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Olson AM, Wood RC, Weigel KM, Yan AJ, Lochner KA, Dragovich RB, Luabeya AK, Yager P, Hatherill M, Cangelosi GA. High-sensitivity detection of Mycobacterium tuberculosis DNA in tongue swab samples. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.26.24311064. [PMID: 39108520 PMCID: PMC11302704 DOI: 10.1101/2024.07.26.24311064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Tongue swab (TS) sampling combined with qPCR to detect Mycobacterium tuberculosis (MTB) DNA is a promising alternative to sputum testing for tuberculosis (TB) diagnosis. In prior studies, the sensitivity of tongue swabbing has usually been lower than sputum. In this study, we evaluated two strategies to improve sensitivity. In one, centrifugation was used to concentrate tongue dorsum bacteria from 2-mL suspensions eluted from high-capacity foam swab samples. The pellets were resuspended as 500-μL suspensions, and then mechanically lysed prior to dual-target qPCR to detect MTB insertion elements IS6110 and IS1081. Fractionation experiments demonstrated that most of the MTB DNA signal in clinical swab samples (99.22% ± 1.46%) was present in the sedimentable fraction. When applied to archived foam swabs collected from 124 South Africans with presumptive TB, this strategy exhibited 83% sensitivity (71/86) and 100% specificity (38/38) relative to sputum MRS (microbiological reference standard; sputum culture and/or Xpert® Ultra). The second strategy used sequence-specific magnetic capture (SSMaC) to concentrate DNA released from MTB cells. This protocol was evaluated on archived Copan FLOQSwabs® flocked swab samples collected from 128 South African participants with presumptive TB. Material eluted into 500 μL buffer was mechanically lysed. The suspensions were digested by proteinase K, hybridized to biotinylated dual-target oligonucleotide probes, and then concentrated ~20-fold using magnetic separation. Upon dual-target qPCR testing of concentrates, this strategy exhibited 90% sensitivity (83/92) and 97% specificity (35/36) relative to sputum MRS. These results point the way toward automatable, high-sensitivity methods for detecting MTB DNA in TS. Importance Improved testing for tuberculosis (TB) is needed. Using a more accessible sample type than sputum may enable the detection of more cases, but it is critical that alternative samples be tested appropriately. Here, we describe two new, highly accurate methods for testing tongue swabs for TB DNA.
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Affiliation(s)
- Alaina M. Olson
- 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
| | - Kris M. Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Alexander J. Yan
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Katherine A. Lochner
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Rane B. Dragovich
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Angelique K. Luabeya
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Paul Yager
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
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Mesman AW, Calderon RI, Hauns L, Pollock NR, Mendoza M, Holmberg RC, Franke MF. Detection of Mycobacterium tuberculosis transrenal DNA in urine samples among adults in Peru. Tuberculosis (Edinb) 2024; 148:102549. [PMID: 39098064 DOI: 10.1016/j.tube.2024.102549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024]
Abstract
Diagnosis of pulmonary tuberculosis (TB) relies on a sputum sample, which cannot be obtained from all symptomatic individuals. Mycobacterium tuberculosis (Mtb) transrenal DNA (trDNA) has been detected in urine, an easily obtainable, noninvasive, alternative sample type. However, reported sensitivities have been variable and likely depend on collection and assay procedures and aspects of trDNA biology. We analyzed three serial urine samples from each of 75 adults with culture-confirmed pulmonary TB disease in Lima, Peru for detection of trDNA using short-fragment real-time PCR. Additionally, we examined host, urine, and sampling factors associated with detection. Overall per-sample sensitivity was 38 % (95 % Confidence Interval [CI] 30-45 %). On an individual level (i.e., any of the three samples positive), sensitivity was 73 % (95 % CI: 62-83 %). Sensitivity was highest among samples from patients with smear-positive TB, 92 % (95 % CI: 62-100 %). Specificity from a single sample from each of 10 healthy controls was 100 % (95 % CI: 69-100 %). Adjusting our assay positivity threshold increased individual-level sensitivity to 88 % (95 % CI: 78-94 %) overall without affecting the specificity. We did not find associations between Mtb trDNA detection and individual characteristics or urine sample characteristics. Overall, our results support the potential of trDNA detection for TB diagnosis.
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Affiliation(s)
- Annelies W Mesman
- Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Ave, Boston, MA, 02115, USA.
| | - Roger I Calderon
- Socios En Salud Sucursal Perú, Av. Javier Prado Este 492, San Isidro, Lima, 15001, Peru.
| | - Laura Hauns
- Akonni Biosystems, 400 Sagner Ave, Frederick, MD, 21701, USA.
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.
| | - Milagros Mendoza
- Socios En Salud Sucursal Perú, Av. Javier Prado Este 492, San Isidro, Lima, 15001, Peru.
| | | | - Molly F Franke
- Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Ave, Boston, MA, 02115, USA.
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3
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Wood RC, Luabeya AK, Dragovich RB, Olson AM, Lochner KA, Weigel KM, Codsi R, Mulenga H, de Vos M, Kohli M, Penn-Nicholson A, Hatherill M, Cangelosi GA. Diagnostic accuracy of tongue swab testing on two automated tuberculosis diagnostic platforms, Cepheid Xpert MTB/RIF Ultra and Molbio Truenat MTB Ultima. J Clin Microbiol 2024; 62:e0001924. [PMID: 38483169 PMCID: PMC11005402 DOI: 10.1128/jcm.00019-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/25/2024] [Indexed: 03/21/2024] Open
Abstract
Tongue dorsum swabbing is a potential alternative to sputum collection for tuberculosis (TB) testing. Previous studies showed that Cepheid Xpert MTB/RIF Ultra (Xpert Ultra) can detect Mycobacterium tuberculosis DNA on tongue swabs stored in buffer, with 72% sensitivity and 100% specificity relative to a sputum microbiological reference standard (sputum MRS). The present study evaluated a more convenient sample collection protocol (dry swab storage), combined with streamlined sample processing protocols, for evaluating two commercial TB diagnostic tests: Xpert Ultra and Molbio Truenat MTB Ultima (MTB Ultima). Copan FLOQSwabs were self-collected or collected by study workers from 321 participants in Western Cape, South Africa. All participants had symptoms suggestive of TB, and 245 of them had sputum MRS-confirmed TB (by sputum MGIT culture and/or Xpert Ultra). One tongue swab per participant was tested on Xpert Ultra, and another tongue swab was tested with MTB Ultima. Xpert Ultra was 75.5% sensitive and 100% specific relative to sputum MRS, similar to previous methods that used swabs stored in buffer. MTB Ultima was 71.6% sensitive and 96.9% specific relative to sputum MRS. When sample lysates that were false-negative or invalid by MTB Ultima were frozen, thawed, and re-tested, MTB Ultima sensitivity rose to 79.1%. Both tests were more sensitive with swabs from participants with higher sputum Xpert Ultra semi-quantitative results. Although additional development could improve diagnostic accuracy, these results further support tongue swabs as easy-to-collect samples for TB testing. IMPORTANCE Tongue dorsum swabbing is a promising alternative to sputum collection for tuberculosis (TB) testing. Our results lend further support for tongue swabs as exceptionally easy-to-collect samples for high-throughput TB testing.
