Resolution of blood RNA signatures fails to discriminate sputum culture status after eight weeks of tuberculosis treatment.

Background There is concerted effort to reduce the burden of 6 months antimicrobial treatment for tuberculosis (TB). Early treatment cessation at 8 weeks is effective for most but incurs increased risk of disease relapse. We tested the hypothesis that blood RNA signatures of TB disease or C-reactive protein (CRP) measurements discriminate microbiological cure after 8 weeks of treatment, as a pre-requisite for a biomarker to stratify risk of relapse. Methods We identified blood RNA signatures of TB disease or cure by systematic review. We evaluated CRP measurements and blood RNA signatures that could be reproduced in genome-wide transcriptomic data from a previously reported longitudinal dataset in pulmonary TB, spanning samples collected pre-treatment, at 2 and 8 weeks of treatment, and after 2 years of follow up. In our primary analysis, we tested discrimination of sputum culture positivity at 8 weeks by contemporary blood RNA and CRP measurements using area under the receiver operating characteristic curve (AUROC) analysis. In secondary analyses, we tested the relationship between biomarker measurements and time to culture positivity as a surrogate for bacterial load in sputum culture positive cases at 8 weeks, and discrimination of sputum culture status at 8 weeks by biomarker measurements at any other time point. Findings We evaluated 12 blood RNA signatures. Blood RNA signature scores normalised over time from TB treatment initiation. 11/44 cases with available blood RNA, CRP and sputum culture results, were sputum culture positive at 8 weeks of treatment. None of the 12 blood RNA signature scores tested achieved statistically significant discrimination between sputum culture-positive vs. negative patients at this time point, with AUROC point estimates of 0.48-0.61. CRP achieved the best AUROC of 0.69 (95% confidence interval 0.52-0.87). None of the contemporary biomarker measurements correlated with bacterial load, and no measurements pre-treatment or at 2 weeks discriminated sputum culture status at 8 weeks. Interpretation The current repertoire of blood RNA signatures of TB and CRP will not provide host response surrogates of microbiological cure to support cessation of TB treatment at 8 weeks. Decoupling of blood transcriptional host-response from the presence of viable bacteria is indicative of subpopulations of Mycobacterium tuberculosis able to colonise the respiratory tract without triggering a detectable immune response. ### Competing Interest Statement JR, MN and ARM hold a patent in relation to blood transcriptomic biomarkers of tuberculosis. All other authors declare no competing interests. ### Funding Statement MN acknowledges support from the Wellcome Trust (207511/Z/17/Z) and NIHR Biomedical Research Funding to UCL and UCLH; RKG acknowledges support from National Institute for Health Research (NIHR302829). ARM acknowledges support from Asthma + Lung UK (ref TB05/11). CJC acknowledges funding from Wellcome Trust (203905/Z/16/Z). BO acknowledges support from an NIHR Academic Clinical Fellowship award. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: UK National Research Ethics services (reference number: 06/Q0605/83) I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The microarray data presented in this study will be made available in an open-access public repository at the time of peer-reviewed publication.