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Syed RR, Catanzaro DG, Colman RE, Cooney CG, Linger Y, Kukhtin AV, Holmberg RC, Norville R, Crudu V, Ciobanu N, Codreanu A, Seifert M, Hillery N, Chiles P, Catanzaro A, Rodwell TC. Clinical Evaluation of the XDR-LFC Assay for the Molecular Detection of Isoniazid, Rifampin, Fluoroquinolone, Kanamycin, Capreomycin, and Amikacin Drug Resistance in a Prospective Cohort. J Clin Microbiol 2023; 61:e0147822. [PMID: 36757183 PMCID: PMC10035299 DOI: 10.1128/jcm.01478-22] [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: 10/05/2022] [Accepted: 01/11/2023] [Indexed: 02/10/2023] Open
Abstract
While the goal of universal drug susceptibility testing has been a key component of the WHO End TB Strategy, in practice, this remains inaccessible to many. Rapid molecular tests for tuberculosis (TB) and antituberculosis drug resistance could significantly improve access to testing. In this study, we evaluated the accuracy of the Akonni Biosystems XDR-TB (extensively drug-resistant TB) TruArray and lateral-flow-cell (XDR-LFC) assay (Akonni Biosystems, Inc., Frederick, MD, USA), a novel assay that detects mutations in seven genes associated with resistance to antituberculosis drugs: katG, the inhA promoter, and the ahpC promoter for isoniazid; rpoB for rifampin; gyrA for fluoroquinolones; rrs and the eis promoter for kanamycin; and rrs for capreomycin and amikacin. We evaluated assay performance using direct sputum samples from 566 participants recruited in a prospective cohort in Moldova over 2 years. The sensitivity and specificity against the phenotypic reference were both 100% for isoniazid, 99.2% and 97.9% for rifampin, 84.8% and 99.1% for fluoroquinolones, 87.0% and 84.1% for kanamycin, 54.3% and 100% for capreomycin, and 79.2% and 100% for amikacin, respectively. Whole-genome sequencing data for a subsample of 272 isolates showed 95 to 99% concordance with the XDR-LFC-reported suspected mutations. The XDR-LFC assay demonstrated a high level of accuracy for multiple drugs and met the WHO's minimum target product profile criteria for isoniazid and rifampin, while the sensitivity for fluoroquinolones and amikacin fell below target thresholds, likely due to the absence of a gyrB target in the assay. With optimization, the XDR-LFC shows promise as a novel near-patient technology to rapidly diagnose drug-resistant tuberculosis.
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Affiliation(s)
- Rehan R Syed
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Donald G Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Rebecca E Colman
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | | | | | | | | | | | - Valeriu Crudu
- Phthisiopneumology Institute, Chișinău, Republic of Moldova
| | - Nelly Ciobanu
- Phthisiopneumology Institute, Chișinău, Republic of Moldova
| | | | - Marva Seifert
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Naomi Hillery
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, California, USA
| | - Peter Chiles
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Antonino Catanzaro
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Timothy C Rodwell
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
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Abstract
We examined Mycobacterium tuberculosis DNA detection from buccal swab samples collected from children in Lima, Peru. DNA was extracted and amplified via real-time polymerase chain reaction. Sensitivity was 21% (95% confidence interval [CI]: 7%-42%) in 24 culture-confirmed tuberculosis cases and 4.6% (95% CI: 1%-13%) in 65 clinically diagnosed unconfirmed cases. Sensitivity was highest for smear-positive tuberculosis. Specificity was 99% in the 199 controls (95% CI: 96%-100%).
