Transposon-sequencing across multiple Mycobacterium abscessus isolates reveals significant functional genomic diversity among strains

Abstract

Mycobacterium 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, Mab clinical isolates are highly genetically diverse. The functional consequence of this diversity remains largely unknown because to date, functional genomic studies in Mab have largely been performed on reference strains. Given the growing public health threat of Mab infections, understanding the functional genomic differences among Mab clinical isolates can provide more insight into how its genetic diversity influences gene essentiality and clinically relevantly phenotypes. To determine the functional genomic diversity among Mab strains, we conducted transposon-sequencing (TnSeq) on 22 genetically diverse clinical isolates. We generated triplicate libraries for 16 M. abscessus subspecies abscessus isolates and single libraries for 6 M. abscessus subspecies massiliense isolates, 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 the Mab core 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 in Mab. Altogether, this study is the first to unveil differences in genetic requirement across Mab clinical isolates and establishes that Mab strains are not only genetically diverse, but also functionally diverse as well.

High‐throughput functional genomics: A (myco)bacterial perspective

“…As the field progresses, there is certain to be an increased embrace of experimental diversity—both in the utilization of different bacterial and host strains, as well as in the types of genetic interactions studied. Instances of this trend are increasingly evident: for example, a pooled CRISPRi screen was used to compare gene vulnerability in M. tuberculosis HN878, a clinical strain, with the standard laboratory strain, M. tuberculosis H37Rv, and revealed differing vulnerabilities in drug targets (Bosch et al, 2021 ), echoing results in M. abscessus in which a Tn screen identified differential essentiality in 563 genes across 22 clinical isolates (Akusobi et al, 2023 ) and E. coli in which differences in gene essentiality were investigated across 18 strains under three conditions (Rousset et al, 2021 ).…”