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. 2021 Aug 6;12:4765. doi: 10.1038/s41467-021-25096-3

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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 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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Fig. 4 — a The content of three datasets. Dataset1 contains the chromosomal genomes and plasmids collected from opportunistic pathogen isolates cultured from a tertiary hospital after 02/20/2019. Dataset1 covers a total of 94 taxa (2,347 chromosomal genomes and 5,910 plasmids). Dataset2 contains 116 metagenomes collected after 02/20/2019 from a tertiary hospital. Dataset3 contains all NCBI pathogen genomes submitted in the last 2 years (02/20/2019 to 02/10/2021). Dataset3 covers a total of 362 taxa (42,481 genomes). ARG sequences of the initial set were searched in three testing datasets using the same criteria described before (90% aa similarity over 80% aa hit length). b the percentage of unique ARGs of different Ranks in hospital plasmids. Asterisk of box represent the p value for fisher exact test. n = 16 (No. of unique ARGs). c The mean abundance of ARGs of different Ranks in 116 hospital metagenomes. Quantiles (represented as bars), mean (represented as points), and standard error (represented as error bars) were computed for all ARGs in an ARG Rank. Asterisk of box represent the p value for one way anova test. n = 1393 (No. of unique ARGs detected in hospital metagenomes). Adjustments were made for multiple comparisons. Data are presented as mean values ± SE (error bars), median values (center of box), and 25%, 75% percentiles (bounds of box). The minima and maxima represent the range of the data. d The percentage of unique ARGs that were found in pathogens after 02/20/2019 and were not detected in pathogens before 02/20/2019. Asterisk of box represent the p value for fisher exact test. n = 76 (No. of unique ARGs newly present in pathogens). Adjustments were made for multiple comparisons. The color represents the rank of ARGs (Rank I on WHO list, Rank I not on WHO list, Rank II-IV). ARGs antibiotic resistance genes.