Conjugative plasmid transfer is limited by prophages but can be overcome by high conjugation rates

Phage predation accelerates the spread of plasmid-encoded antibiotic resistance

Phage predation is generally assumed to reduce microbial proliferation while not contributing to the spread of antibiotic resistance. However, this assumption does not consider the effect of phage predation on the spatial organization of different microbial populations. Here, we show that phage predation can increase the spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth by reshaping spatial organization. Using two strains of the bacterium Escherichia coli, we demonstrate that phage predation slows the spatial segregation of the strains during growth. This increases the number of cell-cell contacts and the extent of conjugation-mediated plasmid transfer between them. The underlying mechanism is that phage predation shifts the location of fastest growth from the biomass periphery to the interior where cells are densely packed and aligned closer to parallel with each other. This creates straighter interfaces between the strains that are less likely to merge together during growth, consequently slowing the spatial segregation of the strains and enhancing plasmid transfer between them. Our results have implications for the design and application of phage therapy and reveal a mechanism for how microbial functions that are deleterious to human and environmental health can proliferate in the absence of positive selection.

Dynamics of antibiotic resistance genes in plasmids and bacteriophages

This brief review explores the intricate interplay between bacteriophages and plasmids in the context of antibiotic resistance gene (ARG) dissemination. Originating from studies in the late 1950s, the review traces the evolution of knowledge regarding extrachromosomal factors facilitating horizontal gene transfer and adaptation in bacteria. Analyzing the gene repertoires of plasmids and bacteriophages, the study highlights their contributions to bacterial evolution and adaptation. While plasmids encode essential and accessory genes influencing host characteristics, bacteriophages carry auxiliary metabolic genes (AMGs) that augment host metabolism. The debate on phages carrying ARGs is explored through a critical evaluation of various studies, revealing contrasting findings from researchers. Additionally, the review addresses the interplay between prophages and plasmids, underlining their similarities and divergences. Based on the available literature evidence, we conclude that plasmids generally encode ARGs while bacteriophages typically do not contain ARGs. But extra-chromosomaly present prophages with plasmid characteristics can encode and disseminate ARGs.

My host's enemy is my enemy: plasmids carrying CRISPR-Cas as a defence against phages

Bacteria are infected by mobile genetic elements like plasmids and virulent phages, and those infections significantly impact bacterial ecology and evolution. Recent discoveries reveal that some plasmids carry anti-phage immune systems like CRISPR-Cas, suggesting that plasmids may participate in the coevolutionary arms race between virulent phages and bacteria. Intuitively, this seems reasonable as virulent phages kill the plasmid's obligate host. However, the efficiency of CRISPR-Cas systems carried by plasmids can be expected to be lower than those carried by the chromosome due to continuous segregation loss, creating susceptible cells for phage amplification. To evaluate the anti-phage protection efficiency of CRISPR-Cas on plasmids, we develop a stochastic model describing the dynamics of a virulent phage infection against which a conjugative plasmid defends using CRISPR-Cas. We show that CRISPR-Cas on plasmids provides robust protection, except in limited parameter sets. In these cases, high segregation loss favours phage outbreaks by generating a population of defenceless cells on which the phage can evolve and escape CRISPR-Cas immunity. We show that the phage's ability to exploit segregation loss depends strongly on the evolvability of both CRISPR-Cas and the phage itself.

The social lives of viruses and other mobile genetic elements: a commentary on Leeks et al. 2023

Illustration of life-histories of phages and plasmids through horizontal and vertical transmission (see Figure 1 for more information).

One Earth: The Equilibrium between the Human and the Bacterial Worlds

Misuse and abuse of antibiotics on humans, cattle, and crops have led to the selection of multi-resistant pathogenic bacteria, the most feared 'superbugs'. Infections caused by superbugs are progressively difficult to treat, with a subsequent increase in lethality: the toll on human lives is predicted to reach 10 million by 2050. Here we review three concepts linked to the growing resistance to antibiotics, namely (i) the Resistome, which refers to the collection of bacterial genes that confer resistance to antibiotics, (ii) the Mobilome, which includes all the mobile genetic elements that participate in the spreading of antibiotic resistance among bacteria by horizontal gene transfer processes, and (iii) the Nichome, which refers to the set of genes that are expressed when bacteria try to colonize new niches. We also discuss the strategies that can be used to tackle bacterial infections and propose an entente cordiale with the bacterial world so that instead of war and destruction of the 'fierce enemy' we can achieve a peaceful coexistence (the One Earth concept) between the human and the bacterial worlds. This, in turn, will contribute to microbial biodiversity, which is crucial in a globally changing climate due to anthropogenic activities.

