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Bunyasi EW, Middelkoop K, Koch A, Hoosen Z, Mulenga H, Luabeya AKK, Shenje J, Mendelsohn SC, Tameris M, Scriba TJ, Warner DF, Wood R, Andrews JR, Hatherill M. Molecular Detection of Airborne Mycobacterium tuberculosis in South African High Schools. Am J Respir Crit Care Med 2022; 205:350-356. [PMID: 34752730 PMCID: PMC8886998 DOI: 10.1164/rccm.202102-0405oc] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Rationale: South African adolescents carry a high tuberculosis disease burden. It is not known if schools are high-risk settings for Mycobacterium tuberculosis (MTB) transmission. Objectives: To detect airborne MTB genomic DNA in classrooms. Methods: We studied 72 classrooms occupied by 2,262 students in two South African schools. High-volume air filtration was performed for median 40 (interquartile range [IQR], 35-54) minutes and assayed by droplet digital PCR (ddPCR)-targeting MTB region of difference 9 (RD9), with concurrent CO2 concentration measurement. Classroom data were benchmarked against public health clinics. Students who consented to individual tuberculosis screening completed a questionnaire and sputum collection (Xpert MTB/RIF Ultra) if symptom positive. Poisson statistics were used for MTB RD9 copy quantification. Measurements and Main Results: ddPCR assays were positive in 13/72 (18.1%) classrooms and 4/39 (10.3%) clinic measurements (P = 0.276). Median ambient CO2 concentration was 886 (IQR, 747-1223) ppm in classrooms versus 490 (IQR, 405-587) ppm in clinics (P < 0.001). Average airborne concentration of MTB RD9 was 3.61 copies per 180,000 liters in classrooms versus 1.74 copies per 180,000 liters in clinics (P = 0.280). Across all classrooms, the average risk of an occupant inhaling one MTB RD9 copy was estimated as 0.71% during one standard lesson of 35 minutes. Among 1,836/2,262 (81.2%) students who consented to screening, 21/90 (23.3%) symptomatic students produced a sputum sample, of which one was Xpert MTB/RIF Ultra positive. Conclusions: Airborne MTB genomic DNA was detected frequently in high school classrooms. Instantaneous risk of classroom exposure was similar to the risk in public health clinics.
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Affiliation(s)
- Erick W. Bunyasi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine,,Department of Pathology
| | | | - Anastasia Koch
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine, and
| | | | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine,,Department of Pathology
| | - Angelique K. K. Luabeya
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine,,Department of Pathology
| | - Justin Shenje
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine,,Department of Pathology
| | - Simon C. Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine,,Department of Pathology
| | - Michele Tameris
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine,,Department of Pathology
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine,,Department of Pathology
| | - Digby F. Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine, and,Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), University of Cape Town, Cape Town, South Africa; and
| | | | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine,,Department of Pathology
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Deviaene M, Weigel KM, Wood RC, Luabeya AKK, Jones-Engel L, Hatherill M, Cangelosi GA. Sample adequacy controls for infectious disease diagnosis by oral swabbing. PLoS One 2020; 15:e0241542. [PMID: 33125422 PMCID: PMC7598519 DOI: 10.1371/journal.pone.0241542] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/16/2020] [Indexed: 12/22/2022] Open
Abstract
Oral swabs are emerging as a non-invasive sample type for diagnosing infectious diseases including Ebola, tuberculosis (TB), and COVID-19. To assure proper sample collection, sample adequacy controls (SACs) are needed that detect substances indicative of samples collected within the oral cavity. This study evaluated two candidate SACs for this purpose. One detected representative oral microbiota (Streptococcus species DNA) and the other, human cells (human mitochondrial DNA, mtDNA). Quantitative PCR (qPCR) assays for the two target cell types were applied to buccal swabs (representing samples collected within the oral cavity) and hand swabs (representing improperly collected samples) obtained from 51 healthy U.S. volunteers. Quantification cycle (Cq) cutoffs that maximized Youden’s index were established for each assay. The streptococcal target at a Cq cutoff of ≤34.9 had 99.0% sensitivity and specificity for oral swab samples, whereas human mtDNA perfectly distinguished between hand and mouth swabs with a Cq cutoff of 31.3. The human mtDNA test was then applied to buccal, tongue, and gum swabs that had previously been collected from TB patients and controls in South Africa, along with “air swabs” collected as negative controls (total N = 292 swabs from 71 subjects). Of these swabs, 287/292 (98%) exhibited the expected Cq values. In a paired analysis the three oral sites yielded indistinguishable amounts of human mtDNA, however PurFlockTM swabs collected slightly more human mtDNA than did OmniSwabsTM (p = 0.012). The results indicate that quantification of human mtDNA cannot distinguish swabs collected from different sites within the mouth. However, it can reliably distinguish oral swabs from swabs that were not used orally, which makes it a useful SAC for oral swab-based diagnosis.
