Retrospective Analysis of Archived Pyrazinamide Resistant Complex Isolates from Uganda-Evidence of Interspecies Transmission.

The contribution of to the proportion of tuberculosis cases in humans is unknown. A retrospective study was undertaken on archived complex (MTBC) isolates from a reference laboratory in Uganda to identify the prevalence of human infection. A total of 5676 isolates maintained in this repository were queried and 136 isolates were identified as pyrazinamide resistant, a hallmark phenotype of . Of these, 1.5% ( = 2) isolates were confirmed as by using regions of difference PCR analysis. The overall size of whole genome sequences (WGSs) of these two isolates were ~4.272 Mb ( Bz_31150 isolated from a captive chimpanzee) and 4.17 Mb ( B2_7505 from a human patient), respectively. Alignment of these genomes against 15 MTBC genome sequences revealed 7248 single nucleotide polumorphisms (SNPs). Theses SNPs were used for phylogenetic analysis that indicated a strong relationship between and the chimpanzee isolate (Bz_31150) while the other genome from the human patient (B2_7505) analyzed did not cluster with any or strains. WGS analysis also revealed multidrug resistance genotypes; these genomes revealed mutations at positions H57D in Bz_31150 and B2_7505. Phenotypically, B2_7505 was an extensively drug-resistant strain and this was confirmed by the presence of mutations in the major resistance-associated proteins for all anti-tuberculosis (TB) drugs, including isoniazid (G (S315T) and A (S94A)), fluoroquinolones (S95T), streptomycin (rrs (R309C)), and rifampin (D435Y, a rare but disputed mutation in ). The presence of these mutations exclusively in the human isolate suggested that these occurred after transmission from cattle. Genome analysis in this study identified in humans and great apes, suggesting possible transmission from domesticated ruminants in the area due to a dynamic and changing interface, which has created opportunity for exposure and transmission.