Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in and .

Bacterial genetic diversity is often described solely using base-pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplication/amplifications are thought to be widespread among bacteria but due to their often-intractable size and instability, comprehensive studies of these mutations are rare. We define a methodology to investigate amplifications in bacterial genomes based on read depth of genome sequence data as a proxy for copy number. We demonstrate the approach with , whose insertion sequence element-rich genome provides extensive scope for amplifications to occur. Analysis of data for 2430 isolates identified 272 putative amplifications, of which 94 % were located at 11 hotspot loci. We demonstrate limited phylogenetic connection for the occurrence of amplifications, suggesting unstable and sporadic characteristics. Genome instability was further described using long-read sequencing via the Nanopore platform, which revealed that clonally derived laboratory cultures produced heterogenous populations rapidly. We extended this research to analyse a population of 1000 isolates of another important pathogen, . We found 590 amplifications in , and like , these occurred primarily at hotspots. Genes amplified in include those involved in motility and respiration, whilst in , functions included intracellular growth and regulation of virulence. Using publicly available short-read data we predicted previously unrecognized, large amplifications in and . This reveals the unrecognized and dynamic genetic diversity of and , highlighting the need for a more holistic understanding of bacterial genetics.