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Affiliation(s)
- Rachel C. Wood
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Angelique K. Luabeya
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Rane B. Dragovich
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Alaina M. Olson
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Katherine A. Lochner
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Kris M. Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Renée Codsi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Department of Pathology, University of Cape Town, Cape Town, South Africa
| | | | | | | | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
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4
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Zhang F, Wang Y, Zhang X, Liu K, Shang Y, Wang W, Liu Y, Li L, Pang Y. Diagnostic accuracy of oral swab for detection of pulmonary tuberculosis: a systematic review and meta-analysis. Front Med (Lausanne) 2024; 10:1278716. [PMID: 38528958 PMCID: PMC10961363 DOI: 10.3389/fmed.2023.1278716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/26/2023] [Indexed: 03/27/2024] Open
Abstract
Objectives Tuberculosis (TB) remains a significant concern in terms of public health, necessitating the timely and accurate diagnosis to impede its advancement. The utilization of oral swab analysis (OSA) presents a promising approach for diagnosing pulmonary TB by identifying Mycobacterium tuberculosis (MTB) within oral epithelial cells. Due to disparities in the diagnostic performance of OSA reported in the original studies, we conducted a meticulous meta-analysis to comprehensively assess the diagnostic efficacy of OSA in pulmonary TB. Methods We conducted a comprehensive investigation across multiple databases, namely PubMed, Cochrane Library, Embase, Web of Science, ClinicalTrials.gov, Chinese BioMedical Literature Database (CBM), China National Knowledge Infrastructure Database (CNKI), and Wanfang China Science and Technology Journal Database to identify relevant studies. Out search query utilized the following keywords: oral swab, buccal swab, tongue swab, tuberculosis, and TB. Subsequently, we employed STATA 16.0 to compute the combined sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio for both the overall and subgroup analyses. Results Our findings indicated that OSA has a combined sensitivity of 0.67 and specificity of 0.95 in individuals with pulmonary TB. Subgroup analysis further revealed that among adult individuals with pulmonary TB, the sensitivity and specificity of OSA were 0.73 and 0.93, respectively. In HIV-negative individuals with pulmonary TB, the sensitivity and specificity were 0.68 and 0.98, respectively. The performance of OSA in detecting pulmonary TB correlated with the bacteria load in sputum. Additionally, the sensitivity for diagnosing pulmonary TB using tongue specimens was higher (0.75, 95% CI: 0.65-0.83) compared to cheek specimens (0.52, 95% CI: 0.34-0.70), while both types of specimens demonstrated high specificity. Conclusions To conclude, oral swabs serve as a promising alternative for diagnosing pulmonary TB, especially in adult patients. In addition, tongue swabs yield better sensitivity than cheek swabs to identify pulmonary TB patients. Systematic review registration identifier: CRD42023421357.
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Affiliation(s)
- Fuzhen Zhang
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yilin Wang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xuxia Zhang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Kewei Liu
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Wei Wang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuanyuan Liu
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Liang Li
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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Srilohasin P, Warit S, Prammananan T, Smithtikarn S, Kanitpun R, Kaewparuehaschai M, Noradechanon K, Meesawat S, Thakaew N, Sakulwittayasuk N, Kemthong T, Palaga T, Malaivijitnond S, Chaiprasert A. Advancing tuberculosis diagnosis and management in cynomolgus macaques using Xpert MTB/RIF ultra assay. Sci Rep 2024; 14:1518. [PMID: 38233591 PMCID: PMC10794203 DOI: 10.1038/s41598-024-51824-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024] Open
Abstract
The detection and management of Mycobacterium tuberculosis complex (MTBC) infection, the causative agent of tuberculosis (TB), in macaques, including cynomolgus macaques (Macaca fascicularis), are of significant concern in research and regions where macaques coexist with humans or other animals. This study explored the utility of the Xpert MTB/RIF Ultra assay, a widely adopted molecular diagnostic tool to diagnose tuberculosis (TB) in humans, to detect DNA from the Mycobacterium tuberculosis complex in clinical samples obtained from cynomolgus macaques. This investigation involved a comprehensive comparative analysis, integrating established conventional diagnostic methodologies, assessing oropharyngeal-tracheal wash (PW) and buccal swab (BS) specimen types, and follow-up assessments at 3-month, 6-month, and 12-month intervals. Our results demonstrated that the Xpert MTB/RIF Ultra assay was able to detect MTBC in 12 of 316 clinical samples obtained from cynomolgus macaques, presenting a potential advantage over bacterial culture and chest radiographs. The Xpert MTB/RIF Ultra assay exhibited exceptional sensitivity (100%) at the animal level, successfully detecting all macaques positive for M. tuberculosis as confirmed by traditional culture methods. The use of PW samples revealed that 5 positive samples from 99 (5.1%) were recommended for testing, compared to 0 samples from 99 buccal swab (BS) samples (0.0%). In particular, the definitive diagnosis of TB was confirmed in three deceased macaques by MTB culture, which detected the presence of the bacterium in tissue autopsy. Our findings demonstrate that the implementation of the Xpert MTB/RIF Ultra assay, along with prompt isolation measures, effectively reduced active TB cases among cynomolgus macaques over a 12-month period. These findings highlight the advance of the Xpert MTB/RIF Ultra assay in TB diagnosis and its crucial role in preventing potential outbreaks in cynomolgus macaques. With its rapidity, high sensitivity, and specificity, the Xpert MTB/RIF Ultra assay can be highly suitable for use in reference laboratories to confirm TB disease and effectively interrupt TB transmission.
