GenePointer - A Software for Automated Identification of Resistance Markers in Bacterial Genomes

Abstract

Antimicrobial resistance has been a growing threat on the horizon for more than 70 years now, and recent improvements in sequencing technology and bioinformatics tools are making it easier to analyze bacterial genomes. To add upon the already existing functionality of PhenotypeSeeker, a program for phenotype prediction from genotypes, the author created the resistance marker identification pipeline, GenePointer. The program aims to identify the elements in bacterial genomes most associated with their resistance phenotypes, using mapping and alignment approaches and is made to provide insight into novel associations to make the study of resistance mechanisms faster and more efficient. The program managed to identify some of the resistance associated genes in two of the three species and antibiotic combinations analyzed. However, the current version of GenePointer did not identify any novel associations and lacks the statistical power to identify all the known resistance genes. The program in its current form is useful for analyzing and summarizing the resistance associated elements in large numbers of genomes at a time and has potential in future developments to improve on the detection of associations.