Harnessing the pangenome for genomic surveillance:Salmonella entericaserotype Typhi as a paradigm Article Swipe
Arancha Peñil-Celis
,
Kaitlin A. Tagg
,
Hattie E. Webb
,
Santiago Redondo
,
Louise Francois Watkins
,
Luis Vielva
,
Chelsey Griffin
,
Justin Y Kim
,
Jason P. Folster
,
M. Pilar Garcillán‐Barcia
,
Fernando de la Cruz
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1101/2023.08.23.554479
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1101/2023.08.23.554479
Public health genomic surveillance systems typically measure genome relatedness and infer molecular epidemiological relationships using chromosomal loci alone – an approximation of vertical evolution, or homology-by-descent. The accessory genome, composed of plasmids and other mobile genetic elements, reflects horizontal gene transfer and serves as an important mechanism of bacterial evolution, enabling rapid adaptation. Measuring homology in the accessory genome – homology-by-admixture – could offer important molecular epidemiological information for public health application. We applied Jaccard Index and a novel genome length distance metric to compute pangenome relatedness for the globally-important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both homology-by-descent and homology-by-admixture in a reticulate network. Jaccard Index Network Analysis revealed structure in the Typhi pangenome that can be harnessed to enhance discriminatory power for surveillance, track antimicrobial resistance, and refine our understanding of homology for outbreak management and prevention. This offers a more intricate, multidimensional framework for understanding pathogen evolution. Significance Statement Bacterial relatedness is often measured and visualized using chromosomal comparison and phylogenetic trees. While valuable, this approach captures only the vertical evolutionary dimension and excludes genetic material acquired or lost through horizontal gene transfer. We present an approach for measuring and visualizing bacterial relatedness using all core and accessory genetic material and discuss the interpretation of resulting reticulate networks of bacterial genomes. In application to Salmonella Typhi, Jaccard Index Network Analysis revealed structure in populations of this pathogen that may be harnessed for public health applications. This approach captures both vertical and horizontal evolutionary dimensions, offering an intricate genetic framework for exploring pathogen evolution.
Related Topics
Concepts
Biology
Horizontal gene transfer
Genome
Salmonella typhi
Genetics
Salmonella enterica
Jaccard index
Bacterial genome size
Homology (biology)
Synteny
Plasmid
Computational biology
Phylogenetic tree
Pathogenicity island
Evolutionary biology
Salmonella
Gene
Artificial intelligence
Bacteria
Escherichia coli
Computer science
Pattern recognition (psychology)
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2023.08.23.554479
- https://www.biorxiv.org/content/biorxiv/early/2023/08/23/2023.08.23.554479.full.pdf
- OA Status
- green
- References
- 63
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4386140830
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4386140830Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1101/2023.08.23.554479Digital Object Identifier
- Title
-
Harnessing the pangenome for genomic surveillance:Salmonella entericaserotype Typhi as a paradigmWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2023Year of publication
- Publication date
-
2023-08-23Full publication date if available
- Authors
-
Arancha Peñil-Celis, Kaitlin A. Tagg, Hattie E. Webb, Santiago Redondo, Louise Francois Watkins, Luis Vielva, Chelsey Griffin, Justin Y Kim, Jason P. Folster, M. Pilar Garcillán‐Barcia, Fernando de la CruzList of authors in order
- Landing page
-
https://doi.org/10.1101/2023.08.23.554479Publisher landing page
- PDF URL
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https://www.biorxiv.org/content/biorxiv/early/2023/08/23/2023.08.23.554479.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
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https://www.biorxiv.org/content/biorxiv/early/2023/08/23/2023.08.23.554479.full.pdfDirect OA link when available
- Concepts
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Biology, Horizontal gene transfer, Genome, Salmonella typhi, Genetics, Salmonella enterica, Jaccard index, Bacterial genome size, Homology (biology), Synteny, Plasmid, Computational biology, Phylogenetic tree, Pathogenicity island, Evolutionary biology, Salmonella, Gene, Artificial intelligence, Bacteria, Escherichia coli, Computer science, Pattern recognition (psychology)Top concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- References (count)
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63Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.enhance | 123 |
| abstract_inverted_index.express | 99 |
