Biology subjects

Top, E. M.

Publications and source records attributed to Top, E. M..

16 recordsLinked to original sources

bioRxiv2026

Horizontal gene transfer by plasmids relaxes the evolutionary constraints of its own tradeoff

Horizontal gene transfer (HGT) is a defining feature of plasmid biology, enabling plasmids to spread between bacterial cells and driving the global dissemination of antibiotic resistance and other adaptive traits. HGT and vertical gene transfer (VGT) have long been assumed to be subject to an evolutionary tradeoff, where improvements in one come at the expense of the other. Yet whether this tradeoff reliably constrains plasmid evolution remains unclear. Through the first cross-literature synthesis examining both transmission traits across 16 studies and 245 plasmid-host pairs, we find mixed empirical evidence: patterns consistent with a tradeoff alongside outcomes that a strict tradeoff should make impossible. We propose that this contradiction is resolved by recognizing that a tradeoff is ensured only when plasmid-host pairs are well-adapted to one another. Because HGT introduces plasmids into novel hosts where this adaptation is disrupted, it systematically creates the very conditions under which near-term evolution need not be bound by a tradeoff. We support this framework empirically by documenting the first mutation that simultaneously improves both transmission modes, arising from a non-coevolved plasmid-host pair. These findings reveal a fundamental irony: the defining feature of plasmid transmission is the very mechanism that relaxes the evolutionary constraints of its own tradeoff.

evolutionary biology↗

bioRxiv2026

Molecular pet or parasite? Exploring selection for vertical and horizontal plasmid transfer

Understanding the environmental conditions that drive selection for increased horizontal plasmid transfer is crucial for predicting the spread of plasmid-encoded antibiotic resistance. In natural systems, plasmids exhibit diverse lifestyles, ranging from "host-centric" strategies, which favor vertical gene transfer (VGT) from mother to daughter cell at the expense of horizontal mobility, to "parasitic" strategies, which favor horizontal gene transfer (HGT) by conjugation at the expense of host fitness. However, laboratory evolution experiments are biased towards host-centric evolution, highlighting a gap in our ability to consistently select for horizontal mobility. To understand this experimental bias, we developed a mathematical model to explore the invasion of pleiotropic transfer mutations. Using local linear stability analysis, we derived an invasion criterion establishing that, for a given pleiotropic cost, the availability of plasmid-free cells determines whether increased transfer is selected. We expanded this model to better represent our previous evolution experiment, in which selection for a host-centric mutant occurred despite the addition of plasmid-free cells and periodic selection for transconjugants. We found that standard batch culture protocols inherently impose strong selective pressure on VGT, heavily limiting the laboratory observation of increases in HGT. We experimentally and theoretically demonstrated that a simple protocol modification--minimizing excess growth by eliminating batch culture passages--effectively tips selection towards HGT. Finally, we performed a parameter sweep to predict the invasion success of hypothetical mutants across HGT-VGT phenotypic space. Our predictive framework can be used to further explore the evolution of plasmid transfer under conditions more representative of natural environments where medically and environmentally relevant plasmids evolve.

microbiology↗

bioRxiv2026

Using Hi-C and target capture to monitor plasmid transfer in the barley rhizosphere

Emergence of multi-drug resistant (MDR) pathogens is facilitated by the mobilization of resistance genes from bacteria in animal and environmental habitats, a process often mediated by plasmids. While fertilization of agricultural soils with manure is hypothesized to serve as a pathway for transferring antimicrobial resistance plasmids to soil and crop bacteria, evidence is limited. In this study, we aimed to determine whether MDR-plasmids from manure transfer in soil, leading to the formation of long-term agricultural resistance reservoirs. To this end, we introduced a known MDR plasmid to agricultural soil where barley was subsequently grown and monitored spread of the plasmid over the course of a growing season (up to 190 days). Our experimental design mimicked conventional agricultural practices at a microcosm scale. A digital droplet PCR approach indicated plasmid transfer in the rhizosphere, which was confirmed by a targeted Hi-C method (termed Hi-C+). This demonstrated transfer of the plasmid to soil bacteria 10 days after barley planting but was not observed afterwards. The new plasmid hosts could not be identified, as plasmid-associated host Hi-C reads were absent from existing databases. This implies these hosts were rare and likely unculturable members of the soil microbiome. Our findings demonstrate that plasmid transfer from manure to soil can occur under conditions reflecting those found in agricultural settings. Furthermore, rare and uncharacterized members of the soil microbiomes may participate in acquiring MDR plasmids from manure bacteria, raising important questions about their role in spreading resistance plasmids.

microbiology↗

bioRxiv2025

Not So Mosaic After All? The Core Genomes of IncP-1 Plasmids Evolve Predominantly Through Vertical Trasmission

