The ecology of plasmid-coded antibiotic resistance: a basic framework for experimental research and modeling

Zwanzig, Martin

doi:10.1016/j.csbj.2020.12.027

Cited by 18 publications

(14 citation statements)

References 127 publications

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“…This suggests that the IncX3 plasmid backbone gene itself has the advantage of mediating the wide spread of bla NDM . The theory of plasmid biology shows that high conjugation efficiency, powerful distribution system, and low fitness cost are three factors to ensure the long-term existence and wide spread of plasmids ( Zwanzig, 2021 ). The T4SS system in the backbone region guarantees the efficiency of plasmid self-conjugation ( Costa et al, 2020 ); the parAB distribution system ensures that progeny plasmids can be assigned to the offspring host, promoting plasmid stability ( Sheng et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

In silico Evolution and Comparative Genomic Analysis of IncX3 Plasmids Isolated From China Over Ten Years

et al. 2021

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IncX3 plasmids are correlated with the dissemination and acquisition of carbapenem resistance in Enterobacteriaceae and have been prevalent in China over the last 10 years. Since the distribution characteristics of IncX3 plasmids across China as well as their evolutionary traits for 10 years remain unclear, here we conducted a retrospective literature review and in silico comparative analysis of IncX3 plasmids in publicly available IncX3 plasmid genomes. IncX3 plasmids distributed in 17 provinces or cities were extracted for analysis, which tend to be specifically associated with hospital-isolated Escherichia coli ST410 from phylogroup A. Although the backbones of IncX3 plasmids have remained highly conservative over the last 10 years, the blaNDM resistance genetic contexts on these plasmids could fall into five subtypes, among which AR_N1_I has been identified in Enterobacter cloacae174 chromosome and AR_N5_I was simultaneously located on IncF and IncA/C plasmids. This suggests that the blaNDM resistance gene environment can spread between different plasmids, between different bacterial genera, or between strains and plasmids, highlighting that it is imperative to adopt more stringent infection control measures targeting IncX3 plasmid spread.

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Section: Discussionmentioning

confidence: 99%

In silico Evolution and Comparative Genomic Analysis of IncX3 Plasmids Isolated From China Over Ten Years

et al. 2021

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“…[92] When computationally feasible, spatially explicit models such as partial differential equations (PDEs) and individual-based models (IBMs) will be helpful to examine the consequences of various model assumptions. [92][93][94]…”

Section: Discussionmentioning

confidence: 99%

Predicting plasmid persistence in microbial communities by coarse‐grained modeling

Wang

Weiss

et al. 2021

BioEssays

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Plasmids are a major type of mobile genetic elements (MGEs) that mediate horizontal gene transfer. The stable maintenance of plasmids plays a critical role in the functions and survival for microbial populations. However, predicting and controlling plasmid persistence and abundance in complex microbial communities remain challenging. Computationally, this challenge arises from the combinatorial explosion associated with the conventional modeling framework. Recently, a plasmid-centric framework (PCF) has been developed to overcome this computational bottleneck. This framework enables the derivation of a simple metric, the persistence potential, to predict plasmid persistence and abundance. Here, we discuss how PCF can be extended to account for plasmid interactions. We also discuss how such model-guided predictions of plasmid fates can benefit from the development of new experimental tools and data-driven computational methods.

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“…Ample evidence for this claim comes from community ecology. In a multihost-multiparasite community, indirect effects cascade across host-parasite interaction networks to affect parasite interactions [40] and the evolution of both hosts and parasites [41]. Moreover, in ecological communities, higherorder interactions are abundant and strongly affect community dynamics [42].…”

Section: Microbe-plasmid Interactions Are Shaped At Multiple Levels O...mentioning

confidence: 99%

Conceptualizing microbe-plasmid communities as complex adaptive systems

Pilosof¹

2023

Preprint

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Plasmids shape microbial communities' diversity, structure, and function. Nevertheless, we lack a mechanistic understanding of how community structure and dynamics emerge from local microbe-plasmid interactions and co-evolution. Addressing this gap is challenging because multiple processes operate simultaneously at multiple levels of organization. For example, immunity operates between a plasmid and a cell, but incompatibility mechanisms regulate coexistence between plasmids. Conceptualizing microbe-plasmid communities as complex adaptive systems is a promising approach to overcoming these challenges. I illustrate how agent-based evolutionary modeling, extended by network analysis, can be used to quantify the relative importance of local processes governing community dynamics. These theoretical developments can advance our understanding of plasmid ecology and evolution, especially when combined with empirical data.

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The ecology of plasmid-coded antibiotic resistance: a basic framework for experimental research and modeling

Cited by 18 publications

References 127 publications

In silico Evolution and Comparative Genomic Analysis of IncX3 Plasmids Isolated From China Over Ten Years

In silico Evolution and Comparative Genomic Analysis of IncX3 Plasmids Isolated From China Over Ten Years

Predicting plasmid persistence in microbial communities by coarse‐grained modeling

Conceptualizing microbe-plasmid communities as complex adaptive systems

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