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. 2018 Aug 2;8:11606. doi: 10.1038/s41598-018-29707-w

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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The workflow for selection and validation of RNA markers for phenotypic measurements of antibiotic susceptibility and resistance. Susceptible and resistant isolates of Neisseria gonorrhoeae are exposed to antibiotics (ABX) for 5, 10, and 15 min. Samples are collected for RNA sequencing at time zero and every 5 min thereafter. Genes demonstrating fold changes in expression (control:treated ratio (C:T ratio)) greater than the threshold of significance (gray line) are identified as differentially expressed (blue: downregulated and orange: upregulated). Candidate markers are selected from the pool of differentially expressed genes and validated by digital PCR.