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Affiliation(s)
- Prapaporn Srilohasin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
| | - Saradee Warit
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Thailand
| | - Therdsak Prammananan
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Thailand
| | - Saijai Smithtikarn
- Division of Tuberculosis, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand
| | - Reka Kanitpun
- National Institute of Animal Health, Bangkok, Thailand
| | | | - Kirana Noradechanon
- Department of National Parks, Wildlife and Plant Conservation, Chachoengsao, Thailand
| | - Suthirote Meesawat
- National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand
| | - Nattakan Thakaew
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
| | | | - Taratorn Kemthong
- National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand
| | - Tanapat Palaga
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Angkana Chaiprasert
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand.
- Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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6
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Church EC, Steingart KR, Cangelosi GA, Ruhwald M, Kohli M, Shapiro AE. Oral swabs with a rapid molecular diagnostic test for pulmonary tuberculosis in adults and children: a systematic review. Lancet Glob Health 2024; 12:e45-e54. [PMID: 38097297 PMCID: PMC10733129 DOI: 10.1016/s2214-109x(23)00469-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/26/2023] [Accepted: 10/07/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Tuberculosis is a leading cause of infectious disease mortality worldwide, but diagnosis of pulmonary tuberculosis remains challenging. Oral swabs are a promising non-sputum alternative sample type for the diagnosis of pulmonary tuberculosis. We aimed to assess the diagnostic accuracy of oral swabs to detect pulmonary tuberculosis in adults and children and suggest research implications. METHODS In this systematic review, we searched published and preprint studies from Jan 1, 2000, to July 5, 2022, from eight databases (MEDLINE, Embase, Scopus, Science Citation Index, medRxiv, bioRxiv, Global Index Medicus, and Google Scholar). We included diagnostic accuracy studies including cross-sectional, cohort, and case-control studies in adults and children from which we could extract or derive sensitivity and specificity of oral swabs as a sample type for the diagnosis of pulmonary tuberculosis against a sputum microbiological (nucleic acid amplification test [NAAT] on sputum or culture) or composite reference standard. FINDINGS Of 550 reports identified by the search, we included 16 eligible reports (including 20 studies and 3083 participants) that reported diagnostic accuracy estimates on oral swabs for pulmonary tuberculosis. Sensitivity on oral swabs ranged from 36% (95% CI 26-48) to 91% (80-98) in adults and 5% (1-14) to 42% (23-63) in children. Across all studies, specificity ranged from 66% (95% CI 52-78) to 100% (97-100), with most studies reporting specificity of more than 90%. Meta-analysis was not performed because of sampling and testing heterogeneity. INTERPRETATION Sensitivity varies in both adults and children when diverse methods are used. Variability in sampling location, swab type, and type of NAAT used in accuracy studies limits comparison. Although data are suggestive that high accuracy is achievable using oral swabs with molecular testing, more research is needed to define optimal methods for using oral swabs as a specimen for tuberculosis detection. The current data suggest that tongue swabs and swab types that collect increased biomass might have increased sensitivity. We would recommend that future studies use these established methods to continue to refine sample processing to maximise sensitivity. FUNDING Bill and Melinda Gates foundation (INV-045721) and FIND (Netherlands Enterprise Agency on behalf of the Minister for Foreign Trade and Development Cooperation [NL-GRNT05] and KfW Development Bank, German Federal Ministry of Education and Research [KFW-TBBU01/02]).
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Affiliation(s)
- E Chandler Church
- HIV Vaccine Trials Network, Fred Hutchinson Cancer Center, Seattle, WA, USA; Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA.
| | - Karen R Steingart
- Honorary Research Fellow, Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Gerard A Cangelosi
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | | | | | - Adrienne E Shapiro
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
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7
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Wood RC, Luabeya AK, Dragovich RB, Olson AM, Lochner KA, Weigel KM, Codsi R, Mulenga H, de Vos M, Kohli M, Penn-Nicholson A, Hatherill M, Cangelosi GA. Tongue swab testing on two automated tuberculosis diagnostic platforms, Cepheid Xpert ® MTB/RIF Ultra and Molbio Truenat ® MTB Ultima. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.10.23296833. [PMID: 37873199 PMCID: PMC10593025 DOI: 10.1101/2023.10.10.23296833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Tongue dorsum swabbing is a potential alternative to sputum collection for tuberculosis (TB) testing. Previous studies showed that Cepheid Xpert® MTB/RIF Ultra (Xpert Ultra) can detect Mycobacterium tuberculosis (MTB) DNA in tongue swabs stored in buffer, with 72% sensitivity and 100% specificity relative to a sputum microbiological reference standard (sputum MRS). The present study evaluated a more convenient sample collection protocol (dry swab storage), combined with streamlined sample processing protocols, for side-by-side analysis using two commercial TB diagnostic tests: Xpert Ultra and Molbio Truenat® MTB Ultima (MTB Ultima). Copan FLOQSwabs were self-collected, or collected by study workers, from 321 participants in Western Cape, South Africa. All participants had symptoms suggestive of TB, and 245 of them had sputum MRS-confirmed TB (by sputum culture and/or Xpert Ultra). One tongue swab per participant was tested on Xpert Ultra and another tongue swab was tested with MTB Ultima. Xpert Ultra was 75.4% sensitive and 100% specific, and MTB Ultima was 71.6% sensitive and 96.9% specific, relative to sputum MRS. When sample lysates that were false-negative by MTB Ultima were frozen, thawed, and re-tested, MTB Ultima sensitivity rose to 79.1%. Both tests were more sensitive with swabs from participants with higher sputum Xpert semi-quantitative results. The protocol for Xpert Ultra enabled fast and easy testing of dry-stored swabs with no loss of accuracy relative to previous methods. MTB Ultima testing of dry-stored swabs exhibited comparable performance to Xpert Ultra. These results further support tongue swabs as easy-to-collect samples for high-throughput TB testing.