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Kukhtin AV, Norville R, Bueno A, Qu P, Parrish N, Murray M, Chandler DP, Holmberg RC, Cooney CG. A Benchtop Automated Sputum-to-Genotype System Using a Lab-on-a-Film Assembly for Detection of Multidrug-Resistant Mycobacterium tuberculosis. Anal Chem 2020; 92:5311-5318. [PMID: 32142258 PMCID: PMC7354060 DOI: 10.1021/acs.analchem.9b05853] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Automated genotyping of drug-resistant Mycobacterium tuberculosis (MTB) directly from sputum is challenging for three primary reasons. First, the sample matrix, sputum, is highly viscous and heterogeneous, posing a challenge for sample processing. Second, acid-fast MTB bacilli are difficult to lyse. And third, there are hundreds of MTB mutations that confer drug resistance. An additional constraint is that MTB is most prevalent where test affordability is paramount. We address the challenge of sample homogenization and cell lysis using magnetic rotation of an external magnet, at high (5000) rpm, to induce the rotation of a disposable stir disc that causes chaotic mixing of glass beads ("MagVor"). Nucleic acid is purified using a pipet tip with an embedded matrix that isolates nucleic acid ("TruTip"). We address the challenge of cost and genotyping multiple mutations using 203 porous three-dimensional gel elements printed on a film substrate and enclosed in a microfluidic laminate assembly ("Lab-on-a-Film"). This Lab-on-a-Film assembly (LFA) serves as a platform for amplification, hybridization, washing, and fluorescent imaging, while maintaining a closed format to prevent amplicon contamination of the workspace. We integrated and automated MagVor homogenization, TruTip purification, and LFA amplification in a multisample, sputum-to-genotype system. Using this system, we report detection down to 43 cfu/mL of MTB bacilli from raw sputum.
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Affiliation(s)
- Alexander V Kukhtin
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
| | - Ryan Norville
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
| | - Arial Bueno
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
| | - Peter Qu
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
| | - Nicole Parrish
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Darrell P Chandler
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
| | - Rebecca C Holmberg
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
| | - Christopher G Cooney
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
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Mesman AW, Soto M, Coit J, Calderon R, Aliaga J, Pollock NR, Mendoza M, Mestanza FM, Mendoza CJ, Murray MB, Lecca L, Holmberg R, Franke MF. Detection of Mycobacterium tuberculosis in pediatric stool samples using TruTip technology. BMC Infect Dis 2019; 19:563. [PMID: 31248383 PMCID: PMC6598370 DOI: 10.1186/s12879-019-4188-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/13/2019] [Indexed: 01/16/2023] Open
Abstract
Background Rapid and accurate diagnosis of childhood tuberculosis (TB) is challenging because children are often unable to produce the sputum sample required for conventional tests. Stool is an alternative sample type that is easy to collect from children, and studies investigating the use of stool for molecular detection of Mycobacterium tuberculosis (Mtb) have led to promising results. Our objective was to evaluate stool as an alternative specimen to sputum for Mtb detection in children. We did so using the TruTip workstation (Akonni Biosystems), a novel automated lysis and extraction platform. Methods We tested stool samples from 259 children aged 0–14 years old, in Lima, Peru who presented with TB symptoms. Following extraction with TruTip, we detected the presence of Mtb DNA by IS6110 real-time PCR. We calculated assay sensitivity in two groups: (1) children with culture confirmed TB (N = 22); and (2) children with clinically-diagnosed unconfirmed TB (N = 84). We calculated specificity among children in whom TB was ruled out (N = 153). Among children who were diagnosed with TB, we examined factors associated with a positive stool test. Results Assay sensitivity was 59% (95% confidence interval [CI]: 39–80%) and 1.2% (95% CI: 0.0–6.5%) in children with culture-confirmed and clinically-diagnosed unconfirmed TB, respectively, and specificity was 97% (95% CI: 93–99%). The assay detected Mtb in stool of 7/7 children with smear-positive TB (100% sensitivity; 95% CI: 59–100%), and in 6/15 of children with smear-negative, culture-confirmed TB (40% sensitivity; 95% CI: 16–68%). Older age, smear positivity, culture positivity, ability to produce sputum and cavitary disease were associated with a positive stool result. Conclusion Testing of stool samples with the TruTip workstation and IS6110 amplification yielded sensitivity and specificity estimates comparable to other tests such as Xpert. Future work should include detection of resistance using the TruTip closed amplification system and assay optimization to improve sensitivity in children with low bacillary loads.
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Affiliation(s)
- Annelies W Mesman
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, USA
| | - Martin Soto
- Socios En Salud Sucursal (Partners In Health), Lima, Peru
| | - Julia Coit
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, USA
| | - Roger Calderon
- Socios En Salud Sucursal (Partners In Health), Lima, Peru
| | - Juan Aliaga
- Socios En Salud Sucursal (Partners In Health), Lima, Peru
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, USA
| | | | | | | | - Megan B Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, USA
| | - Leonid Lecca
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, USA.,Socios En Salud Sucursal (Partners In Health), Lima, Peru
| | | | - Molly F Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, USA.
