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Characteristics of the 1,728 clinical isolates. A A histogram showing the number of pairwise <t>SNP</t> differences. B A histogram showing the number of isolates that carry each of the 6,976 pangenome genes. C Geography of the phylogenetic neighborhood of the clinical clade. The SNP-based maximum <t>likelihood</t> <t>phylogeny</t> contains all environmental isolates identified in the NCBI Pathogen Detection database within 1000 cgMLST alleles of the clinical clade. Only select bootstrap values that highlight the separation between the clinical and environmental isolates are shown for clarity. The clinical clade (blue), which is only represented by ten isolates here, is nested within a larger clade (magenta) of ten isolates collected from California and one isolate from Washington, collected between 2010 and 2017. The sister clade (orange) contains isolates from California, New Mexico, and Mexico collected between 2014 and 2020. The phylogeny was inferred using GARLI (with 1,000 bootstraps) with the SNP matrix generated by the CFSAN SNP Pipeline
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Characteristics of the 1,728 clinical isolates. A A histogram showing the number of pairwise <t>SNP</t> differences. B A histogram showing the number of isolates that carry each of the 6,976 pangenome genes. C Geography of the phylogenetic neighborhood of the clinical clade. The SNP-based maximum <t>likelihood</t> <t>phylogeny</t> contains all environmental isolates identified in the NCBI Pathogen Detection database within 1000 cgMLST alleles of the clinical clade. Only select bootstrap values that highlight the separation between the clinical and environmental isolates are shown for clarity. The clinical clade (blue), which is only represented by ten isolates here, is nested within a larger clade (magenta) of ten isolates collected from California and one isolate from Washington, collected between 2010 and 2017. The sister clade (orange) contains isolates from California, New Mexico, and Mexico collected between 2014 and 2020. The phylogeny was inferred using GARLI (with 1,000 bootstraps) with the SNP matrix generated by the CFSAN SNP Pipeline
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Characteristics of the 1,728 clinical isolates. A A histogram showing the number of pairwise <t>SNP</t> differences. B A histogram showing the number of isolates that carry each of the 6,976 pangenome genes. C Geography of the phylogenetic neighborhood of the clinical clade. The SNP-based maximum <t>likelihood</t> <t>phylogeny</t> contains all environmental isolates identified in the NCBI Pathogen Detection database within 1000 cgMLST alleles of the clinical clade. Only select bootstrap values that highlight the separation between the clinical and environmental isolates are shown for clarity. The clinical clade (blue), which is only represented by ten isolates here, is nested within a larger clade (magenta) of ten isolates collected from California and one isolate from Washington, collected between 2010 and 2017. The sister clade (orange) contains isolates from California, New Mexico, and Mexico collected between 2014 and 2020. The phylogeny was inferred using GARLI (with 1,000 bootstraps) with the SNP matrix generated by the CFSAN SNP Pipeline
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Characteristics of the 1,728 clinical isolates. A A histogram showing the number of pairwise <t>SNP</t> differences. B A histogram showing the number of isolates that carry each of the 6,976 pangenome genes. C Geography of the phylogenetic neighborhood of the clinical clade. The SNP-based maximum <t>likelihood</t> <t>phylogeny</t> contains all environmental isolates identified in the NCBI Pathogen Detection database within 1000 cgMLST alleles of the clinical clade. Only select bootstrap values that highlight the separation between the clinical and environmental isolates are shown for clarity. The clinical clade (blue), which is only represented by ten isolates here, is nested within a larger clade (magenta) of ten isolates collected from California and one isolate from Washington, collected between 2010 and 2017. The sister clade (orange) contains isolates from California, New Mexico, and Mexico collected between 2014 and 2020. The phylogeny was inferred using GARLI (with 1,000 bootstraps) with the SNP matrix generated by the CFSAN SNP Pipeline
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Characteristics of the 1,728 clinical isolates. A A histogram showing the number of pairwise <t>SNP</t> differences. B A histogram showing the number of isolates that carry each of the 6,976 pangenome genes. C Geography of the phylogenetic neighborhood of the clinical clade. The SNP-based maximum <t>likelihood</t> <t>phylogeny</t> contains all environmental isolates identified in the NCBI Pathogen Detection database within 1000 cgMLST alleles of the clinical clade. Only select bootstrap values that highlight the separation between the clinical and environmental isolates are shown for clarity. The clinical clade (blue), which is only represented by ten isolates here, is nested within a larger clade (magenta) of ten isolates collected from California and one isolate from Washington, collected between 2010 and 2017. The sister clade (orange) contains isolates from California, New Mexico, and Mexico collected between 2014 and 2020. The phylogeny was inferred using GARLI (with 1,000 bootstraps) with the SNP matrix generated by the CFSAN SNP Pipeline
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Characteristics of the 1,728 clinical isolates. A A histogram showing the number of pairwise <t>SNP</t> differences. B A histogram showing the number of isolates that carry each of the 6,976 pangenome genes. C Geography of the phylogenetic neighborhood of the clinical clade. The SNP-based maximum <t>likelihood</t> <t>phylogeny</t> contains all environmental isolates identified in the NCBI Pathogen Detection database within 1000 cgMLST alleles of the clinical clade. Only select bootstrap values that highlight the separation between the clinical and environmental isolates are shown for clarity. The clinical clade (blue), which is only represented by ten isolates here, is nested within a larger clade (magenta) of ten isolates collected from California and one isolate from Washington, collected between 2010 and 2017. The sister clade (orange) contains isolates from California, New Mexico, and Mexico collected between 2014 and 2020. The phylogeny was inferred using GARLI (with 1,000 bootstraps) with the SNP matrix generated by the CFSAN SNP Pipeline
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Characteristics of the 1,728 clinical isolates. A A histogram showing the number of pairwise SNP differences. B A histogram showing the number of isolates that carry each of the 6,976 pangenome genes. C Geography of the phylogenetic neighborhood of the clinical clade. The SNP-based maximum likelihood phylogeny contains all environmental isolates identified in the NCBI Pathogen Detection database within 1000 cgMLST alleles of the clinical clade. Only select bootstrap values that highlight the separation between the clinical and environmental isolates are shown for clarity. The clinical clade (blue), which is only represented by ten isolates here, is nested within a larger clade (magenta) of ten isolates collected from California and one isolate from Washington, collected between 2010 and 2017. The sister clade (orange) contains isolates from California, New Mexico, and Mexico collected between 2014 and 2020. The phylogeny was inferred using GARLI (with 1,000 bootstraps) with the SNP matrix generated by the CFSAN SNP Pipeline

