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

UNLABELLED

) is a clinically significant pathogen and a highly genetically diverse species due to its large accessory genome. The functional consequence of this diversity remains unknown mainly because, to date, functional genomic studies in have been primarily performed on reference strains. Given the growing public health threat of infections, understanding the functional genomic differences among clinical isolates can provide more insight into how its genetic diversity influences gene essentiality, clinically relevant phenotypes, and importantly, potential drug targets. To determine the functional genomic diversity among strains, we conducted transposon-sequencing (TnSeq) on 21 genetically diverse clinical isolates, including 15 . subsp. isolates and 6 . subsp. isolates, cataloging all the essential and non-essential genes in each strain. Pan-genome analysis revealed a core set of 3,845 genes and a large accessory genome of 11,507. We identified 259 core essential genes across the 21 clinical isolates and 425 differentially required genes, representing ~10% of the core genome. We also identified genes whose requirements were subspecies, lineage, and isolate-specific. Finally, by correlating TnSeq profiles, we identified 19 previously uncharacterized genetic networks in . Altogether, we find that clinical isolates are not only genetically diverse but functionally diverse as well.

IMPORTANCE

This study investigates the genetic diversity of (), a bacteria known for causing difficult-to-treat infections. Researchers performed transposon-sequencing (TnSeq) on 21 different clinical isolates of to identify essential and non-essential genes in each strain. Through this analysis, they identified core genes required for growth across all strains. Interestingly, they also identified genes whose requirement for growth or "essentiality" were subspecies, lineage, and isolate-specific. This study reveals that s genetic diversity translates into significant functional differences among clinical isolates. Insights from this paper lay essential groundwork for future studies exploring the biological and clinical implications of genetic diversity in clinical isolates. Understanding this diversity could guide targeted therapies and offer new insights into managing infections caused by , a growing public health concern.