AUTHOR=Xiong Xuekai , Wang Rui , Deng Dachuan , Chen Yingyu , Liu Han , Wang Tianqi , Wang Jieru , Zhu Xiaojie , Zhu Xifang , Zhu Yongqiang , Lu Xinyan , Chen Huanchun , Zheng Huajun , Guo Aizhen 

TITLE=Comparative Genomics of a Bovine Mycobacterium tuberculosis Isolate and Other Strains Reveals Its Potential Mechanism of Bovine Adaptation

JOURNAL=Frontiers in Microbiology

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.02500

DOI=10.3389/fmicb.2017.02500

ISSN=1664-302X

ABSTRACT=<p>The <italic>Mycobacterium tuberculosis</italic> complex causes tuberculosis (TB) in humans and other animal species, but <italic>Mycobacterium tuberculosis</italic> has a distinct host preference to humans. The present study aimed to determine whether a bovine <italic>M. tb</italic> strain 1458 has evolved some genetic properties in their genome that might be associated with their bovine adaptation. The genome of the <italic>M. tb</italic> strain 1458 was sequenced and subjected to an extensive comparative genomic analysis. A phylogenetic analysis showed that strain 1458 is most closely related to a Chinese <italic>M. tb</italic> strain, CCDC5079, of the same Beijing family. Compared with three human <italic>M. tb</italic> Beijing family strains, the strain 1458 has the fewest unique genes. However, there are most (21) IS<italic>6110</italic> insertion sequences in the strain 1458 genome at either intragenic or intergenic sites, resulting in the interruption of 11 genes including three PPE family-encoding genes (PPE16, PPE38, and PPE59). Only the strain 1458 genome has the upstream insertion in <italic>esxS</italic> and <italic>phoP</italic> genes. PCR confirmed four upstream insertions and qPCR determined that transcription of <italic>esxS, phoP, dnaN</italic>, and <italic>ctpD</italic> genes differed significantly between <italic>M. tb</italic> strain 1458 and H37Rv or <italic>M. bovis</italic>. A Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that the genes affected by non-synonymous SNPs are enriched in RNA polymerase. Moreover, 127 of the 133 unique SNPs in strain 1458 are either different to those in the <italic>M. bovis</italic> genome. In conclusion, some critical genes responsible for bacterial virulence and immunogenicity were interrupted in the genome of bovine <italic>M. tb</italic> strain 1458 by IS insertions and non-synonymous SNPs, which might contribute to its bovine adaptation, and the modification of its virulence and immunogenicity in cattle.</p>