Whole-Genome Sequencing for Antimicrobial Resistance Detection: A Simulation-Based Evaluation of WHO-Recommended Workflow in Pakistan

Abstract

Objectives: To evaluate the performance and feasibility of whole-genome sequencing works for detecting antimicrobial resistance and to determine whether it is practical to use in Pakistan, using a simulation-based model based on the World Health Organization’s antimicrobial resistance genome sequencing guidelines.

Methodology: A simulation model was developed according to the guidelines described in World Health Organization (WHO) report for detection of Antimicrobial Resistance using Whole Genome Sequencing (WGS). Simulation inputs included common AMR genes circulating in Pakistan (mecA, blaCTX-M, blaNDM-1, blaOXA-48, aac(6')-Ib), pathogenic species profiles, and metadata recommendations. Evidence from WHO-recommended WGS workflows was used for AMR detection and validation.

Results: Simulated WGS workflows showed high predicted accuracy for AMR gene detection (94–100%), virulence factor identification (≥90%), plasmid and mobile genetic element (MGE) resolution, and outbreak-level genomic typing. WGS reduced theoretical AMR detection time from 48–72 hours (phenotypic methods) to <12 hours post-culture. WHO-recommended quality metrics including ≥30× coverage, Q30 base accuracy, appropriate metadata capture, and standardized laboratory workflows were achievable within Pakistan health care system, though limited by workforce training, bioinformatics infrastructure.

Conclusion: WGS is a feasible and highly accurate method for detecting antimicrobial resistance (AMR) in Pakistan. Using WGS according to the World Health Organization (WHO) recommended standards can greatly improve Pakistan's national AMR surveillance system.