Genomic sequencing of clinical isolates

The problem of antimicrobial resistance needs action on many fronts. We need to minimise usage of antibiotics in humans as well as in animal husbandry. We need better disease prevention methods. We need newer drugs that will be effective against pathogens and so on. But to succeed on all these fronts we need to have an effective surveillance of AMR. Currently, surveillance is primarily done through phenotypic means all over India. While clinically important, such surveillance tells us little about the underlying genomic changes that result in resistance. 

We work with a few tertiary healthcare centres in the Western and Northern region of India where we perform regular genomic surveillance for AMR. We sequence the genomes of pathogens listed as priority by Indian Council of Medical Research such as Carbapenem resistant gram-negative bacteria like Klebsiella pneumoniae and Escherichia coli, Methicillin resistant Staphylococcus aureus, Vancomycin-resistant Enterococci etc. We also perform genomic surveillance for a few emerging threats like Strenotrophomonas maltophilia. 

Whole-genome sequencing of the clinical isolates provides us a wealth of information including the genetic underpinnings of the observed resistance, resistance elements going together and location of the resistance conferring gene (whether on the bacterial chromosome or plasmid). This information is not only useful for the purpose of surveillance but also helpful in building cutting-edge diagnostic tools and predicting the spread of resistance