Kinuyo, Lowary, Todd L., Pinter, Abraham, Mitarai, Satoshi, Moreau, Emmanuel, Schumacher, Samuel G., and Denkinger, Claudia M.

Subjects
Tuberculosis -- Diagnosis, Biochemical assays -- Usage, Lipoarabinomannan -- Health aspects, Urinalysis -- Methods, Health care industry
Abstract

BACKGROUND. Inadequate tuberculosis (TB) diagnostics are a major hurdle in the reduction of disease burden, and accurate point-of-care tests (POCTs) are urgently needed. We assessed the diagnostic accuracy of Fujifilm SILVAMP TB lipoarabinomannan (FujiLAM) POCT for TB diagnosis in HIV-negative outpatients and compared it with Alere Determine TB LAM Ag (AlereLAM) POCT and a laboratory-based ultrasensitive electrochemiluminescence LAM research assay (EclLAM). METHODS. In this multicenter diagnostic test accuracy study, we recruited HIV-negative adults with symptoms suggestive of pulmonary TB presenting to outpatient health care centers in Peru and South Africa. Urine samples were tested using FujiLAM, AlereLAM, and EclLAM, and the diagnostic accuracy was assessed against a microbiological reference standard (MRS) and a composite reference standard. RESULTS. Three hundred seventy-two HIV-negative participants were included and the prevalence of microbiologically confirmed TB was 30%. Compared with the MRS, the sensitivities of AlereLAM, FujiLAM, and EclLAM were 10.8% (95% confidence interval [CI] 6.3%-18.0%), 53.2% (95% CI 43.9%-62.1%), and 66.7% (95% CI 57.5%-74.7%), respectively. The specificities of AlereLAM, FujiLAM, and EclLAM were 92.3% (95% CI 88.5%-95.0%), 98.9% (95% CI 96.7%-99.6%), and 98.1% (95% CI 95.6%-99.2%), respectively. Positive likelihood ratios of AlereLAM, FujiLAM, and EclLAM were 1.4, 46.2, and 34.8, respectively, and positive predictive values were 37.5%, 95.2%, and 93.7%, respectively. CONCLUSION. Compared with AlereLAM, FujiLAM detected 5 times more patients with TB in HIV-negative participants, had a high positive predictive value, and has the potential to improve rapid diagnosis of TB at the point-of-care. EclLAM demonstrated that additional sensitivity gains are possible, which highlights LAM's potential as a biomarker. Additional research is required to assess FujiLAM's performance in prospective cohorts, its cost-effectiveness, and its impact in real-world clinical settings. FUNDING. Global Health Innovative Technology Fund, the UK Department for International Development, the Dutch Ministry of Foreign Affairs, the Bill and Melinda Gates Foundation, the Australian Department of Foreign Affairs and Trade, the German Federal Ministry of Education and Research through Kreditanstalt fur Wiederaufbau, and the NIH and National Institute of Allergy and Infectious Diseases., Introduction Tuberculosis (TB) is the leading single infectious cause of death worldwide, with more than 1.5 million deaths in 2018 (1). The high rate of unreported TB (estimated at 3.0 [...]

Published
2020
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34. Respiratory Syncytial Virus Reinfections in Children in Western Australia

Author

Foley, David A., primary, Minney-Smith, Cara A., additional, Lee, Wei Hao, additional, Oakes, Daniel B., additional, Hazelton, Briony, additional, Ford, Timothy J., additional, Wadia, Ushma, additional, Sikazwe, Chisha, additional, Moore, Hannah C., additional, Nicol, Mark P., additional, Levy, Avram, additional, and Blyth, Christopher C., additional

Published
2023
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36. Genomic epidemiology of Streptococcus pneumoniae serotype 16F lineages

Author

Mokaya, Jolynne, primary, Mellor, Kate C., additional, Murray, Gemma G. R., additional, Kalizang’oma, Akuzike, additional, Lekhuleni, Cebile, additional, Zar, Heather J., additional, Nicol, Mark P., additional, McGee, Lesley, additional, Bentley, Stephen D., additional, Lo, Stephanie W., additional, and Dube, Felix, additional

Published
2023
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37. A Blueprint to Address Research Gaps in the Development of Biomarkers for Pediatric Tuberculosis

Author

Nicol, Mark Patrick, Gnanashanmugam, Devasena, Browning, Renee, Click, Eleanor S, Cuevas, Luis E, Detjen, Anne, Graham, Steve M, Levin, Michael, Makhene, Mamodikoe, Nahid, Payam, Perez-Velez, Carlos M, Reither, Klaus, Song, Rinn, Spiegel, Hans ML, Worrell, Carol, Zar, Heather J, and Walzl, Gerhard

Subjects
Prevention, Infectious Diseases, Tuberculosis, Pediatric, Rare Diseases, Pediatric Research Initiative, Infection, Good Health and Well Being, Biological Specimen Banks, Biomarkers, Biomedical Research, Child, Delivery of Health Care, Humans, National Institutes of Health (U.S.), Pediatrics, Specimen Handling, United States, tuberculosis, children, diagnosis, biomarker, blueprint, Biological Sciences, Medical and Health Sciences, Microbiology
Abstract

Childhood tuberculosis contributes significantly to the global tuberculosis disease burden but remains challenging to diagnose due to inadequate methods of pathogen detection in paucibacillary pediatric samples and lack of a child-specific host biomarker to identify disease. Accurately diagnosing tuberculosis in children is required to improve case detection, surveillance, healthcare delivery, and effective advocacy. In May 2014, the National Institutes of Health convened a workshop including researchers in the field to delineate priorities to address this research gap. This blueprint describes the consensus from the workshop, identifies critical research steps to advance this field, and aims to catalyze efforts toward harmonization and collaboration in this area.

