The sampling bottleneck in antimicrobial susceptibility testing: consequences and paths forward.

Area of Science:

• Microbiology
• Clinical Diagnostics
• Antimicrobial Resistance

Background:

• Conventional antimicrobial susceptibility testing (AST) relies on small bacterial inocula, potentially missing low-frequency resistant subpopulations within complex within-host environments.
• While often clinically insignificant in immunocompetent hosts, these subpopulations can emerge in high-risk scenarios like persistent infections or in profoundly immunocompromised individuals.

Purpose of the Study:

• To outline the biological basis of the sampling constraint in AST.
• To identify clinical contexts where this limitation is most impactful.
• To discuss adjunct strategies complementing standard AST.

Main Methods:

• Review of biological principles underlying AST sampling limitations.
• Analysis of clinical scenarios and patient populations at higher risk.
• Discussion of population-based and sequencing-informed adjunct testing approaches.

Main Results:

• Identified a sampling bottleneck in conventional AST due to small inocula.
• Highlighted the clinical relevance of low-frequency resistant subpopulations in specific patient groups and infection types.
• Proposed complementary diagnostic strategies to address AST limitations.

Conclusions:

• Standard AST methods may not fully capture the complexity of within-host bacterial resistance.
• Awareness of AST limitations is crucial for antimicrobial stewardship, especially in high-risk patients.
• Targeted adjunct methods can enhance diagnostic accuracy in select clinical situations.