Genome entropy and network centrality contrast exploration and exploitation in evolution of foodborne pathogens
Creative Commons Attribution license..
Modelling evolution of foodborne pathogens is crucial for mitigation and prevention of outbreaks. We apply network-theoretic and information-theoretic methods to trace evolutionary pathways ofSalmonellaTyphimurium in New South Wales, Australia, by studying whole genome sequencing surveillance data over a five-year period which included several outbreaks. The study derives both undirected and directed genotype networks based on genetic proximity, and relates the network's structural property (centrality) to its functional property (prevalence). The centrality-prevalence space derived for the undirected network reveals a salient exploration-exploitation distinction across the pathogens, further quantified by the normalised Shannon entropy and the Fisher information of the corresponding shell genome. This distinction is also analysed by tracing the probability density along evolutionary paths in the centrality-prevalence space. We quantify the evolutionary pathways, and show that pathogens exploring the evolutionary search-space during the considered period begin to exploit their environment (their prevalence increases resulting in outbreaks), but eventually encounter a bottleneck formed by epidemic containment measures.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:20 |
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| Enthalten in: |
Physical biology - 20(2023), 4 vom: 02. Juni |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Chang, Sheryl L [VerfasserIn] |
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| Links: |
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| Themen: |
Entropy |
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| Anmerkungen: |
Date Completed 05.06.2023 Date Revised 13.06.2023 published: Electronic Citation Status MEDLINE |
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| doi: |
10.1088/1478-3975/acd899 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM357272056 |
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| 245 | 1 | 0 | |a Genome entropy and network centrality contrast exploration and exploitation in evolution of foodborne pathogens |
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| 520 | |a Creative Commons Attribution license. | ||
| 520 | |a Modelling evolution of foodborne pathogens is crucial for mitigation and prevention of outbreaks. We apply network-theoretic and information-theoretic methods to trace evolutionary pathways ofSalmonellaTyphimurium in New South Wales, Australia, by studying whole genome sequencing surveillance data over a five-year period which included several outbreaks. The study derives both undirected and directed genotype networks based on genetic proximity, and relates the network's structural property (centrality) to its functional property (prevalence). The centrality-prevalence space derived for the undirected network reveals a salient exploration-exploitation distinction across the pathogens, further quantified by the normalised Shannon entropy and the Fisher information of the corresponding shell genome. This distinction is also analysed by tracing the probability density along evolutionary paths in the centrality-prevalence space. We quantify the evolutionary pathways, and show that pathogens exploring the evolutionary search-space during the considered period begin to exploit their environment (their prevalence increases resulting in outbreaks), but eventually encounter a bottleneck formed by epidemic containment measures | ||
| 650 | 4 | |a Journal Article | |
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| 650 | 4 | |a Fisher information | |
| 650 | 4 | |a Salmonella Typhimurium | |
| 650 | 4 | |a entropy | |
| 650 | 4 | |a evolutionary dynamics | |
| 650 | 4 | |a genotype network | |
| 650 | 4 | |a network centrality | |
| 650 | 4 | |a shell genome | |
| 700 | 1 | |a Suster, Carl J E |e verfasserin |4 aut | |
| 700 | 1 | |a Rockett, Rebecca J |e verfasserin |4 aut | |
| 700 | 1 | |a Svahn, Adam J |e verfasserin |4 aut | |
| 700 | 1 | |a Cliff, Oliver M |e verfasserin |4 aut | |
| 700 | 1 | |a Arnott, Alicia |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Qinning |e verfasserin |4 aut | |
| 700 | 1 | |a Kim, Rady |e verfasserin |4 aut | |
| 700 | 1 | |a Suliman, Basel |e verfasserin |4 aut | |
| 700 | 1 | |a Gall, Mailie |e verfasserin |4 aut | |
| 700 | 1 | |a Sorrell, Tania C |e verfasserin |4 aut | |
| 700 | 1 | |a Sintchenko, Vitali |e verfasserin |4 aut | |
| 700 | 1 | |a Prokopenko, Mikhail |e verfasserin |4 aut | |
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