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. 2021 Dec 9;11:23749. doi: 10.1038/s41598-021-02505-7

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© The Author(s) 2021

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Heatmap of 15 observed clinically relevant PJI-associated pathogens. Samples by group are depicted above the heatmap, with the following colors: orange (aseptic joints), red (infected joints), and green (primary joints). Heatmap of PJI-associated pathogens observed in metatranscriptomic [MT] (a) and metagenomic [MG] (b) synovial fluid samples. Boxes represent CPM-r normalized counts of each pathogen within synovial fluid samples. Stars (*) represent pathogens identified by library preparation and culture-based methods while an X indicates that the pathogen was identified by culture but not sequencing. Infected synovial fluid samples from the MT dataset yielded differential clustering from remaining samples, with only one infected sample (SF-32), plotting distinctly from other infected samples (a). Heatmaps were generated using pheatmap version 1.0.12 (https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf) and ggplot2 version 3.3.5 (https://cran.r-project.org/web/packages/ggplot2/ggplot2.pdf) within R 3.6.1 (https://www.R-project.org/). Parts of the heatmap marked with stars (*) and X were added using Adobe Photoshop version 21 (https://www.adobe.com/products/photoshop).