Novel approach to antibiogram analysis: looking at the composite resistance phenotype

Expression of Interest Title: Data challenge – Novel approach to antibiogram analysis: looking at the composite resistance phenotype
Team 9049, led by Shraddha Karve of Ashoka University, India, with Rintu Kutum (Ashoka University), Devojit Sarma (ICMR,NIREH, India), Vasundhara Karthikeyan (Ashoka University) and Ragul N (Ashoka University)

Summary of Research:

We are an academic team of five researchers who are deeply interested in the problem of rising antimicrobial resistance. We hail from diverse backgrounds of data science, microbiology, biochemistry, epidemiology and evolutionary biology. We work as a part of consortium that is tackling several aspects of AMR in India. Areas of interest include, but are not limited to, clinical surveillance, wastewater surveillance, AMR in animals and applications of genomics in AMR. Our team focuses on the clinical aspect of AMR. We are currently working with two hospital groups with half a dozen hospitals each in northern and western regions of India. We have collected the retrospective antibiograms and some associated clinical data of more than 60 thousand isolates till date from these hospitals. The data spans over the period of five years. Apart from the routine analysis for the prevalence and time trends of priority pathogenic species in India, we focus on the specific antibiotic susceptibility profiles of certain microbes. For instance, we have observed that carbapenem resistance in gram negative bacteria may or may not be accompanied with the extended beta lactate resistance or colistin resistance. Additionally, distribution of these specific resistance profiles changes with specimen or in-patient/out-patient status. After finding out the prevalence of the specific resistance profiles for a region we sequence the genomes of these bugs in the prospective arm of our study. Whole genome sequencing provides rich insights into the molecular mechanisms of resistance and molecular signatures of a particular resistance profile. The location of resistance conferring element, whether on chromosome or plasmid, indicates how fast the resistance might spread. As a newly formed consortium we are keen to visualise our data on the global AMR backdrop. We want to know the similarities and differences in the prevalence of the specific resistance profiles as well as their distributions across specimen and wards. We also want to contrast the time trends of the resistance. We also plan to compare our observations with the Indian data from Pfizer and Venatorx.

Requested Datasets:

Data Contributor: Pfizer Inc.

Data Contributor: Pfizer Inc.

Bedaquiline Drug Resistance Assessment in MDR-TB (DREAM)
Data Contributor: Johnson & Johnson

GEARS (Global Evaluation of Antimicrobial Resistance via Surveillance)
Data Contributor: Venatorx Pharmaceuticals

Data Contributor: Paratek Pharmaceuticals, Inc.

Data Contributor: Shionogi

SOAR 201818
Data Contributor: GSK