Genomic analyses of Mycobacterium tuberculosis from human lung resections reveal a high frequency of polyclonal infections

11 páginas, 5 figuras, 1 tablaPolyclonal infections occur when at least two unrelated strains of the same pathogen are detected in an individual. This has been linked to worse clinical outcomes in tuberculosis, as undetected strains with different antibiotic resistance profiles can lead to treatment failure. Here, we examine the amount of polyclonal infections in sputum and surgical resections from patients with tuberculosis in the country of Georgia. For this purpose, we sequence and analyse the genomes of Mycobacterium tuberculosis isolated from the samples, acquired through an observational clinical study (NCT02715271). Access to the lung enhanced the detection of multiple strains (40% of surgery cases) as opposed to just using a sputum sample (0-5% in the general population). We show that polyclonal infections often involve genetically distant strains and can be associated with reversion of the patient's drug susceptibility profile over time. In addition, we find different patterns of genetic diversity within lesions and across patients, including mutational signatures known to be associated with oxidative damage; this suggests that reactive oxygen species may be acting as a selective pressure in the granuloma environment. Our results support the idea that the magnitude of polyclonal infections in high-burden tuberculosis settings is underestimated when only testing sputum samples.The authors were supported by projects SAF2016-77346-R and PID2019-104477RB-I00 awarded to IC and the grant BES-2017-079656 awarded to MM by the Spanish Ministry of Economy and Competitiveness and Ministry of Science, the ERC project 638553-TBACCELERATE awarded to IC, Spanish Government-FEDER Funds through CV contract CPII18/00031 and grant PI16/01511, and Generalitat Valencia Grant to I.C. (code PROMETEO/2020/012). The grant providers played no part in study design, data collection, and analysis, or the preparation of the manuscript.Peer reviewe