Published
2015

42. Global patterns in monthly activity of influenza virus, respiratory syncytial virus, parainfluenza virus, and metapneumovirus: a systematic analysis

Author

Acacio, Sozinho, Alonso, Wladimir J, Antonio, Martin, Ayora Talavera, Guadalupe, Badarch, Darmaa, Baillie, Vicky L, Barrera-Badillo, Gisela, Bigogo, Godfrey, Broor, Shobha, Bruden, Dana, Buchy, Philippe, Byass, Peter, Chipeta, James, Clara, Wilfrido, Dang, Duc-Anh, de Freitas Lázaro Emediato, Carla Cecília, de Jong, Menno, Díaz-Quiñonez, José Alberto, Do, Lien Anh Ha, Fasce, Rodrigo A, Feng, Luzhao, Ferson, Mark J, Gentile, Angela, Gessner, Bradford D, Goswami, Doli, Goyet, Sophie, Grijalva, Carlos G, Halasa, Natasha, Hellferscee, Orienka, Hessong, Danielle, Homaira, Nusrat, Jara, Jorge, Kahn, Kathleen, Khuri-Bulos, Najwa, Kotloff, Karen L, Lanata, Claudio F, Lopez, Olga, Lopez Bolaños, Maria Renee, Lucero, Marilla G, Lucion, Florencia, Lupisan, Socorro P, Madhi, Shabir A, Mekgoe, Omphile, Moraleda, Cinta, Moyes, Jocelyn, Mulholland, Kim, Munywoki, Patrick K, Naby, Fathima, Nguyen, Thanh Hung, Nicol, Mark P, Nokes, D James, Noyola, Daniel E, Onozuka, Daisuke, Palani, Nandhini, Poovorawan, Yong, Rahman, Mustafizur, Ramaekers, Kaat, Romero, Candice, Schlaudecker, Elizabeth P, Schweiger, Brunhilde, Seidenberg, Phil, Simoes, Eric A F, Singleton, Rosalyn, Sistla, Sujatha, Sturm-Ramirez, Katharine, Suntronwong, Nungruthai, Sutanto, Agustinus, Tapia, Milagritos D, Thamthitiwat, Somsak, Thongpan, Ilada, Tillekeratne, Gayani, Tinoco, Yeny O, Treurnicht, Florette K, Turner, Claudia, Turner, Paul, van Doorn, Rogier, Van Ranst, Marc, Visseaux, Benoit, Waicharoen, Sunthareeya, Wang, Jianwei, Yoshida, Lay-Myint, Zar, Heather J, Li, You, Reeves, Rachel M, Wang, Xin, Bassat, Quique, Brooks, W Abdullah, Cohen, Cheryl, Moore, David P, Nunes, Marta, Rath, Barbara, Campbell, Harry, and Nair, Harish

Published
2019
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45. Mixed Mycobacterium tuberculosis Complex Infections and False-Negative Results for Rifampin Resistance by GeneXpert MTB/RIF Are Associated with Poor Clinical Outcomes

Author

Zetola, Nicola M, Shin, Sanghyuk S, Tumedi, Kefentse A, Moeti, Keletso, Ncube, Ronald, Nicol, Mark, Collman, Ronald G, Klausner, Jeffrey D, and Modongo, Chawangwa

Subjects
Clinical Research, Rare Diseases, Tuberculosis, Infectious Diseases, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Infection, Good Health and Well Being, Adult, Aged, Aged, 80 and over, Antitubercular Agents, Bacteriological Techniques, Cohort Studies, Coinfection, Drug Resistance, Bacterial, False Negative Reactions, Humans, Male, Microbial Sensitivity Tests, Middle Aged, Molecular Diagnostic Techniques, Mycobacterium tuberculosis, Retrospective Studies, Rifampin, Sensitivity and Specificity, Treatment Outcome, Tuberculosis, Multidrug-Resistant, Young Adult, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Microbiology
Abstract

The Xpert MTB/RIF (Xpert) assay is becoming a principal screening tool for diagnosing rifampin-resistant Mycobacterium tuberculosis complex (MTBC) infection. However, little is known about the performance of the Xpert assay in infections with both drug-sensitive and drug-resistant strains (mixed MTBC infections). We assessed the performance of the Xpert assay for detecting rifampin resistance using phenotypic drug sensitivity testing (DST) as the reference standard in 370 patients with microbiologically proven pulmonary tuberculosis. Mixed MTBC infections were identified genetically through 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) analysis. Logistic regression was used to identify the factors associated with poor (defined as treatment failure, default, and death from any cause) or good (defined as cure or successful treatment completion) clinical outcomes. The analytic sensitivity of the Xpert assay for detecting rifampin resistance was assessed in vitro by testing cultures containing different ratios of drug-sensitive and drug-resistant organisms. Rifampin resistance was detected by the Xpert assay in 52 (14.1%) and by phenotypic DST in 55 (14.9%) patients. Mixed MTBC infections were identified in 37 (10.0%) patients. The Xpert assay was 92.7% (95% confidence interval [CI], 82.4% to 97.9%) sensitive for detecting rifampin resistance and 99.7% (95% CI, 98.3% to 99.9%) specific. When restricted to patients with mixed MTBC infections, Xpert sensitivity was 80.0% (95% CI, 56.3 to 94.3%). False-negative Xpert results (adjusted odds ratio [aOR], 6.6; 95% CI,1.2 to 48.2) and mixed MTBC infections (aOR, 6.5; 95% CI, 2.1 to 20.5) were strongly associated with poor clinical outcome. The Xpert assay failed to detect rifampin resistance in vitro when

Published
2014

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