P-1791. Understanding Clinical Application of Whole Genome Sequencing for Antimicrobial Resistance

TL;DR

This paper reviews how whole genome sequencing can help manage antibiotic-resistant infections in clinical settings, highlighting its potential and current limitations.

Contribution

The study systematically reviews recent literature to assess the clinical use of whole genome sequencing for antimicrobial resistance management.

Findings

WGS aids in detecting novel resistance patterns and improving genotype-phenotype correlations for antibiotic susceptibility.

Only a few studies evaluated clinical outcomes, and most did not use WGS in real-time for patient management.

There is a need for standardized guidelines to integrate WGS into routine clinical microbiology testing.

Abstract

Antimicrobial resistance (AR) remains a growing global concern, as detailed by U.S. Centers for Disease Control and Prevention (CDC) in the 2021-2022 “Antimicrobial Resistance Threats in the United States” report. Whole genome sequencing (WGS) is a powerful tool for enhancing our capacity to better address increasing threats of antimicrobial-resistant pathogens. However, integration of WGS and analysis into routine clinical microbiology laboratory testing is still evolving.

We conducted a literature review to identify documented use cases of WGS data for patient management of antimicrobial-resistant bacterial healthcare-associated infections. The review was completed on PubMed using combinations of pre-defined key terms including “whole genome sequencing”, “antibiotic resistance”, “clinical management”, and “(Gram positive or Gram negative)”. The search was limited to articles published from 2020-2025 that covered a specific example of WGS data relating to understanding patient management.

Out of 27 total articles, 15 environmental and agricultural studies were excluded. These 12 articles covered Gram-positive and Gram-negative bacteria, causing various infections. All studies included a WGS component and some evaluation of AR, although the specific antibiotics evaluated varied. Few studies (n=3) evaluated a clinical outcome. Four papers discussed potential impact in patient management. However, this was not done in real-time. In most studies (n=10), WGS aided in detecting novel resistance patterns, enhancing our understanding of these mechanisms, and improving genotype-phenotype correlations for antibiotic susceptibility.

These studies support that real-time WGS has the potential to be a powerful tool for clinical management in treating Gram-negative AR infections, providing rapid and precise genetic insights to guide antibiotic selection. There is an urgent need for development of standardized guidelines to allow labs to integrate WGS as a clinical test. Additionally, WGS contributes to protecting the public’s health by expanding our understanding of emerging resistance mechanisms and advancing the field’s ability to track and respond to AR threats.

All Authors: No reported disclosures