A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids

Microbial organisms have diverse populations, where using a single linear reference sequence in comparative studies introduces reference-bias in downstream analyses, and leads to a failure to account for variability in the population. Recently, pan-genome graphs have emerged as an alternative to the traditional linear reference with many successful applications and a rapid increase in the number of methods available in the literature. Despite this enthusiasm, there has been no attempt at exploring these graph construction methods in depth, demonstrating their practical use. In this study, we aim to develop a general guide to help researchers who may want to incorporate pan-genomes in their analyses of microbial organisms. We evaluated the state-of- the art pan-genome construction tools to model a collection of 70 Acinetobacter baumannii strains. Our results suggest that all tools produced pan-genome graphs conforming to our expectations based on previous literature, and that their approach to homologue detection is likely to be the most influential in determining the final size and complexity of the pan-genome. The graphs overlapped most in the core pan-genome content while the cloud genes varied significantly among tools. We propose an alternative approach for pan-genome construction by combining two of the tools, Panaroo and Ptolemy, to further exploit them in downstream analyses, and demonstrate the effectiveness of our pipeline for structural variant calling in beta-lactam resistance genes in the same set of A. baumannii isolates, identifying various transposon structures for carbapenem resistance in chromosome, as well as plasmids. We identify a novel plasmid structure in two multidrug-resistant clinical isolates that had previously been studied, and which could be important for their resistance phenotypes