 Ahmed also has interest in comparative genomics of bacterial pathogens obtained from single patients at different occasions and this approach nurtures his concept of 'chronological evolution and replicative genomics' as tools to study host-microbe interaction over time.Ahmed's group has developed a widely used multilocus sequence typing scheme for species level identification of pathogenic "Leptospira" with a potential to replace the highly ambiguous serotyping method that currently is used for Leptospiral strain identification.Ahmed has also worked extensively on the nomenclature, taxonomic status, genome sequencing and functional characterization of Mycobacterium indicus pranii, a non-pathogenic mycobacterial species with very high translational promise as an immunotherapeutic.