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Affiliation(s)
- Rachel C Wood
- University of Washington, Department of Environmental and Occupational Health Sciences, Seattle, United States of America
| | - Angelique K Luabeya
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Rane B Dragovich
- University of Washington, Department of Environmental and Occupational Health Sciences, Seattle, United States of America
| | - Alaina M Olson
- University of Washington, Department of Environmental and Occupational Health Sciences, Seattle, United States of America
| | - Katherine A Lochner
- University of Washington, Department of Environmental and Occupational Health Sciences, Seattle, United States of America
| | - Kris M Weigel
- University of Washington, Department of Environmental and Occupational Health Sciences, Seattle, United States of America
| | - Renée Codsi
- University of Washington, Department of Environmental and Occupational Health Sciences, Seattle, United States of America
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Department of Pathology, University of Cape Town, Cape Town, South Africa
| | | | | | | | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease & Molecular Medicine and Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Gerard A Cangelosi
- University of Washington, Department of Environmental and Occupational Health Sciences, Seattle, United States of America
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8
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Savage HR, Rickman HM, Burke RM, Odland ML, Savio M, Ringwald B, Cuevas LE, MacPherson P. Accuracy of upper respiratory tract samples to diagnose Mycobacterium tuberculosis: a systematic review and meta-analysis. THE LANCET. MICROBE 2023; 4:e811-e821. [PMID: 37714173 PMCID: PMC10547599 DOI: 10.1016/s2666-5247(23)00190-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 09/17/2023]
Abstract
BACKGROUND Pulmonary tuberculosis due to Mycobacterium tuberculosis can be challenging to diagnose when sputum samples cannot be obtained, which is especially problematic in children and older people. We systematically appraised the performance characteristics and diagnostic accuracy of upper respiratory tract sampling for diagnosing active pulmonary tuberculosis. METHODS In this systematic review and meta-analysis, we searched MEDLINE, Cinahl, Web of Science, Global Health, and Global Health Archive databases for studies published between database inception and Dec 6, 2022 that reported on the accuracy of upper respiratory tract sampling for tuberculosis diagnosis compared with microbiological testing of sputum or gastric aspirate reference standard. We included studies that evaluated the accuracy of upper respiratory tract sampling (laryngeal swabs, nasopharyngeal aspirate, oral swabs, saliva, mouth wash, nasal swabs, plaque samples, and nasopharyngeal swabs) to be tested for microbiological diagnosis of tuberculous (by culture and nucleic acid amplification tests) compared with a reference standard using either sputum or gastric lavage for a microbiological test. We included cohort, case-control, cross-sectional, and randomised controlled studies that recruited participants from any community or clinical setting. We excluded post-mortem studies. We used a random-effects meta-analysis with a bivariate hierarchical model to estimate pooled sensitivity, specificity, and diagnostics odds ratio (DOR; odds of a positive test with disease relative to without), stratified by sampling method. We assessed bias using QUADAS-2 criteria. This study is registered with PROSPERO (CRD42021262392). FINDINGS We screened 10 159 titles for inclusion, reviewed 274 full texts, and included 71, comprising 119 test comparisons published between May 13, 1933, and Dec 19, 2022, in the systematic review (53 in the meta-analysis). For laryngeal swabs, pooled sensitivity was 57·8% (95% CI 50·5-65·0), specificity was 93·8% (88·4-96·8), and DOR was 20·7 (11·1-38·8). Nasopharyngeal aspirate sensitivity was 65·2% (52·0-76·4), specificity was 97·9% (96·0-99·0), and DOR was 91·0 (37·8-218·8). Oral swabs sensitivity was 56·7% (44·3-68·2), specificity was 91·3% (CI 81·0-96·3), and DOR was 13·8 (5·6-34·0). Substantial heterogeneity in diagnostic accuracy was found, probably due to differences in reference and index standards. INTERPRETATION Upper respiratory tract sampling holds promise to expand access to tuberculosis diagnosis. Exploring historical methods using modern microbiological techniques might further increase options for alternative sample types. Prospective studies are needed to optimise accuracy and utility of sampling methods in clinical practice. FUNDING UK Medical Research Council, Wellcome, and UK Foreign, Commonwealth and Development Office.
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Affiliation(s)
- Helen R Savage
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Hannah M Rickman
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK; Public Health Group, Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
| | - Rachael M Burke
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK; Public Health Group, Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
| | - Maria Lisa Odland
- Public Health Group, Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Martina Savio
- The LIGHT Consortium, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Beate Ringwald
- The LIGHT Consortium, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Luis E Cuevas
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Peter MacPherson
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK; Public Health Group, Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; School of Health and Wellbeing, University of Glasgow, Glasgow, UK
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9
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Codsi R, Errett NA, Luabeya AK, Van As D, Hatherill M, Shapiro AE, Lochner KA, Vingino AR, Kohn MJ, Cangelosi GA. Preferences of healthcare workers using tongue swabs for tuberculosis diagnosis during COVID-19. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001430. [PMID: 37676852 PMCID: PMC10484421 DOI: 10.1371/journal.pgph.0001430] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 08/02/2023] [Indexed: 09/09/2023]
Abstract
Healthcare workers (HCWs) who come into contact with tuberculosis (TB) patients are at elevated risk of TB infection and disease. The collection and handling of sputum samples for TB diagnosis poses exposure risks to HCWs, particularly in settings where aerosol containment is limited. An alternative sample collection method, tongue swabbing, was designed to help mitigate this risk, and is under evaluation in multiple settings. This study assessed risk perceptions among South African HCWs who used tongue swabbing in TB diagnostic research during the COVID-19 pandemic. We characterized their context-specific preferences as well as the facilitators and barriers of tongue swab use in clinical and community settings. Participants (n = 18) were HCWs with experience using experimental tongue swabbing methods at the South African Tuberculosis Vaccine Initiative (SATVI). We used key informant semi-structured interviews to assess attitudes toward two tongue swab strategies: Provider-collected swabbing (PS) and supervised self-swabbing (SSS). Responses from these interviews were analyzed by rapid qualitative analysis and thematic analysis methods. Facilitators included aversion to sputum (PS and SSS), perceived safety of the method (SSS), and educational resources to train patients (SSS). Barriers included cultural stigmas, as well as personal security and control of their work environment when collecting swabs in community settings. COVID-19 risk perception was a significant barrier to the PS method. Motivators for HCW use of tongue swabbing differed substantially by use case, and whether the HCW has the authority and agency to implement safety precautions in specific settings. These findings point to a need for contextually specific educational resources to enhance safety of and adherence to the SSS collection method.
