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. 2019 Jan 24;9:487. doi: 10.1038/s41598-018-37422-9

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© The Author(s) 2019

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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Transcriptome comparison between MDR versus antibiotic-susceptible strains. (A) Seventy-eight genes that satisfied two parameters (fold change >2, FDR < 0.05) were selected among the antibiotic-susceptible (PAO1, Y31) and MDR strains (Y71, Y82, Y89) by the edgeR tool. These genes were lined up next to the heat map. TMM-normalized read counts of samples were converted to log2. After each gene was averaged from five samples, the average was subtracted from the read count of each gene. If the last calculated value was high, it was displayed in the heat map in red; when it was low, it was displayed in blue, as shown in the Color Key (top left). Hierarchical clustering was performed on the basis of genes and samples. (B) 64 genes that exhibited decreased expression (>2-fold) in the MDR strains were used for a functional gene network using STRING. The box drawn with the solid line was the group related to quorum sensing, and box drawn with the dashed line was the group related to the type VI secretion system.