Transposon-sequencing across multipleMycobacterium abscessusisolates reveals significant functional genomic diversity among strains

Abstract

AbstractMycobacterium abscessus (Mab)clinical isolates have large accessory genomes that are comprised of plasmids, prophages, and genomic islands acquired by horizontal gene transfer. Due to their large accessory genomes, Mabclinical isolates are highly genetically diverse. The functional consequence of this diversity remains largely unknown because to date, functional genomic studies inMabhave largely been performed on reference strains. Given the growing public health threat ofMabinfections, understanding the functional genomic differences amongMabclinical isolates can provide more insight into how its genetic diversity influences gene essentiality and clinically relevantly phenotypes. To determine the functional genomic diversity amongMabstrains, we conducted transposon-sequencing (TnSeq) on 22 genetically diverse clinical isolates. We generated triplicate libraries for 16M. abscessus subspecies abscessusisolates and single libraries for 6M. abscessus subspecies massilienseisolates, cataloguing all the essential and non-essential genes in each strain. We identified 562 genes that were differentially required across the 22 clinical isolates, representing ∼15% of theMabcore genome. We also identified genes whose requirements were sub-species, lineage, and isolate specific. Finally, we identified 10,198 pairs of genes whose genetic requirements were significantly correlated and ultimately identified 19 previously uncharacterized genetic networks inMab. Altogether, this study is the first to unveil differences in genetic requirement acrossMabclinical isolates and establishes thatMabstrains are not only genetically diverse, but also functionally diverse as well.