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Affiliation(s)
- Renée Codsi
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Nicole A. Errett
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Angelique K. Luabeya
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Danelle Van As
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Adrienne E. Shapiro
- Departments of Global Health and Medicine (Infectious Diseases) University of Washington, Seattle, WA, United States of America
| | - Katherine A. Lochner
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Alexandria R. Vingino
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Marlana J. Kohn
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, United States of America
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
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10
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Mesman AW, Calderon RI, Hauns L, Pollock NR, Mendoza M, Holmberg RC, Franke MF. Detection of Mycobacterium tuberculosis transrenal DNA in urine samples among adult patients in Peru. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.26.23293199. [PMID: 37546779 PMCID: PMC10402216 DOI: 10.1101/2023.07.26.23293199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Diagnosis of tuberculosis (TB) relies on a sputum sample, which cannot be obtained from all symptomatic patients. Mycobacterium tuberculosis (Mtb) transrenal DNA (trDNA) has been detected in urine, an easily obtainable, noninvasive, alternative sample type. However, reported sensitivities have been variable and likely depend on collection/assay procedures and aspects of trDNA biology. We analyzed three serial urine samples from each of 75 adults with culture-confirmed pulmonary TB disease in Lima, Peru for detection of trDNA using short-fragment real-time PCR. Additionally, we examined host, urine, and sampling factors associated with detection. Overall sample sensitivity was 38% (95% Confidence Interval [CI] 30-45%). On a patient level (i.e., any of three samples positive), sensitivity was 73% (95% CI: 62-83%). Sensitivity was highest among samples from patients with smear-positive TB, 92% (95% CI: 62-100%). Specificity from a single sample from each of 10 healthy controls was 100% (95% CI: 69-100%). Adjusting our assay positivity threshold increased patient-level sensitivity to 88% (95% CI: 78-94%) overall without affecting the specificity. We did not find associations between Mtb trDNA detection and either patient characteristics or urine sample characteristics. Overall, our results support the potential of trDNA detection for TB diagnosis.
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Affiliation(s)
- Annelies W Mesman
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA
| | | | | | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA
| | | | | | - Molly F Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA
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11
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Wang Y, He Y, Wang L, Zhang YA, Wang MS. Diagnostic Yield of Nucleic Acid Amplification Tests in Oral Samples for Pulmonary Tuberculosis: A Systematic Review and Meta-analysis. Open Forum Infect Dis 2023; 10:ofad082. [PMID: 36937246 PMCID: PMC10019807 DOI: 10.1093/ofid/ofad082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
The diagnostic accuracy of oral specimen nucleic acid amplification tests (NAATs) for pulmonary tuberculosis (PTB) remains controversial. We performed a systematic review according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, including studies that reported the diagnostic yield of NAATs in oral samples for PTB diagnosis. The pooled estimates, including those of sensitivity and specificity, were calculated, and a meta-regression was performed to investigate heterogeneity, which was determined using χ2 and I² tests. A total of 23 articles were included, and the pooled sensitivity, specificity, and area under the curve of NAATs in oral samples for PTB diagnosis were 50% (95% CI, 37%-63%), 97% (95% CI, 93%-99%), and 0.89 (95% CI, 86%-92%; I 2 = 99%; chi-square, 169.61; P < .001), respectively. Our data demonstrated that NAATs using oral samples have a less satisfactory sensitivity and high specificity for PTB diagnosis. However, due to significant heterogeneity, such as heterogeneity in age, the results should be interpreted with caution.
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Affiliation(s)
| | | | - Li Wang
- Department of Lab Medicine, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Yan-An Zhang
- Correspondence: Yan-An Zhang, BS, Department of Cardiovascular Medicine, Shandong Public Health Clinical Center, 46# Lishan Road, Jinan, 250013, PR China (); or Mao-Shui Wang, MS, Department of Lab Medicine, Shandong Public Health Clinical Center, 46# Lishan Road, Jinan, 250013, PR China ()
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12
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Codsi R, Errett NA, Luabeya AK, Hatherill M, Shapiro AE, Lochner KA, Vingino AR, Kohn MJ, Cangelosi GA. Preferences of health care workers using tongue swabs for tuberculosis diagnosis during COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.12.06.22283185. [PMID: 36523414 PMCID: PMC9753790 DOI: 10.1101/2022.12.06.22283185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Healthcare workers (HCW) who come into contact with tuberculosis (TB) patients are at elevated risk of TB infection and disease. The collection and handling of sputum samples for TB diagnosis poses exposure risks to HCW, particularly in settings where aerosol containment is limited. An alternative sample collection method, tongue swabbing, was designed to help mitigate this risk, and is under evaluation in multiple settings. This study assessed risk perceptions among South African HCW who used tongue swabbing in TB diagnostic research during the COVID-19 pandemic. We characterized their context-specific preferences as well as the facilitators and barriers of tongue swab use in clinical and community settings. Participants (n=18) were HCW with experience using experimental tongue swabbing methods at the South African Tuberculosis Vaccine Initiative (SATVI). We used key informant semi-structured interviews to assess attitudes toward two tongue swab strategies: Provider-collected swabbing (PS) and supervised self-swabbing (SSS). Responses from these interviews were analyzed by rapid qualitative analysis and thematic analysis methods. Facilitators included aversion to sputum (PS and SSS), perceived safety of the method (SSS), and educational resources to train patients (SSS). Barriers included cultural stigmas, as well as personal security and control of their work environment when collecting swabs in community settings. COVID-19 risk perception was a significant barrier to the PS method. Motivators for HCW use of tongue swabbing differed substantially by use case, and whether the HCW has the authority and agency to implement safety precautions in specific settings. These findings point to a need for contextually specific educational resources to enhance safety of and adherence to the SSS collection method.
