Related Experiment Video
Updated: Nov 2, 2025
09:32
Oral Bacterial Infection and Shedding in Drosophila melanogaster
Published on: May 31, 2018
12.0K
Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric
Daniel Dawson1, David Rasmussen2,3, Xinxia Peng2,4
1Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.
Journal of the Royal Society, Interface
|June 8, 2021
Summary
Distinguishing direct and indirect transmission in epidemics is challenging. Phylodynamic methods can infer transmission routes, but pathogen ecology and population structure critically influence reconstruction accuracy.
Area of Science:
- Epidemiology
- Evolutionary Biology
- Computational Biology
Background:
- Direct (host-to-host) and indirect (environmental) transmission routes often coexist in epidemics, making differentiation difficult.
- Phylodynamic reconstruction, integrating epidemiological and genomic data, offers a method to infer epidemic transmission trees.
- Environmental factors and differing pathogen evolution rates can complicate phylogenetic inference.
Purpose of the Study:
- To evaluate the effectiveness of phylodynamic methods in distinguishing direct and indirect transmission pathways.
- To investigate how pathogen evolution, environmental conditions, and transmission proportions impact phylogenetic inference.
- To assess the influence of pathogen lifestyle on transmission route reconstruction.
Main Methods:
- Simulated epidemics using a network-based transmission model incorporating direct and indirect transmission.
- Varied direct/indirect transmission proportions, host mutation rates, and environmental pathogen growth conditions.
- Reconstructed transmission trees using the phylodynamic tool SCOTTI (structured coalescent transmission tree inference).
Main Results:
- Accurate phylodynamic inference is limited by insufficient pathogen genetic diversity.
- Transmission routes and pathogen lifestyle significantly altered pathogen population structure.
- Reconstruction success and the ability to distinguish direct vs. indirect pathways were influenced by pathogen ecology.
Conclusions:
- Phylodynamic methods are valuable for inferring transmission routes but are sensitive to pathogen characteristics.
- Understanding pathogen ecology and population structure in both host and non-host environments is crucial for accurate phylodynamic analysis.
- Prior ecological knowledge enhances the reliability of phylodynamic inference in complex epidemic scenarios.
Related Concept Videos
01:20Infection
9.5K
When a pathogen enters the body and reproduces, it can cause an infection, damage body cells, and cause illness symptoms that eventually lead to disease. Therefore, its prevention requires breaking the chain of infection.
The chain begins with pathogens: bacteria, viruses, fungi, prions, or parasites such as protozoa helminths. These can be present on the skin as transient or resident flora, or they can be acquired from the environment. Identifying and treating the type of infection and...
The chain begins with pathogens: bacteria, viruses, fungi, prions, or parasites such as protozoa helminths. These can be present on the skin as transient or resident flora, or they can be acquired from the environment. Identifying and treating the type of infection and...
9.5K
01:16Transduction
417
Among the three main modes of HGT—transformation, conjugation, and transduction—transduction is unique in that it is mediated by bacteriophages, or bacterial viruses.Transduction occurs in two ways. Generalized transduction occurs during the lytic cycle of a bacteriophage infection. In this process, bacteriophages infect bacterial cells, replicate within them, and ultimately cause cell lysis, releasing newly assembled virions. Occasionally, random fragments of the bacterial genome...
417
02:39Gene Flow
36.4K
Gene flow is the transfer of genes among populations, resulting from either the dispersal of gametes or from the migration of individuals.
36.4K
02:54Evolutionary Relationships through Genome Comparisons
6.5K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.5K
01:16Viral Replication: Lysogenic Cycle
584
The lysogenic cycle is a crucial viral replication strategy that allows bacteriophages to persist within host cells without immediately destroying them. This process is primarily observed in temperate phages, such as bacteriophage lambda (λ), which infects Escherichia coli. The cycle allows the viral genome to persist across bacterial generations while keeping host cells viable.Integration of the Viral GenomeUpon infection, bacteriophage lambda attaches to the bacterial surface and injects...
584
02:05Gene Evolution - Fast or Slow?
7.6K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.6K