Rapid and Accurate Antibiotic Susceptibility Determination of tet (X)-Positive E. coli Using RNA Biomarkers

• Published in: Microbiology spectrum Vol. 9; no. 2; p. e0064821
• Main Authors: Zhang, Haijie, Li, Yan, Jiang, Yongjia, Lu, Xiaoyu, Li, Ruichao, Peng, Daxin, Wang, Zhiqiang, Liu, Yuan
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 31.10.2021
• Subjects: Anti-Bacterial Agents - pharmacology; antibiotic resistance; antibiotic susceptibility determination; Antimicrobial Chemotherapy; bacteria; Bacteria - drug effects; Bacteria - genetics; Biomarkers; Escherichia coli - drug effects; Escherichia coli - genetics; Escherichia coli - isolation & purification; Gene Expression Regulation, Bacterial; Humans; Methods and Protocols; Microbial Sensitivity Tests - methods; Plasmids; RNA; tet(X); tigecycline; Tigecycline - pharmacology; Transcriptome; tet(X); bacteria; antibiotic resistance; tigecycline; antibiotic susceptibility determination
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/Spectrum.00648-21

The emergence and prevalence of novel plasmid-mediated tigecycline resistance genes, namely, (X) and their variants, pose a serious threat to public health worldwide. Rapid and accurate antibiotic susceptibility testing (AST) that can simultaneously detect the genotype and phenotype of (X)-positive bacteria may contribute to the deployment of an effective antibiotic arsenal, mortality reduction, and a decrease in the use of broad-spectrum antimicrobial agents. However, current bacterial growth-based AST methods, such as broth microdilution, are time consuming and delay the prompt treatment of infectious diseases. Here, we developed a rapid RNA-based AST (RBAST) assay to effectively distinguish (X)-positive and -negative strains. RBAST works by detecting specific mRNA expression signatures in bacteria after short-term tigecycline exposure. As a proof of concept, a panel of clinical isolates was characterized successfully by using the RBAST method, with a 3-h assay time and 87.9% accuracy (95% confidence interval [CI], 71.8% to 96.6%). Altogether, our findings suggest that RNA signatures upon antibiotic exposure are promising biomarkers for the development of rapid AST, which could inform early antibiotic choices. Infections caused by multidrug-resistant (MDR) Gram-negative pathogens are an increasing threat to global health. Tigecycline is one of the last-resort antibiotics for the treatment of these complicated infections; however, the emergence of plasmid-encoded tigecycline resistance genes, namely, (X), severely diminishes its clinical efficacy. Currently, there is a lack of rapid and accurate antibiotic susceptibility testing (AST) for the detection of (X)-positive bacteria. In this study, we developed a rapid and robust RNA-based antibiotic susceptibility determination (RBAST) assay to effectively distinguish (X)-negative and -positive strains using specific RNA biomarkers in bacteria after tigecycline exposure. Using this RBAST method, we successfully characterized a set of clinical strains in 3 h. Our data indicate that the RBAST assay is useful for identifying (X)-positive Escherichia coli.