Genome-wide host loci regulate M. tuberculosis fitness in immunodivergent mice.

The factors that determine the outcome of clinical tuberculosis lie within both the host and the pathogen, Mycobacterium tuberculosis (Mtb). The advent of recombinant inbred mouse panels and next-generation transposon mutagenesis and sequencing approaches has enabled dissection of the host-pathogen interface for mammalian and pathogen genetic determinants of disease outcome. To identify host and pathogen genetic drivers of Mtb infection, we infected 19 genotypes from the BXD panel, bred from Mtb-resistant C57BL/6J (B6) and Mtb-susceptible DBA/2J (D2), with a comprehensive library of transposon mutants (TnSeq). The survival of each of the ~4000 bacterial mutants within each distinct host was quantified and leveraged as refined “endophenotypes”, directly reporting on the infection microenvironment. We leveraged QTL mapping to associate each varying bacterial fitness endophenotype to the host genome and identified 140 significant host-pathogen quantitative trait loci (hpQTL). This host-pathogen interaction screen reinforces the utility of bacterial mutant libraries as precise reporters of host immunological microenvironment during infection and highlights host gene candidates for further investigation. Subject mice (19 BXD strains, C57BL/6J, and DBA/2J) were infected via tail vein injection with a saturated M. tuberculosis Himar1 transposon library. Animals were sacrificed after 4 weeks, and TnSeq was performed after library recovery from harvested spleens. In the majority of cases, two replicates were obtained per mouse strain, 5 replicates in the case of in vitro-cultured libraries.