Variation in pre-therapy levels of selected Mycobacterium tuberculosis transcripts in sputum and their relationship with 2-month culture conversion

Background: The abundance of transcripts arising from Mycobacterium tuberculosis (MTB) in sputum pre-chemotherapy may enhance our understanding of factors influencing treatment response. We hypothesized that differences in the prevalence of pre-existing slowly metabolizing MTB in sputum may be partially responsible for differences in the rate of sputum clearance during treatment. Methods: Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used to characterize a selected limited transcription profile of MTB in sputum pre-chemotherapy and assess inter-individual variation. The difference in cycle threshold (Ct) per gene, normalized to 16S, between exponential/stationary phase culture and sputum was calculated and stratified by 2-month culture converter status. Results: HIV-1 uninfected patients with rifampicin-susceptible tuberculosis provided sputum pre-chemotherapy; 11 patients were negative for MTB culture after two months of therapy and 8 remained culture-positive. Increased icl1 and prpD and rpsN2:rpsN1 in sputum relative to culture suggested cholesterol utilization and a low-zinc environment respectively. Increased hspX and decreased atpA and nuoG relative to exponential culture suggested a slowly metabolizing subpopulation of MTB. While the the hspX hi atpA lo nuoG lo signal varied, we did not observe statistically significant enrichment of this phenotype in the non-converter population nor an association with MTB-lineage. Conclusion: Differential abundance of selected informative transcripts suggested a metabolically less-active subpopulation with a prevalence that varied between individual untreated patients.