| abstract_inverted_index.genetic | 36, 180, 204, 253 |
| abstract_inverted_index.genome, | 29 |
| abstract_inverted_index.genomic | 3 |
| abstract_inverted_index.measure | 7 |
| abstract_inverted_index.present | 190 |
| abstract_inverted_index.systems | 5 |
| abstract_inverted_index.through | 185 |
| abstract_inverted_index.(Typhi), | 96 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.Analysis | 111, 225 |
| abstract_inverted_index.acquired | 182 |
| abstract_inverted_index.approach | 171, 192, 242 |
| abstract_inverted_index.captures | 172, 243 |
| abstract_inverted_index.composed | 30 |
| abstract_inverted_index.distance | 82 |
| abstract_inverted_index.enabling | 51 |
| abstract_inverted_index.enterica | 93 |
| abstract_inverted_index.excludes | 179 |
| abstract_inverted_index.genomes. | 216 |
| abstract_inverted_index.homology | 55, 136 |
| abstract_inverted_index.material | 181, 205 |
| abstract_inverted_index.measured | 159 |
| abstract_inverted_index.network. | 107 |
| abstract_inverted_index.networks | 213 |
| abstract_inverted_index.offering | 250 |
| abstract_inverted_index.outbreak | 138 |
| abstract_inverted_index.pathogen | 91, 151, 232, 257 |
| abstract_inverted_index.plasmids | 32 |
| abstract_inverted_index.reflects | 38 |
| abstract_inverted_index.revealed | 112, 226 |
| abstract_inverted_index.serotype | 94 |
| abstract_inverted_index.transfer | 41 |
| abstract_inverted_index.vertical | 23, 175, 245 |
| abstract_inverted_index.Bacterial | 155 |
| abstract_inverted_index.Measuring | 54 |
| abstract_inverted_index.Statement | 154 |
| abstract_inverted_index.accessory | 28, 58, 203 |
| abstract_inverted_index.bacterial | 49, 197, 215 |
| abstract_inverted_index.dimension | 177 |
| abstract_inverted_index.elements, | 37 |
| abstract_inverted_index.exploring | 256 |
| abstract_inverted_index.framework | 148, 254 |
| abstract_inverted_index.harnessed | 121, 236 |
| abstract_inverted_index.important | 46, 65 |
| abstract_inverted_index.intricate | 252 |
| abstract_inverted_index.measuring | 194 |
| abstract_inverted_index.mechanism | 47 |
| abstract_inverted_index.molecular | 12, 66 |
| abstract_inverted_index.pangenome | 86, 117 |
| abstract_inverted_index.resulting | 211 |
| abstract_inverted_index.structure | 113, 227 |
| abstract_inverted_index.transfer. | 188 |
| abstract_inverted_index.typically | 6 |
| abstract_inverted_index.valuable, | 169 |
| abstract_inverted_index.Salmonella | 92, 220 |
| abstract_inverted_index.comparison | 164 |
| abstract_inverted_index.evolution, | 24, 50 |
| abstract_inverted_index.evolution. | 152, 258 |
| abstract_inverted_index.horizontal | 39, 186, 247 |
| abstract_inverted_index.intricate, | 146 |
| abstract_inverted_index.management | 139 |
| abstract_inverted_index.reticulate | 106, 212 |
| abstract_inverted_index.visualized | 161 |
| abstract_inverted_index.adaptation. | 53 |
| abstract_inverted_index.application | 218 |
| abstract_inverted_index.chromosomal | 16, 163 |
| abstract_inverted_index.dimensions, | 249 |
| abstract_inverted_index.graphically | 98 |
| abstract_inverted_index.information | 68 |
| abstract_inverted_index.populations | 229 |
| abstract_inverted_index.prevention. | 141 |
| abstract_inverted_index.relatedness | 9, 87, 156, 198 |
| abstract_inverted_index.resistance, | 130 |
| abstract_inverted_index.visualizing | 196 |
| abstract_inverted_index.Significance | 153 |
| abstract_inverted_index.application. | 72 |
| abstract_inverted_index.evolutionary | 176, 248 |
| abstract_inverted_index.phylogenetic | 166 |
| abstract_inverted_index.surveillance | 4 |
| abstract_inverted_index.antimicrobial | 129 |
| abstract_inverted_index.applications. | 240 |
| abstract_inverted_index.approximation | 21 |
| abstract_inverted_index.relationships | 14 |
| abstract_inverted_index.surveillance, | 127 |
| abstract_inverted_index.understanding | 134, 150 |
| abstract_inverted_index.discriminatory | 124 |
| abstract_inverted_index.interpretation | 209 |
| abstract_inverted_index.epidemiological | 13, 67 |
| abstract_inverted_index.multidimensional | 147 |
| abstract_inverted_index.globally-important | 90 |
| abstract_inverted_index.homology-by-descent | 101 |
| abstract_inverted_index.homology-by-descent. | 26 |
| abstract_inverted_index.homology-by-admixture | 61, 103 |
| cited_by_percentile_year | |
| corresponding_author_ids | https://openalex.org/A5044677733, https://openalex.org/A5017358738 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 11 |
| corresponding_institution_ids | https://openalex.org/I13134134, https://openalex.org/I4210102893 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/10 |
| sustainable_development_goals[0].score | 0.6499999761581421 |
| sustainable_development_goals[0].display_name | Reduced inequalities |
| citation_normalized_percentile.value | 0.1475194 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |