On modelling environmentally transmitted pathogens

Lanzas, Cristina; Davies, Kale; Erwin, Samantha; Dawson, Daniel E.

doi:10.1098/rsfs.2019.0056

Cited by 25 publications

(18 citation statements)

References 37 publications

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“…Like simulated movement, the disease transmission process occurred probabilistically, in discrete time, and on a spatially explicit landscape. However, a mean field approximation of the transmission process can be conceptualized as [37]:…”

Section: Plos Computational Biologymentioning

confidence: 99%

A mechanistic, stigmergy model of territory formation in solitary animals: Territorial behavior can dampen disease prevalence but increase persistence

2020

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Although movement ecology has leveraged models of home range formation to explore the effects of spatial heterogeneity and social cues on movement behavior, disease ecology has yet to integrate these potential drivers and mechanisms of contact behavior into a generalizable disease modeling framework. Here we ask how dynamic territory formation and maintenance might contribute to disease dynamics in a territorial, solitary predator for an indirectly transmitted pathogen. We developed a mechanistic individual-based model where stigmergy-the deposition of signals into the environment (e.g., scent marking, scraping)dictates local movement choices and long-term territory formation, but also the risk of pathogen transmission. Based on a variable importance analysis, the length of the infectious period was the single most important variable in predicting outbreak success, maximum prevalence, and outbreak duration. Host density and rate of pathogen decay were also key predictors. We found that territoriality best reduced maximum prevalence in conditions where we would otherwise expect outbreaks to be most successful: slower recovery rates (i.e., longer infectious periods) and higher conspecific densities. However, for slower pathogen decay rates, stigmergy-driven movement increased outbreak durations relative to random movement simulations. Our findings therefore support a limited version of the "territoriality benefits" hypothesis-where reduced home range overlap leads to reduced opportunities for pathogen transmission, but with the caveat that reduction in outbreak severity may increase the likelihood of pathogen persistence. For longer infectious periods and higher host densities, key trade-offs emerged between the strength of pathogen load, the strength of the stigmergy cue, and the rate at which those two quantities decayed; this finding raises interesting questions about the evolutionary nature of these competing processes and the role of possible feedbacks between parasitism and territoriality. This work also highlights the importance of considering social cues as part of the movement landscape in order to better understand the consequences of individual behaviors on population level outcomes.

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Section: Plos Computational Biologymentioning

confidence: 99%

A mechanistic, stigmergy model of territory formation in solitary animals: Territorial behavior can dampen disease prevalence but increase persistence

2020

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“…Finally, Lanzas et al [43] brings attention to the challenges of explicitly modelling environmental transmission. The authors provide a conceptual framework to organize pathogens based on the role that non-host habitats play in the pathogen life cycle.…”

Section: Enteric Diseasesmentioning

confidence: 99%

“…To inform these complex models, new methods of data collection and analysis [31,41] are needed to explain how different scales are connected and modelled. Modelling frameworks [35,43] as well as looking at both top-down and bottom-up approaches to multiscale modelling of disease systems are helpful in harmonizing findings from the expanding literature within these different disease systems. Beyond these methods for piecing together models across scales, new analytical techniques hold promise for integrating models and data across scales.…”

Section: Analytical Approaches To Modelling Multiscale Systemsmentioning

confidence: 99%

“…Enteric disease research tends to emphasize the within-host [38] as well as explicit modelling of processes external to the host, which we could classify as modelling the environment [39,40]. While emphasis on these particular scales may be appropriate to these disease systems, new empirical methods of linking scales [31,41] as well as modelling frameworks [35,43] and analytical methods [45,47] may allow researchers to explore connections among the full system of scales in physical size, population size, time and environmental context (figure 1) to determine whether the scales that have been emphasized are truly the drivers of dynamics for these diseases.…”

Section: Analytical Approaches To Modelling Multiscale Systemsmentioning

confidence: 99%

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Multi-scale dynamics of infectious diseases

et al. 2019

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“…Once in the non-host environment, some pathogens can then re-enter hosts without the need for direct contact between hosts. The ability to persist and/or reproduce within the non-host environment has numerous implications for the transmission of pathogens [1].…”

Section: Introductionmentioning

confidence: 99%

Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen

Dawson

Rasmussen

Peng

et al. 2021

J. R. Soc. Interface.

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Indirect (environmental) and direct (host–host) transmission pathways cannot easily be distinguished when they co-occur in epidemics, particularly when they occur on similar time scales. Phylodynamic reconstruction is a potential approach to this problem that combines epidemiological information (temporal, spatial information) with pathogen whole-genome sequencing data to infer transmission trees of epidemics. However, factors such as differences in mutation and transmission rates between host and non-host environments may obscure phylogenetic inference from these methods. In this study, we used a network-based transmission model that explicitly models pathogen evolution to simulate epidemics with both direct and indirect transmission. Epidemics were simulated according to factorial combinations of direct/indirect transmission proportions, host mutation rates and conditions of environmental pathogen growth. Transmission trees were then reconstructed using the phylodynamic approach SCOTTI (structured coalescent transmission tree inference) and evaluated. We found that although insufficient diversity sets a lower bound on when accurate phylodynamic inferences can be made, transmission routes and assumed pathogen lifestyle affected pathogen population structure and subsequently influenced both reconstruction success and the likelihood of direct versus indirect pathways being reconstructed. We conclude that prior knowledge of the likely ecology and population structure of pathogens in host and non-host environments is critical to fully using phylodynamic techniques.

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On modelling environmentally transmitted pathogens

Cited by 25 publications

References 37 publications

A mechanistic, stigmergy model of territory formation in solitary animals: Territorial behavior can dampen disease prevalence but increase persistence

A mechanistic, stigmergy model of territory formation in solitary animals: Territorial behavior can dampen disease prevalence but increase persistence

Multi-scale dynamics of infectious diseases

Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen

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