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. 2022 Dec 30;14:147. doi: 10.1186/s13073-022-01150-7

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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. 1 — Population structure of a complete collection of E. coli clinical isolates for a 1-year period at a US hospital. A cgMLST-based minimum spanning tree of 2075 E. coli isolates. Isolates belonging to the main phylogenetic groups observed in this study are circled and labeled. The dominant STs are shaded in light gray and the proportion of MDR (red) and non-MDR (gray) isolates within specific STs is indicated by pie charts. B Pie charts indicate the prevalence of MDR (red) primary isolates (27%) was similar to the prevalence of MDR isolates in primary isolates predicted to be part of clusters of transmission (35%) (Table 1)