A mathematician's guide to plasmids: an introduction to plasmid biology for modellers

Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.

Conjugation's Toolkit: the Roles of Nonstructural Proteins in Bacterial Sex

Bacterial conjugation, a form of horizontal gene transfer, relies on a type 4 secretion system (T4SS) and a set of nonstructural genes that are closely linked. These nonstructural genes aid in the mobile lifestyle of conjugative elements but are not part of the T4SS apparatus for conjugative transfer, such as the membrane pore and relaxosome, or the plasmid maintenance and replication machineries. While these nonstructural genes are not essential for conjugation, they assist in core conjugative functions and mitigate the cellular burden on the host. This review compiles and categorizes known functions of nonstructural genes by the stage of conjugation they modulate: dormancy, transfer, and new host establishment. Themes include establishing a commensalistic relationship with the host, manipulating the host for efficient T4SS assembly and function and assisting in conjugative evasion of recipient cell immune functions. These genes, taken in a broad ecological context, play important roles in ensuring proper propagation of the conjugation system in a natural environment.

A multifunctional Fe2O3@MoS2@SDS Z-scheme nanocomposite: NIR enhanced bacterial inactivation, degradation antibiotics and inhibiting ARGs dissemination

To fight the flourishment of drug-resistant bacteria caused by antibiotics and the dissemination of antibiotic resistance genes (ARGs), it is of great urgency to develop multifunctional non-antibiotic agents with residual antibiotics elimination, and ARGs dissemination inhibition properties. Herein, sodium dodecyl sulfate (SDS) was modified onto the surface of Fe2O3 @MoS2 by ultrasonic method to obtain the Z-scheme, multifunctional Fe2O3 @MoS2 @SDS nanocomposites. The Fe2O3 @MoS2 @SDS (weight ratio of Fe2O3 @MoS2 and SDS was 1:1) was selected as the optimal agent. Under NIR irradiation, the Fe2O3 @MoS2 @SDS had a photothermal conversion efficiency of 45.96%, and could generate plenty of reactive oxygen species (ROS) at the same time. Under the synergy of photothermal and photodynamic, the antibacterial efficiency of Fe2O3 @MoS2 @SDS to E. coli, MRSA and P. aeruginosa could reach 99.95%, 99.97% and 99.58%, respectively, indicating excellent photothermal-photodynamic therapy (PPT) effect. The Fe2O3 @MoS2 @SDS also displayed photocatalytic activity in degradation of tetracycline (TC). The degradation rate of TC could reach 92.3% after 2 h of visible light irradiation. The obtained results indicated that a promising Fe2O3 @MoS2 @SDS composite based multifunctional nanoplatform could be constructed for NIR induced bacterial inactivation, antibiotics degradation and ARGs dissemination inhibition.

Ecological dynamics of plasmid transfer and persistence in microbial communities

Plasmids are a major driver of horizontal gene transfer in prokaryotes, allowing the sharing of ecologically important accessory traits between distantly related bacterial taxa. Within microbial communities, interspecies transfer of conjugative plasmids can rapidly drive the generation genomic innovation and diversification. Recent studies are starting to shed light on how the microbial community context, that is, the bacterial diversity together with interspecies interactions that occur within a community, can alter the dynamics of conjugative plasmid transfer and persistence. Here, I summarise the latest research exploring how community ecology can both facilitate and impose barriers to the spread of conjugative plasmids within complex microbial communities. Ultimately, the fate of plasmids within communities is unlikely to be determined by any one individual host, rather it will depend on the interacting factors imposed by the community in which it is embedded.