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Affiliation(s)
- Renée Codsi
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Nicole A. Errett
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Angelique K. Luabeya
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Adrienne E. Shapiro
- Departments of Global Health and Medicine (Infectious Diseases) University of Washington, Seattle, WA, USA
| | - Katherine A. Lochner
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Alexandria R. Vingino
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Marlena J. Kohn
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
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13
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Complementary Nonsputum Diagnostic Testing for Tuberculosis in People with HIV Using Oral Swab PCR and Urine Lipoarabinomannan Detection. J Clin Microbiol 2022; 60:e0043122. [PMID: 35913145 PMCID: PMC9383113 DOI: 10.1128/jcm.00431-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Testing for mycobacterial lipoarabinomannan (LAM) in urine is a practical but insensitive alternative to sputum testing to diagnose tuberculosis (TB) in people with HIV (PWH). Here, we evaluated urine LAM testing alongside PCR-based tests for Mycobacterium tuberculosis (MTB) DNA in tongue swabs. We hypothesized that the two nonsputum samples would deliver complementary, not redundant, results. The study included 131 South African patients of whom 64 (48.1%) were confirmed to have TB by GeneXpert MTB/RIF Ultra (Xpert Ultra) or culture analysis of sputum. A total of 120 patients (91.6%) were coinfected with HIV and 130 yielded a valid urine LAM result (Alere DETERMINE LAM Ag). Tongue swab samples were tested by IS6110-targeted qPCR with a quantification cycle (Cq) cutoff of 32. Relative to reference sputum testing (TB culture and Xpert Ultra), combined urine LAM and oral swab testing (either sample positive) was significantly more sensitive than either nonsputum sample alone (57% sensitivity for combined testing versus 35% and 39% sensitivity for urine LAM and tongue swabs; P = 0.01 and 0.04, respectively). Specificity of combined testing (neither sample positive) was 97%. On average, tongue swab-positive participants had higher sputum signal strength than urine-LAM positive participants, as measured by sputum Xpert Ultra Cq value (P = 0.037). A subset of tongue swabs (N = 18) was also tested by using Xpert Ultra, which reproduced true positive and true negative IS6110 qPCR results and resolved the two false-positive tongue swabs. With further development, tongue swabs and urine may feasibly serve as complementary nonsputum samples for diagnosis of TB in PWH.
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14
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Cox H, Workman L, Bateman L, Franckling-Smith Z, Prins M, Luiz J, Van Heerden J, Ah Tow Edries L, Africa S, Allen V, Baard C, Zemanay W, Nicol MP, Zar HJ. Oral Swab Specimens Tested With Xpert MTB/RIF Ultra Assay for Diagnosis of Pulmonary Tuberculosis in Children: A Diagnostic Accuracy Study. Clin Infect Dis 2022; 75:2145-2152. [PMID: 35579497 PMCID: PMC9761885 DOI: 10.1093/cid/ciac332] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/28/2022] [Accepted: 04/25/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Microbiologic diagnosis of childhood tuberculosis may be difficult. Oral swab specimens are a potential noninvasive alternative to sputum specimens for diagnosis. METHODS This was a prospective diagnostic accuracy study of oral swab specimens (buccal and tongue) for pulmonary tuberculosis diagnosis in children (aged ≤ 15 years) in 2 South African hospital sites. Children with cough of any duration as well as a positive tuberculin skin test result, tuberculosis contact, loss of weight, or chest radiograph suggestive of pulmonary tuberculosis were enrolled. Two induced sputum specimens were tested with Xpert MTB/RIF (or Xpert MTB/RIF Ultra) assay and liquid culture. Oral swab specimens were obtained before sputum specimens, frozen, and later tested with Xpert MTB/RIF Ultra. Children were classified as microbiologically confirmed tuberculosis, unconfirmed tuberculosis (receipt of tuberculosis treatment), or unlikely tuberculosis according to National Institutes of Health consensus definitions based on sputum microbiologic results. RESULTS Among 291 participants (median age [interquartile range], 32 [14-73] months), 57 (20%) had human immunodeficiency virus (HIV), and 87 (30%) were malnourished; 90 (31%) had confirmed pulmonary tuberculosis (rifampicin resistant in 6 [7%] ), 157 (54%), unconfirmed pulmonary tuberculosis, and 44 (15%), unlikely tuberculosis. A single oral swab specimen was obtained from 126 (43%) of the participants (tongue in 96 and buccal in 30) and 2 swab specimens from 165 (57%) (tongue in 110 and buccal in 55). Sensitivity was low (22% [95% confidence interval, 15%-32%]) for all swab specimens combined (with confirmed pulmonary tuberculosis as reference), but specificity was high (100% [91%-100%]). The highest sensitivity was 33% (95% confidence interval, 15%-58%) among participants with HIV. The overall yield was 6.9% with 1 oral swab specimen and 7.2% with 2. CONCLUSIONS Use of the Xpert MTB/RIF Ultra assay with oral swab specimens provides poor yield for microbiologic pulmonary tuberculosis confirmation in children.
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Affiliation(s)
- Helen Cox
- Correspondence: H. Cox, University of Cape Town, Anzio Road, Observatory, 7925 Cape Town, South Africa ()
| | - Lesley Workman
- Department of Paediatrics and Child Health and South African Medical Research Council Unit on Child and Adolescent Health, University of Cape Town and Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Lindy Bateman
- Department of Paediatrics and Child Health and South African Medical Research Council Unit on Child and Adolescent Health, University of Cape Town and Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Zoe Franckling-Smith
- Department of Paediatrics and Child Health and South African Medical Research Council Unit on Child and Adolescent Health, University of Cape Town and Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Margaretha Prins
- Department of Paediatrics and Child Health and South African Medical Research Council Unit on Child and Adolescent Health, University of Cape Town and Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Juaneta Luiz
- Department of Paediatrics and Child Health and South African Medical Research Council Unit on Child and Adolescent Health, University of Cape Town and Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Judi Van Heerden
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Lemese Ah Tow Edries
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Samantha Africa
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Veronica Allen
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Cynthia Baard
- Department of Paediatrics and Child Health and South African Medical Research Council Unit on Child and Adolescent Health, University of Cape Town and Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Widaad Zemanay
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
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15
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Abstract
Efforts to control transmissible infectious diseases rely on the ability to screen large populations, ideally in community settings. These efforts can be limited by the requirement for invasive or logistically difficult collection of patient samples, such as blood, urine, stool, sputum, and nasopharyngeal swabs. Oral sampling is an appealing, noninvasive alternative that could greatly facilitate high-throughput sampling in community settings. Oral sampling has been described for the detection of dozens of human pathogens, including pathogens whose primary sites of infection are outside of the oral cavity, such as the respiratory pathogens Mycobacterium tuberculosis and SARS-CoV-2. Oral sampling can demonstrate active infections as well as resolving or previous infections, the latter through the detection of antibodies. Its potential applications are diverse, including improved diagnosis in special populations (e.g., children), population surveillance, and infectious disease screening. In this minireview, we address the use of oral samples for the detection of diseases that primarily manifest outside the oral cavity. Focusing on well-supported examples, we describe applications for such methods and highlight their potential advantages and limitations in medicine, public health, and research.
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Affiliation(s)
- Ethan D. Valinetz
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
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16
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Flores JA, Coit J, Mendoza M, Leon SR, Konda K, Lecca L, Franke MF. Is exclusive breastfeeding for six-months protective against pediatric tuberculosis? Glob Health Action 2021; 14:1861922. [PMID: 33393436 PMCID: PMC7782219 DOI: 10.1080/16549716.2020.1861922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Experts recommend exclusive breastfeeding from birth to six months because it protects against deadly childhood illness, including respiratory tract infections and diarrhea. We hypothesized that exclusive breastfeeding would decrease the risk of active tuberculosis (TB) in children. We analyzed cross-sectional data from 279 children in Lima, Peru aged 6 to 59 months with TB symptoms and a close adult contact with TB. Mothers self-reported breastfeeding, and children were evaluated for TB per national guidelines. To quantify the association between exclusive breastfeeding and TB, we estimated prevalence ratios using a generalized linear model with a log link, binomial distribution, and robust variance. Twenty-two percent of children were diagnosed with TB and 72% were exclusively breastfed for six months. We found no evidence that six months of exclusive breastfeeding was associated with TB disease in either bivariate analyses (prevalence ratio [PR] = 1.5; 95%CI = 0.8–2.5) or multivariable analyses adjusting for sex and socioeconomic status (adjusted PR = 1.6; 95%[CI] = 0.9–2.7). In post hoc analyses among children whose close TB contact was their mother, we found evidence of a weak positive association between breastfeeding and TB (aPR = 2.1; 95%[CI] = 0.9–4.9). This association was not apparent among children whose close contact was not the mother (aPR = 1.2; 95%[CI] = 0.6–2.4). Our results raise the possibility that children who are breastfed by mothers with TB may be at increased risk for TB, given the close contact. Due to the cross-sectional study design, these results should be interpreted with caution. If these findings are confirmed in longitudinal analyses, future interventions could aim to minimize TB transmission from mothers with TB to breastfeeding infants.
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Affiliation(s)
- Juan A Flores
- Escuela Profesional de Tecnología Médica, Universidad Privada San Juan Bautista , Lima, Peru.,Facultad de Salud Pública, Universidad Peruana Cayetano Heredia , Lima, Peru
| | - Julia Coit
- Department of Global Health and Social Medicine, Harvard Medical School , Boston, MA, USA
| | - Milagros Mendoza
- Direction of Research, Socios En Salud at Partners in Health , Lima, Peru
| | - Segundo R Leon
- Escuela Profesional de Tecnología Médica, Universidad Privada San Juan Bautista , Lima, Peru
| | - Kelika Konda
- Division of Infectious Diseases, University of California , Los Angeles, CA, USA.,Center for Interdisciplinary Studies in Sexuality, AIDS and Society, and Laboratory of Sexual Health, Universidad Peruana Cayetano Heredia , Lima, Peru
| | - Leonid Lecca
- Direction of Research, Socios En Salud at Partners in Health , Lima, Peru
| | - Molly F Franke
- Department of Global Health and Social Medicine, Harvard Medical School , Boston, MA, USA
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17
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Pollock NR, MacIntyre AT, Blauwkamp TA, Blair L, Ho C, Calderon R, Franke MF. Detection of Mycobacterium tuberculosis cell-free DNA to diagnose TB in pediatric and adult patients. Int J Tuberc Lung Dis 2021; 25:403-405. [PMID: 33977910 DOI: 10.5588/ijtld.21.0055] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- N R Pollock
- Department of Laboratory Medicine, Boston Children´s Hospital and Harvard Medical School, Boston, MA
| | | | | | - L Blair
- Karius Inc, Redwood City, CA, USA
| | - C Ho
- Karius Inc, Redwood City, CA, USA
| | - R Calderon
- Socios En Salud Sucursal Peru, Lima, Peru, Programa Acadêmico de Tuberculose, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - M F Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
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18
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Wood RC, Andama A, Hermansky G, Burkot S, Asege L, Job M, Katumba D, Nakaye M, Mwebe SZ, Mulondo J, Bachman CM, Nichols KP, Le Ny ALM, Ortega C, Olson RN, Weigel KM, Olson AM, Madan D, Bell D, Cattamanchi A, Worodria W, Semitala FC, Somoskovi A, Cangelosi GA, Minch KJ. Characterization of oral swab samples for diagnosis of pulmonary tuberculosis. PLoS One 2021; 16:e0251422. [PMID: 33999938 PMCID: PMC8128230 DOI: 10.1371/journal.pone.0251422] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
Oral swab analysis (OSA) has been shown to detect Mycobacterium tuberculosis (MTB) DNA in patients with pulmonary tuberculosis (TB). In previous analyses, qPCR testing of swab samples collected from tongue dorsa was up to 93% sensitive relative to sputum GeneXpert, when 2 swabs per patient were tested. The present study modified sample collection methods to increase sample biomass and characterized the viability of bacilli present in tongue swabs. A qPCR targeting conserved bacterial ribosomal rRNA gene (rDNA) sequences was used to quantify bacterial biomass in samples. There was no detectable reduction in total bacterial rDNA signal over the course of 10 rapidly repeated tongue samplings, indicating that swabs collect only a small portion of the biomass available for testing. Copan FLOQSwabs collected ~2-fold more biomass than Puritan PurFlock swabs, the best brand used previously (p = 0.006). FLOQSwabs were therefore evaluated in patients with possible TB in Uganda. A FLOQSwab was collected from each patient upon enrollment (Day 1) and, in a subset of sputum GeneXpert Ultra-positive patients, a second swab was collected on the following day (Day 2). Swabs were tested for MTB DNA by manual IS6110-targeted qPCR. Relative to sputum GeneXpert Ultra, single-swab sensitivity was 88% (44/50) on Day 1 and 94.4% (17/18) on Day 2. Specificity was 79.2% (42/53). Among an expanded sample of Ugandan patients, 62% (87/141) had colony-forming bacilli in their tongue dorsum swab samples. These findings will help guide further development of this promising TB screening method.