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Beall SG, Cantera J, Diaz MH, Winchell JM, Lillis L, White H, Kalnoky M, Gallarda J, Boyle DS. Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings. PLoS One 2019; 14:e0215753. [PMID: 30998749 PMCID: PMC6472818 DOI: 10.1371/journal.pone.0215753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/16/2019] [Indexed: 01/20/2023] Open
Abstract
Infectious disease nucleic acid amplification technologies (NAAT) have superior sensitivity, specificity, and rapid time to result compared to traditional microbiological methods. Recovery of concentrated, high quality pathogen nucleic acid (NA) from complex specimen matrices is required for optimal performance of several NA amplification/detection technologies such as polymerase chain reaction (PCR). Fully integrated NAAT platforms that enable rapid sample-to-result workflows with minimal user input are generally restricted to larger reference lab settings, and their complexity and cost are prohibitive to widespread implementation in resource limited settings (RLS). Identification of component technologies for incorporation of reliable and affordable sample preparation with pathogen NA amplification/detection into an integrated platform suitable for RLS, is a necessary first step toward achieving the overarching goal of reducing infectious disease-associated morbidity and mortality globally. In the current study, we evaluate the performance of six novel NA extraction technologies from different developers using blinded panels of stool, sputum and blood spiked with variable amounts of quality-controlled DNA- and/or RNA-based microbes. The extraction efficiencies were semi-quantitatively assessed using validated real-time reverse transcription (RT)-PCR assays specific for each microbe and comparing target-specific RT-PCR results to those obtained with reference NA extraction methods. The technologies were ranked based on overall diagnostic accuracy (analytical sensitivity and specificity). Sample input and output volumes, total processing time, user-required manual steps and cost estimates were also examined for suitability in RLS. Together with the performance analysis, these metrics were used to select the more suitable candidate technologies for further optimization of integrated NA amplification and detection technologies for RLS.
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Affiliation(s)
- Shivani G. Beall
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, Georgia, United States of America
| | | | - Maureen H. Diaz
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, Georgia, United States of America
| | - Jonas M. Winchell
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, Georgia, United States of America
| | | | | | | | - James Gallarda
- Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
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Kukhtin AC, Sebastian T, Golova J, Perov A, Knickerbocker C, Linger Y, Bueno A, Qu P, Villanueva M, Holmberg RC, Chandler DP, Cooney CG. Lab-on-a-Film disposable for genotyping multidrug-resistant Mycobacterium tuberculosis from sputum extracts. LAB ON A CHIP 2019; 19:1217-1225. [PMID: 30801596 PMCID: PMC6461559 DOI: 10.1039/c8lc01404c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We describe a Lab-on-a-Film disposable that detects multidrug-resistant tuberculosis (MDR-TB) from sputum extracts. The Lab-on-a-Film disposable consists of 203 gel elements that include DNA sequences (probes) for 37 mutations, deletions, or insertion elements across 5 genes (including an internal control). These gel elements are printed on a flexible film, which costs approximately 500 times less than microarray glass. The film with printed gel elements is then laminated to additional rollable materials (films) to form a microfluidic flow cell. We combined multiplex amplification and hybridization steps in a single microfluidic chamber, without buffer exchanges or other manipulations up to and throughout hybridization. This flow cell also incorporates post hybridization wash steps while retaining an entirely closed-amplicon system, thus minimizing the potential for sample or amplicon cross-contamination. We report analytical sensitivity of 32 cfu mL-1 across all MDR-TB markers and detection of MDR-TB positive clinical specimens using an automated TruTip workstation for extraction and the Lab-on-a-Film disposable for amplification and detection of the extracts.
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Affiliation(s)
- Alexander C Kukhtin
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, USA.
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Watson RL, de Koff EM, Bogaert D. Characterising the respiratory microbiome. Eur Respir J 2019; 53:13993003.01711-2018. [PMID: 30487204 DOI: 10.1183/13993003.01711-2018] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/05/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Rebecca L Watson
- Center for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK.,Both authors contributed equally
| | - Emma M de Koff
- Dept of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands.,Spaarne Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands.,Both authors contributed equally
| | - Debby Bogaert
- Center for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK.,Dept of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
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