Abstract
Real-time polymerase chain reaction (PCR) has reshaped bacterial infectious disease diagnostics, yet important interpretive gaps remain regarding the relationship among molecular detection, cycle threshold (Ct) values, microbial viability, culture findings, and phenotypic antimicrobial susceptibility. In particular, Ct values are frequently overinterpreted as direct surrogates for viable bacterial burden, and PCR–culture discordance may be interpreted without sufficient consideration of the distinct biological information provided by each method. This review therefore aims to clarify the complementary biological and analytical roles of PCR and bacterial culture, critically examine the determinants and limitations of Ct interpretation and PCR–culture discordance, and provide a practical framework for integrating molecular detection, culture, and antimicrobial susceptibility testing (AST) into clinically and stewardship-informed decision-making. The genotypic lens of PCR (detection of target nucleic acid and resistance genes) is contrasted with the phenotypic lens of bacterial culture and AST, emphasizing that genotype and phenotype distinguish biological layers and account for common PCR–culture discordance. Evidence on Ct variability, assay design, inhibition, and panel scope is synthesized to demonstrate why Ct is inherently assay-specific and non-portable across platforms. Accordingly, MIQE-aligned quality safeguards and assay-specific principles are presented to guide the interpretation of Ct values. Bedside decision tables then integrate Ct patterns, specimen sterility, and patient acuity to support treatment, observation, or additional testing. As a narrative review of heterogeneous evidence, this synthesis does not provide pooled estimates or a uniform risk-of-bias assessment. The proposed Ct categories and clinical framework should therefore be viewed as assay-specific guidance, not universally validated thresholds. Finally, a stepwise workflow is outlined in which PCR is used for rapid rule-in, while culture and AST are retained for confirmation, de-escalation, and dosing. This integrated approach reframes Ct as a qualified signal rather than a standalone truth, supporting faster yet biologically grounded and stewardship-consistent infectious disease management.
Description
Copyright: © 2026 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Publisher
MDPI
Date of publication
Fall 2026
Language
english
Persistent identifier
http://hdl.handle.net/10950/5212
Document Type
Article
Recommended Citation
Carpenter, R. E., Krouse, A., & Vincent, A. (2026). From colonies to copies: Integrating PCR, culture, and AST in bacterial diagnostics. Applied Microbiology, 6(9), Article 107. https://doi.org/10.3390/applmicrobiol6090107
Publisher Citation
Carpenter, R. E., Krouse, A., & Vincent, A. (2026). From colonies to copies: Integrating PCR, culture, and AST in bacterial diagnostics. Applied Microbiology, 6(9), Article 107. https://doi.org/10.3390/applmicrobiol6090107