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Fig. 3 | Genome Medicine

Fig. 3

From: PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks

Fig. 3

Epidemiological timeline of the long-term outbreak. a Phylogenetic tree of core-genome SNV differences (left) with corresponding locations of each variant relative to the first outbreak isolate that was obtained from p40 (right). Non-synonymous and synonymous variants are highlighted in black and gray, respectively. Isolates in subclades sharing three or more variants (shaded areas) are identified by distinct tip symbols at each branch. b PathoSPOT timeline integrating genomic and epidemiological data. Rows correspond to patients, with admission periods in hospital wards shown as horizontal bars, colored as in a. Sequenced isolates are shown as different symbols matching those used in the phylogenetic tree in a. Shaded arcs signify ward-level patient overlap within 24 h. Other positive or negative clinical test results are indicated by gray symbols, with a key shown below. The scale is shown at the top. c Summary of key outbreak events in wards, derived from the epidemiological timeline. See the main text for details. All date information in this figure was recoded to protect health information. An interactive version of this figure is available at https://pathospot.org/?fig=3

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