ArticleSystematic biology2018
Modeling the Growth and Decline of Pathogen Effective Population Size Provides Insight into Epidemic Dynamics and Drivers of Antimicrobial Resistance.
Article in Systematic biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
76 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Key questions for modelling COVID-19 exit strategies.Proceedings. Biological sciences · 2020Pooled it
- Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region.Genome research · 2020Trial
- AcceleratingProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Convergent evolution of ST2 and ST164 mediates dissemination of the blaAnnals of clinical microbiology and antimicrobials · 2026Article
- Genomic epidemiology ofMicrobial genomics · 2026Article
- DiagnoDating: diagnostics for dated phylogenies in microbial population genetics.Molecular biology and evolution · 2026Article
- Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss.Nature ecology & evolution · 2026Article
- Five-decade global expansion of Staphylococcus argenteus ST2250 shapes antimicrobial resistance dynamics.npj antimicrobials and resistance · 2026Article
- Global emergence and evolution ofmSystems · 2026Article
- Quantifying the real-world impact of antibiotic use and genetic determinants of resistance on gonococcal dynamics.Nature microbiology · 2026Article
- Genomic insights into the rapid rise ofVirulence · 2025Article
- Emergence and regional evolution of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae ST11 in China.BMC genomics · 2025Article
- Lineage-specific evolution and resistance-virulence divergence inAntimicrobial agents and chemotherapy · 2025Article
- MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions.PLoS computational biology · 2025Article
- Genome analysis ofMicrobial genomics · 2025Article
- How does date-rounding affect phylodynamic inference for public health?PLoS computational biology · 2025Article
- Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii.Nature communications · 2025Article
- Genomic survey of multidrug resistant Salmonella enterica serovar Minnesota clones in chicken products.npj antimicrobials and resistance · 2025Article
- Methicillin-resistantFrontiers in microbiology · 2025Article
- The dissemination of multidrug-resistant and hypervirulentEmerging microbes & infections · 2024Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Nonparametric population genetic modeling provides a simple and flexible approach for studying demographic history and epidemic dynamics using pathogen sequence data. Existing Bayesian approaches are premised on stochastic processes with stationary increments which may provide an unrealistic prior for epidemic histories which feature extended period of exponential growth or decline. We show that nonparametric models defined in terms of the growth rate of the effective population size can provide a more realistic prior for epidemic history. We propose a nonparametric autoregressive model on the growth rate as a prior for effective population size, which corresponds to the dynamics expected under many epidemic situations. We demonstrate the use of this model within a Bayesian phylodynamic inference framework. Our method correctly reconstructs trends of epidemic growth and decline from pathogen genealogies even when genealogical data are sparse and conventional skyline estimators erroneously predict stable population size. We also propose a regression approach for relating growth rates of pathogen effective population size and time-varying variables that may impact the replicative fitness of a pathogen. The model is applied to real data from rabies virus and Staphylococcus aureus epidemics. We find a close correspondence between the estimated growth rates of a lineage of methicillin-resistant S. aureus and population-level prescription rates of $\beta$-lactam antibiotics. The new models are implemented in an open source R package called skygrowth which is available at https://github.com/mrc-ide/skygrowth.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.