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Affiliation(s)
- Meagan Deviaene
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kris M. Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Rachel C. Wood
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Angelique K. K. Luabeya
- Department of Pathology, South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Lisa Jones-Engel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Mark Hatherill
- Department of Pathology, South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Bunyasi EW, Mulenga H, Luabeya AKK, Shenje J, Mendelsohn SC, Nemes E, Tameris M, Wood R, Scriba TJ, Hatherill M. Regional changes in tuberculosis disease burden among adolescents in South Africa (2005-2015). PLoS One 2020; 15:e0235206. [PMID: 32609738 PMCID: PMC7329123 DOI: 10.1371/journal.pone.0235206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 06/11/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Adolescents in the Western Cape Province of South Africa had high force of Mycobacterium tuberculosis (MTB) infection (14% per annum) and high TB incidence (710 per 100,000 person-years) in 2005. We describe subsequent temporal changes in adolescent TB disease notification rates for the decade 2005-2015. METHOD We conducted an analysis of patient-level adolescent (age 10-19 years) TB disease data, obtained from an electronic TB register in the Breede Valley sub-district, Western Cape Province, South Africa, for 2005-2015. Numerators were annual TB notifications (HIV-related and HIV-unrelated); denominators were mid-year population estimates. Period averages of TB rates were obtained using time series modeling. Temporal trends in TB rates were explored using the Mann-Kendall test. FINDINGS The average adolescent TB disease notification rate was 477 per 100,000 for all TB patients (all-TB) and 361 per 100,000 for microbiologically-confirmed patients. The adolescent all-TB rate declined by 45% from 662 to 361 per 100,000 and the microbiologically-confirmed TB rate by 38% from 492 to 305 per 100,000 between 2005-2015, driven mainly by rapid decreases for the period 2005-2009. There was a statistically significant negative temporal trend in both all-TB (per 100,000) (declined by 48%; from 662 to 343; p = 0·028) and microbiologically confirmed TB (per 100,000) (declined by 49%; from 492 to 252; p = 0·027) for 2005-2009, which was not observed for the period 2009-2015 (rose 5%; from 343 to 361; p = 0·764 and rose 21%; from 252 to 305; p = 1·000, respectively). INTERPRETATION We observed an encouraging fall in adolescent TB disease rates between 2005-2009 with a subsequent plateau during 2010-2015, suggesting that additional interventions are needed to sustain initial advances in TB control.
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Affiliation(s)
- Erick Wekesa Bunyasi
- South African Tuberculosis Vaccine Initiative, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Angelique K. K. Luabeya
- South African Tuberculosis Vaccine Initiative, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Justin Shenje
- South African Tuberculosis Vaccine Initiative, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Simon C. Mendelsohn
- South African Tuberculosis Vaccine Initiative, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Michele Tameris
- South African Tuberculosis Vaccine Initiative, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Robin Wood
- Desmond Tutu HIV Center, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Bunyasi EW, Geldenhuys H, Mulenga H, Shenje J, Luabeya AKK, Tameris M, Nemes E, Mahomed H, Rozot V, Wood R, Scriba T, Andrews JR, Hatherill M. Temporal trends in the prevalence of Mycobacterium tuberculosis infection in South African adolescents. Int J Tuberc Lung Dis 2020; 23:571-578. [PMID: 31097065 DOI: 10.5588/ijtld.18.0283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
<sec id="st1"> <title>SETTING</title> South Africa. </sec> <sec id="st2"> <title>OBJECTIVE</title> 1) To measure changes in the adolescent prevalence of latent tuberculous infection (LTBI) between 2005 and 2015, and 2) to evaluate medium-term impact of TB control measures on LTBI prevalence. </sec> <sec id="st3"> <title>DESIGN</title> We compared baseline data from a cohort study (2005-2007) and a vaccine trial (2014-2015) which enrolled adolescents from the same eight South African high schools. LTBI was defined based on QuantiFERON®-TB Gold In-Tube test positivity. </sec> <sec id="st4"> <title>RESULTS</title> We analysed data from 4880 adolescents between 2005 and 2007, and 1968 adolescents between 2014 and 2015, when the average LTBI prevalence was respectively 43.8% (95%CI 28.4-59.1) vs. 48.5% (95%CI 41.1-55.8). Age-specific LTBI prevalence increased between the ages 12 and 18 years by 13% only in lower socio-economic quintile schools, where the average LTBI prevalence was unchanged between the two periods (54% vs. 53%). In the highest socio-economic quintile schools, LTBI prevalence did not increase with age; however, the average LTBI prevalence increased from 20% to 38% between the two periods. </sec> <sec id="st5"> <title>CONCLUSION</title> Adolescent LTBI prevalence remained high and constant over a decade, suggesting that Mycobacterium tuberculosis transmission to children was not impacted in the medium term by effective TB control efforts. Trends in adolescent LTBI prevalence should be interpreted in the context of the sociodemographic factors that affect the risk of transmission before and during adolescence. </sec>.
