Flankophile: a bioinformatic pipeline for prokaryotic genomic synteny analysis

Abstract

ABSTRACT Analysis of flanking region sequences can be useful when comparing mobile prokaryotic sequences from different bacterial isolates or metagenomes. Here, we report a new bioinformatics tool, a pipeline called Flankophile, which can analyze flanking regions and sequence variants. The main feature of Flankophile is that it visualizes flanking region synteny and sequence variants in publication-ready plots with distance trees, gene annotations, and metadata. Antimicrobial resistance is a significant threat to human health, and surveillance of the spread of antimicrobial resistance is essential. The study of acquired antimicrobial resistance genes (ARGs) is an obvious use case for Flankophile due to the typically diverse genetic context of the genes. Flanking sequences offer a stronger epidemiological signal than the gene sequence alone. To demonstrate Flankophile, we applied it to 2,057 sequenced bacterial isolates and 273 metagenomes from humans and pigs in Denmark and compared the ARGs found in each host reservoir. Gene variant results showed that just ca. 4% of all unique ARG variants found ( N = 1,052) were detected in samples from both humans and pigs. Flanking region analysis of ARG variants frequently detected in this study showed multiple examples of genes where the entire 3,000-base pair flanking region was identical in samples from both hosts but also cases where no overlap was observed, and the clustering showed a complete separation of the samples from pigs and the samples from humans. IMPORTANCE The Flankophile pipeline enables the analysis and visualization of flanking regions of prokaryotic sequences of interest on large data sets in one step and in a consistent manner. A specific tool for flanking region analysis with automated visualization has not been developed before, and Flankophile will make flanking region analysis easier and accessible to more people. Flankophile will be especially useful in the field of genomic epidemiology of acquired antimicrobial resistance genes. Here, information from flanking region sequences can be instrumental in rejecting or supporting the possibility of a recent common source of the same resistance gene found in different samples.