Broad-host-range plasmids of the incompatibility group IncP-1 play an important role in bacterial evolution by disseminating genes between diverse bacteria. This includes the notable spread of antibiotic resistance genes to bacterial pathogens that increasingly threaten human health. A better understanding of the evolution of genetic elements like IncP-1 plasmids that underwrite bacterial adaptation is required to counter this threat. Here we examined the evolutionary history of IncP-1 plasmids by utilizing the large increase in published genomes and advancing techniques for lineage-based detection of microbial recombination. We specifically tested whether IncP-1 backbone genes evolve primarily (1) through vertical transmission, or (2) horizontally through homologous recombination between distinct plasmids. Our key finding is the IncP-1 plasmid backbone evolves predominantly through vertical transmission, which was supported by a nucleotide-level mapping of backbone recombination. We also showed via a phylogeny of 187 IncP-1 plasmids that established subgroup categories are well-supported. Finally, we examined factors that are potentially associated with IncP-1 subgroup diversification, including a gene related to plasmid-host adaptation and accessory genes like antibiotic and resistance metals. While some IncP-1 subgroups do correlate with certain categories of accessory genes, it remains unknown if these are causes or consequences of subgroup diversification.

evolutionary biology↗

bioRxiv2024

Comparative genomic analysis identifies potential adaptive variation and virulence factors in Mycoplasma ovipneumoniae

Mycoplasma ovipneumoniae is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared M. ovipneumoniae genomes for 99 samples from six countries (Australia, Bosnia and Herzegovina, Brazil, China, France, USA) and four host species (domestic sheep, domestic goats, bighorn sheep, caribou). Core genome sequences of M. ovipneumoniae assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4%) of accessory genes (i.e., genes found only in a subset of assemblies) compared to core genes (i.e., genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three M. ovipneumoniae genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall our results provide evidence that adaptation of M. ovipneumoniae has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways. The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species. Data SummaryRaw sequence data and genome assemblies generated for this study have been deposited with the National Center for Biotechnology Information (NCBI) under BioProject number PRJNA1070810. Assemblies are also currently available for download through Dryad with the following link: https://datadryad.org/stash/share/aNet7o-xag3PTjJ0_A_BDoOPUpHHshArGW1eJMfLYl4 NCBI accession numbers and associated metadata for each assembly are available in the Supplemental Materials. DNA sequences extracted from these assemblies for four genetic markers (gyrB, rpoB, 16S, IGS) are available in the Supplemental Materials. Analysis code is available at https://github.com/kimandrews/Movi and an interactive phylogeny is available at https://nextstrain.org/community/narratives/kimandrews/Movi Impact statementMycoplasma ovipneumoniae causes respiratory disease in wild and domestic sheep and goats around the world, resulting in economic losses for the domestic sheep industry and severe population declines for wild species. Disease outcomes vary widely within and between host species, and this variation could be influenced by genomic differences across bacterial strains. We compared M. ovipneumoniae genomes from six countries and four host species and found species-level divergence for strains from domestic goats versus domestic sheep, indicating separate evolutionary origins in these two host species. All wildlife strains fell within these two groups, providing evidence that these strains originated by transmission from domestic populations. We identified genes potentially involved in adaptation to hosts, which could be responsible for differences in disease outcomes across bacterial strains and host species. Many of these genes had functions related to carbon metabolism, a potential virulence factor for Mycoplasmas.

evolutionary biology↗

bioRxiv2024

Evolution of a Plasmid Regulatory Circuit Ameliorates Plasmid Fitness Cost

Plasmids play a major role in rapid adaptation of bacteria by facilitating horizontal transfer of diverse genes, most notably those conferring antibiotic resistance. While most plasmids that replicate in a broad range of bacteria also persist well in diverse hosts, there are exceptions that are poorly understood. We investigated why a broad-host range plasmid, pBP136, originally found in clinical Bordetella pertussis isolates, quickly became extinct in laboratory Escherichia coli populations. Through experimental evolution we found that inactivation of a previously uncharacterized plasmid gene, upf31, drastically improved plasmid maintenance in E. coli. This gene inactivation resulted in decreased transcription of the global plasmid regulators (korA, korB, and korC) and numerous genes in their regulons. It also caused transcriptional changes in many chromosomal genes primarily related to metabolism. In silico analyses suggested that the change in plasmid transcriptome may be initiated by Upf31 interacting with the plasmid regulator KorB. Expression of upf31 in trans negatively affected persistence of pBP136{Delta}upf31 as well as the closely related archetypal IncP-1{beta} plasmid R751, which is stable in E. coli and natively encodes a truncated upf31 allele. Our results demonstrate that while the upf31 allele in pBP136 might advantageously modulate gene expression in its original host, B. pertussis, it has harmful effects in E. coli. Thus, evolution of a single plasmid gene can change the range of hosts in which that plasmid persists, due to effects on the regulation of plasmid gene transcription.