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Affiliation(s)
- E W Bunyasi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town
| | - H Geldenhuys
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town
| | - H Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town
| | - J Shenje
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town
| | - A K K Luabeya
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town
| | - M Tameris
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town
| | - E Nemes
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town
| | - H Mahomed
- Department of Health, Western Cape and Division of Community Health, Stellenbosch University, Stellenbosch, South Africa
| | - V Rozot
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town
| | - R Wood
- The Desmond Tutu HIV Centre, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - T Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town
| | - J R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - M Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town
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Bunyasi EW, Luabeya AKK, Tameris M, Geldenhuys H, Mulenga H, Landry BS, Scriba TJ, Schmidt BM, Hanekom WA, Mahomed H, McShane H, Hatherill M. Impact of isoniazid preventive therapy on the evaluation of long-term effectiveness of infant MVA85A vaccination. Int J Tuberc Lung Dis 2018. [PMID: 28633702 PMCID: PMC5502581 DOI: 10.5588/ijtld.16.0709] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
SETTING: South Africa. OBJECTIVE: To evaluate the long-term effectiveness of infant modified vaccinia Ankara virus-expressing antigen 85A (MVA85A) vaccination against tuberculosis (TB). DESIGN: We analysed data from a double-blind randomised placebo-controlled Phase 2b MVA85A infant TB vaccine trial (2009–2012), with extended post-trial follow-up (2012–2014). Isoniazid preventive therapy (IPT) was provided by public health services according to national guidelines. The primary outcome was curative treatment for TB disease. Survival analysis and Poisson regression were used for study analysis. RESULTS: Total follow-up was 10 351 person-years of observation (pyo). Median follow-up age was 4.8 years (interquartile range 4.4–5.2). There were 328 (12%) TB cases. TB disease incidence was 3.2/100 pyo (95%CI 2.8–3.5) overall, and respectively 3.3 (95%CI 2.9–3.9) and 3.0 (95%CI 2.6–3.5)/100 pyo in the MVA85A vaccine and placebo arms. A total of 304 children (11%) received IPT, with respectively 880 and 9471 pyo among IPT and non-IPT recipients. There were 23 (7.6%) TB cases among 304 IPT recipients vs. 305 (12.9%) among 2374 non-IPT recipients (P = 0.008). IPT effectiveness was 85% (95%CI 76–91). CONCLUSION: Extended follow-up confirms no long-term effectiveness of infant MVA85A vaccination, but a six-fold reduction in TB risk can be attributed to IPT. National TB programmes in high TB burden countries should ensure optimal implementation of IPT for eligible children.
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Affiliation(s)
- E W Bunyasi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - A K K Luabeya
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - M Tameris
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - H Geldenhuys
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - H Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | | | - T J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - B-M Schmidt
- Department of Social and Behavioral Sciences, School of Public Health and Family Medicine, University of Cape Town, Cape Town
| | - W A Hanekom
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - H Mahomed
- Department of Health, Western Cape and Division of Community Health, Stellenbosch University, Stellenbosch, South Africa
| | - H McShane
- Jenner Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - M Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
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