CRISPR Detection of Circulating Cell-Free Mycobacterium tuberculosis DNA in Adults and Children, Including Children with HIV: A Molecular Diagnostics Study

Authors

Zhen Huang
Sylvia M LaCourse
Alexander W Kay
Joshua Stern
Jaclyn N Escudero
Brady M Youngquist
Wenshu Zheng
Debrah Vambe
Muyalo Dlamini
Godwin Mtetwa
Lisa M Cranmer
Irene Njuguna
Dalton C Wamalwa
Elizabeth Maleche-Obimbo
Donald G Catanzaro
Christopher J Lyon
Grace John-Stewart
Andrew DiNardo
Anna M Mandalakas
Bo Ning
Tony Y Hu

Publication Date

7-1-2022

Journal

The Lancet Microbe

DOI

10.1016/S2666-5247(22)00087-8

PMID

35659882

PMCID

PMC9300929

PubMedCentral® Posted Date

7-21-2022

PubMedCentral® Full Text Version

Author MSS

Published Open-Access

yes

Keywords

Adult, Cell-Free Nucleic Acids, Child, Clustered Regularly Interspaced Short Palindromic Repeats, HIV Infections, Humans, Kenya, Mycobacterium tuberculosis, Pathology, Molecular, Sensitivity and Specificity, Tuberculosis, Lymph Node, United States

Abstract

BACKGROUND: Tuberculosis remains a leading cause of global mortality, especially for adults and children living with HIV (CLHIV) underdiagnosed by sputum-based assays. Non-sputum-based assays are needed to improve tuberculosis diagnosis and tuberculosis treatment monitoring. Our aim in this study was to determine whether ultrasensitive detection of Mycobacterium tuberculosis cell-free DNA (Mtb-cfDNA) in blood can diagnose tuberculosis and evaluate tuberculosis treatment responses.

METHODS: In this molecular diagnostics study we analysed archived serum from two patient populations evaluated for tuberculosis in Eswatini and Kenya to detect Mtb-cfDNA, analysing serum from all individuals who had both sufficient serum volumes and clear diagnostic results. An optimised CRISPR-mediated tuberculosis (CRISPR-TB) assay was used to detect Mtb-cfDNA in serum at enrolment from adults and children with presumptive tuberculosis and their asymptomatic household contacts, and at enrolment and during tuberculosis treatment from a cohort of symptomatic CLHIV at high risk for tuberculosis, who provided longitudinal serum at enrolment and during tuberculosis treatment.

FINDINGS: CRISPR-TB identified microbiologically and clinically confirmed tuberculosis cases in the predominantly HIV-negative Eswatini adult cohort with 96% sensitivity (27 [96%] of 28, 95% CI 80-100) and 94% specificity (16 [94%] of 17, 71-100), and with 83% sensitivity (5 [83%] of 6, 36-100) and 95% specificity (21 [95%] of 22, 77-100) in the paediatric cohort, including all six cases of extrapulmonary tuberculosis. In the Kenyan CLHIV cohort, CRISPR-TB detected all (13 [100%] of 13, 75-100) confirmed tuberculosis cases and 85% (39 [85%] of 46, 71-94) of unconfirmed tuberculosis cases diagnosed by non-microbiological clinical findings. CLHIV who were CRISPR-TB positive at enrolment had a 2·4-times higher risk of mortality by 6 months after enrolment. Mtb-cfDNA signal decreased after tuberculosis treatment initiation, with near or complete Mtb-cfDNA clearance by 6 months after tuberculosis treatment initiation.

INTERPRETATION: CRISPR-mediated detection of circulating Mtb-cfDNA shows promise to increase the identification of paediatric tuberculosis and HIV-associated tuberculosis, and potential for early diagnosis and rapid monitoring of tuberculosis treatment responses.

FUNDING: US Department of Defense, National Institute of Child Health and Human Development, National Institute of Allergy and Infectious Diseases, University of Washington Center for AIDS Research, and the Weatherhead Presidential Endowment fund.