Journal: BMC Genomics

Article Title: Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation

doi: 10.1186/s12864-023-09245-0

Figure Lengend Snippet: Characteristics of the 1,728 clinical isolates. A A histogram showing the number of pairwise SNP differences. B A histogram showing the number of isolates that carry each of the 6,976 pangenome genes. C Geography of the phylogenetic neighborhood of the clinical clade. The SNP-based maximum likelihood phylogeny contains all environmental isolates identified in the NCBI Pathogen Detection database within 1000 cgMLST alleles of the clinical clade. Only select bootstrap values that highlight the separation between the clinical and environmental isolates are shown for clarity. The clinical clade (blue), which is only represented by ten isolates here, is nested within a larger clade (magenta) of ten isolates collected from California and one isolate from Washington, collected between 2010 and 2017. The sister clade (orange) contains isolates from California, New Mexico, and Mexico collected between 2014 and 2020. The phylogeny was inferred using GARLI (with 1,000 bootstraps) with the SNP matrix generated by the CFSAN SNP Pipeline

Article Snippet: The phylogeny was inferred using GARLI (with 1,000 bootstraps) with the SNP matrix generated by the CFSAN SNP Pipeline To assess if the clinical clade was associated with a geographical location, the previous SNP analysis was extended to include all closely related (within 1,000 cgMLST alleles of the clinical isolates) environmental isolates from the National Center for Biotechnology Information (NCBI) Pathogen Detection database (Fig. C).

Techniques: Generated