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. 2022 Dec 2;10:208. doi: 10.1186/s40168-022-01407-8

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© The Author(s) 2022

Open AccessThis 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 4 — Genome-level analysis reveals transmission between hospital and urban environments. A Phylogenetic tree based on the concatenation of 120 conserved prokaryotic marker genes including 383 high- and medium-quality MAGs recovered from the urban environment and 15 high-resolution K. pneumoniae genomes sequenced from hospital-associated infections (ST-11 outbreak). Tree branches are colored according to taxonomy (phylum level). B Zoom-in the monophyletic clade corresponding to family Enterobacteriaceae. Tips are colored according to species and branches are grouped according to sample origin (ST-11 outbreak or environment). K. pneumoniae MAG recovered from sample CPB-17 (bin.7) is highlighted to show its phylogenetic association with K. pneumoniae nosocomial isolates recovered from the outbreak. C Boxplot showing the number of SNPs separating CBP-17_bin.7 from outbreak-associated K. pneumoniae ST-11 genomes or a global collection of non-outbreak K. pneumoniae ST-11 genomes