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Affiliation(s)
- Rachel C. Wood
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Alfred Andama
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Gleda Hermansky
- Intellectual Ventures Laboratory, Bellevue, Washington, United States of America
| | - Stephen Burkot
- Intellectual Ventures’ Global Good Fund, Bellevue, Washington, United States of America
| | - Lucy Asege
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - David Katumba
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Martha Nakaye
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Jerry Mulondo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Christine M. Bachman
- Intellectual Ventures’ Global Good Fund, Bellevue, Washington, United States of America
| | - Kevin P. Nichols
- Intellectual Ventures Laboratory, Bellevue, Washington, United States of America
| | - Anne-Laure M. Le Ny
- Intellectual Ventures Laboratory, Bellevue, Washington, United States of America
| | - Corrie Ortega
- Intellectual Ventures Laboratory, Bellevue, Washington, United States of America
| | - Rita N. Olson
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Kris M. Weigel
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Alaina M. Olson
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Damian Madan
- Intellectual Ventures Laboratory, Bellevue, Washington, United States of America
| | - David Bell
- Intellectual Ventures’ Global Good Fund, Bellevue, Washington, United States of America
| | - Adithya Cattamanchi
- Division of Pulmonary and Critical Care Medicine and Center for Tuberculosis, Zuckerberg San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - William Worodria
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fred C. Semitala
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Akos Somoskovi
- Intellectual Ventures’ Global Good Fund, Bellevue, Washington, United States of America
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Kyle J. Minch
- Intellectual Ventures Laboratory, Bellevue, Washington, United States of America
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19
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Wong M, Coit JM, Mendoza M, Chiang SS, Marin H, Galea JT, Lecca L, Franke MF. Incident Tuberculosis Diagnoses in Children at High Risk for Disease. Open Forum Infect Dis 2021; 8:ofab075. [PMID: 33738322 PMCID: PMC7953651 DOI: 10.1093/ofid/ofab075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/10/2021] [Indexed: 11/29/2022] Open
Abstract
We followed 35 children meeting a research definition for unconfirmed tuberculosis (TB) but in whom a pediatric pulmonologist did not diagnose or treat TB. After a median follow-up of 16.4 months, most children were not diagnosed with TB following a comprehensive evaluation. However, 2 were diagnosed with TB, demonstrating high TB risk (6%; exact 95% CI, 1%–19%). In some contexts, researchers may wish to supplement these research definitions with clinical decision data and longitudinal follow-up in order to improve specificity.
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Affiliation(s)
| | - Julia M Coit
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Silvia S Chiang
- Department of Pediatrics, Alpert Medical School of Brown University, Providence, Rhode Island, USA.,Center for International Health Research, Rhode Island Hospital, Providence, Rhode Island, USA
| | | | - Jerome T Galea
- School of Social Work, University of South Florida, Tampa, Florida, USA.,College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Leonid Lecca
- Socios En Salud Sucursal Peru, Lima, Peru.,Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Molly F Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
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Molecular detection of Mycobacterium tuberculosis from buccal swabs among adult in Peru. Sci Rep 2020; 10:22231. [PMID: 33335256 PMCID: PMC7746708 DOI: 10.1038/s41598-020-79297-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/07/2020] [Indexed: 11/18/2022] Open
Abstract
Tuberculosis (TB) diagnosis relies on a sputum sample, which cannot be easily obtained from all symptomatic patients. Mycobacterium tuberculosis DNA can be detected from oral swabs, a noninvasive, safe alternative sample type; however, reported sensitivities have been variable and likely depend on sample collection, processing procedures and host characteristics. We analyzed three buccal swab samples from 123 adults with culture-confirmed TB in Lima, Peru. We compared the sensitivity and specificity of two sample collection devices (OmniSwab and EasiCollect FTA cards) and examined factors associated with detection. DNA was extracted with a commercially available kit and detected via real-time PCR IS6110 amplification. Overall sensitivity for buccal samples was 51% (95% Confidence Interval [CI] 42–60%). Specificity from a single sample among healthy controls was 96.7% (95% CI 83–99.9%). Positive sputum smear and cavitary disease, correlates of disease burden, were associated with detection via buccal swab. Although we observed higher sensitivities with the Omniswab samples, this appeared to be due primarily to differences in patient characteristics (e.g., cavitary disease). Overall, our findings support the potential for a buccal sample-based TB assay. Future work should focus on assay optimization and streamlining the assay workflow.
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