microbiology↗

bioRxiv2023

Detection of rare plasmid hosts using a targeted Hi-C approach

Despite the significant role plasmids play in microbial evolution, there is limited knowledge of their ecology, evolution, and transfer in microbial communities. Therefore, we developed and implemented a novel approach to identify rare plasmid hosts by combining Hi-C, a proximity ligation method, with enrichment for plasmid-specific DNA. We hereafter refer to this Hi-C enrichment approach as Hi-C+. Our experimental design mimicked scenarios in which the transfer of an antimicrobial resistance plasmid from a donor to a recipient in soil was increasingly rare. We established that Hi-C can link a plasmid to its host in soil when the relative abundance of that plasmid-host pair is as low as 0.001%. The Hi-C+ method further improved the detection limit of Hi-C 100-fold and allowed identification of plasmid hosts at the genus level. Therefore, Hi-C+ will facilitate the exploration of the ecological and evolutionary pathways that affect the spread of plasmids in natural environments. TeaserIn this study we demonstrate that a target-enriched Hi-C approach can identify rare hosts of a given plasmid in soil.

molecular biology↗

bioRxiv2022

Evolutionary crowdsourcing: alignment of fitness landscapes allows cross-species adaptation of a horizontally transferred gene

Genes that undergo horizontal gene transfer (HGT) evolve in different genomic backgrounds as they move between hosts, in contrast to genes that evolve under strict vertical inheritance. Despite the ubiquity of HGT in microbial communities, the effects of host-switching on gene evolution have been understudied. Here, we present a novel framework to examine the consequences of host-switching on gene evolution by probing the existence and form of host-dependent mutational effects. We started exploring the effects of HGT on gene evolution by focusing on an antibiotic resistance gene (encoding a beta-lactamase) commonly found on conjugative plasmids in Enterobacteriaceae pathogens. By reconstructing the resistance landscape for a small set of mutationally connected alleles in three enteric species (Escherichia coli, Salmonella enterica, and Klebsiella pneumoniae), we uncovered that the landscape topographies were largely aligned with very low levels of host-dependent mutational effects. By simulating gene evolution with and without HGT using the species-specific empirical landscapes, we found that evolutionary outcomes were similar despite HGT. These findings suggest that the adaptive evolution of a mobile gene in one species can translate to adaptation in another species. In such a case, vehicles of cross-species HGT such as plasmids enable a distributed form of genetic evolution across a bacterial community, where species can crowdsource adaptation from other community members. The role of evolutionary crowdsourcing on the evolution of bacteria merits further investigation.

evolutionary biology↗

bioRxiv2022

Antimicrobial resistance genes predict plasmid generalism and network structure in wastewater

Plasmids are mobile genetic elements that can act as mutualists or parasites to their bacterial hosts depending on their accessory genes and environment. Ecological network theory predicts that mutualists, such as plasmids with antimicrobial resistance (AMR) genes in the presence of antimicrobials, should act as generalists, while plasmids without beneficial genes are expected to be more specialised. Therefore, whether the relationship between plasmid and host is mutualistic or antagonistic is likely to have a strong impact on the formation of interaction network structures and the spread of AMR genes across microbial networks. Here we re-analyse Hi-C metagenome data from wastewater samples and identify plasmid signatures with machine learning to generate a natural host-plasmid network. We found that AMR-carrying plasmids indeed interacted with more hosts than non-AMR plasmids (on average 14 versus 3, respectively). The AMR plasmid-host subnetwork showed a much higher connectedness and nestedness than the subnetwork associated with non-AMR plasmids. The overall network was clustered around Proteobacteria and AMR-carrying plasmids giving them a crucial role in network connectivity. Therefore, by forming mutualistic networks with their hosts, beneficial AMR plasmids lead to more connected network structures that ultimately share a larger gene pool of AMR genes across the network.

microbiology↗

bioRxiv2022

Biofilms preserve transmissibility of a multi-drug resistance plasmid

Self-transmissible multidrug resistance (MDR) plasmids are a major health concern because they can spread antibiotic resistance to pathogens. Even though most pathogens form biofilms, little is known about how MDR plasmids persist and evolve in biofilms. We hypothesize that (i) biofilms act as refugia of MDR plasmids by retaining them in the absence of antibiotics longer than well-mixed planktonic populations, and that (ii) the evolutionary trajectories that account for the improvement of plasmid persistence over time differ between biofilms and planktonic populations. In this study, we evolved Acinetobacter baumannii with an MDR plasmid in biofilm and planktonic populations with and without antibiotic selection. In the absence of selection biofilm populations were better able to maintain the MDR plasmid than planktonic populations. In planktonic populations plasmid persistence improved rapidly but was accompanied by a loss of genes required for the horizonal transfer of plasmids. In contrast, in biofilms most plasmids retained their transfer genes, but on average plasmid persistence improved less over time. Our results showed that biofilms can act as refugia of MDR plasmids and favor the horizontal mode of plasmid transfer, which has important implications for the spread of MDR.

