Integrating Scalable Genome Sequencing into Microbiology Laboratories for Routine AMR Surveillance

Abstract

Antimicrobial resistance (AMR) is considered a global threat, and novel drug discovery needs to be complemented with systematic and standardized epidemiological surveillance. Surveillance data are currently generated using phenotypic characterization. However, due to poor scalability, this approach does little for true epidemiological investigations. There is a strong case for whole-genome sequencing (WGS) to enhance the phenotypic data. To establish global AMR surveillance using WGS, we developed a laboratory implementation approach that we applied within the NIHR Global Health Research Unit (GHRU) on Genomic Surveillance of Antimicrobial Resistance. In this paper, we outline the laboratory implementation at four units, in Colombia, India, Nigeria, and the Philippines. The journey to embedding WGS capacity was split into four phases: Assessment, Assembly, Optimization, and Reassessment. We show that onboarding WGS capabilities can greatly enhance the real-time processing power within regional and national AMR surveillance initiatives, despite the high initial investment in laboratory infrastructure and maintenance. Countries looking to introduce WGS as a surveillance tool could begin by sequencing select Global Antimicrobial Resistance Surveillance System (GLASS) priority pathogens that can demonstrate the standardization and impact genome sequencing has in tackling AMR.

Circulation of Third-Generation Cephalosporin Resistant Salmonella Typhi in Mumbai, India

“…The evidence of persistent transmission of this high-risk lineage in a location with high burden of typhoid fever calls for active surveillance and effective prevention measures to avert a large outbreak and international dissemination, as seen with XDR S. Typhi carrying the ESBL gene bla CTX-M-15 in an IncY plasmid in neighboring Pakistan [ 5 ]. Through technology transfer and capacity building, the Central Research Laboratory at KIMS, Bangalore, is now equipped to carry out whole genome sequencing [ 22 ] and bioinformatics analysis [ 23 ] locally to support genomic surveillance.…”

Circulation of third-generation cephalosporin resistant Salmonella Typhi in Mumbai, India

“…The evidence of persistent transmission of this high-risk lineage calls for active surveillance and effective prevention measures to avert a large outbreak [31] and global dissemination [32,33]. Through technology transfer and capacity building, the Central Research Laboratory at KIMS, Bangalore, is now equipped to carry out whole genome sequencing [34] and bioinformatics analysis [35] locally to support genomic surveillance.…”