microbiology↗

bioRxiv2021

A Broadly Conserved Deoxycytidine Deaminase Protects Bacteria from Phage Infection

The El Tor biotype of Vibrio cholerae is responsible for perpetuating the longest cholera pandemic in recorded history (1961-current). The genomic islands VSP-1 and -2 are two understudied genetic features that distinguish El Tor from previous pandemics. To understand their utility, we calculated the co-occurrence of VSP genes across bacterial genomes. This analysis predicted the previously uncharacterized vc0175, herein renamed deoxycytidylate deaminase Vibrio (dcdV), is in a gene network with dncV, a cyclic GMP-AMP synthase involved in phage defense. DcdV consists of two domains, a P-loop kinase and a deoxycytidylate deaminase, that are required for the deamination of dCTP and dCMP, inhibiting phage predation by corrupting cellular nucleotide concentrations. Additionally, DcdV is post-translationally inhibited by a unique noncoding RNA encoded 5 of the dcdV locus. DcdV homologs are conserved in bacteria and eukaryotes and our results identify V. cholerae DcdV as the founding member of a previously undescribed bacterial phage defense system.

microbiology↗

bioRxiv2021

Estimating the rate of plasmid transfer with an adapted Luria-Delbrück fluctuation analysis and a case study on the evolution of plasmid transfer rate

To increase our basic understanding of the ecology and evolution of conjugative plasmids, we need a reliable estimate of their rate of transfer between bacterial cells. However, accurate estimates of plasmid transfer have remained elusive due to biological and experimental complexity. Current methods to measure transfer rate can be confounded by many factors. A notable example involves plasmid transfer between different strains or species where the rate that one type of cell donates the plasmid is not equal to the rate at which the other cell type donates. Asymmetry in these rates has the potential to bias or constrain current transfer estimates, thereby limiting our capabilities for estimating transfer in microbial communities. Inspired by the classic fluctuation analysis of Luria and Delbruck, we develop a novel approach, the Luria-Delbruck method ( LDM), for estimating plasmid transfer rate. Our new approach embraces the stochasticity of conjugation departing from the current deterministic population dynamic methods. In addition, the LDM overcomes obstacles of traditional methods by not being affected by different growth and transfer rates for each population within the assay. Using stochastic simulations and experiments, we show that the LDM has high accuracy and precision for estimation of transfer rates compared to the most widely used methods, which can produce estimates that differ from the LDM estimate by orders of magnitude. Significance StatementConjugative plasmids play significant roles in the ecology and evolution of microbial communities. Notably, antibiotic resistance genes are often encoded on conjugative plasmids. Thus, conjugation--the transfer of a plasmid copy from one cell to another--is a common way for antibiotic resistance to spread between important clinical pathogens. For both public health modeling and a basic understanding of microbial population biology, accurate estimates of this fundamental rate are of great consequence. We show that widely used methods can lead to biased estimates, deviating from true values by several orders of magnitude. Therefore, we developed a new approach, inspired by the classic fluctuation analysis of Luria and Delbruck, for accurately assessing the rate of plasmid conjugation under a variety of conditions.

microbiology↗

bioRxiv2020

Contagious Antibiotic Resistance: Plasmid Transfer Among Bacterial Residents of the Zebrafish Gut

By characterizing the trajectories of antibiotic resistance gene transfer in bacterial communities such as the gut microbiome, we will better understand the factors that influence this spread of resistance. Our aim was to investigate the host network of a multi-drug resistance broad-host-range plasmid in the culturable gut microbiome of zebrafish. This was done through in vitro and in vivo conjugation experiments with Escherichia coli as donor of the plasmid pB10::gfp. When this donor was mixed with the extracted gut microbiome, only transconjugants of Aeromonas veronii were detected. In separate matings between the same donor and four prominent isolates from the gut microbiome, the plasmid transferred to two of these four isolates, A. veronii and Plesiomonas shigelloides, but not to Shewanella putrefaciens and Vibrio mimicus. When these A. veronii and P. shigelloides transconjugants were the donors in matings with the same four isolates, the plasmid now also transferred from A. veronii to S. putrefaciens. P. shigelloides was unable to donate the plasmid and V. mimicus was unable to acquire it. Finally, when the E. coli donor was added in vivo to zebrafish through their food, plasmid transfer was observed in the gut but only to Achromobacter sp., a rare member of the gut microbiome. This work shows that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome depends on the donor-recipient species combinations and therefore their spatial arrangement. It also suggests that rare gut microbiome members should not be ignored as potential reservoirs of multi-drug resistance plasmids from food. ImportanceTo understand how antibiotic resistance plasmids end up in human pathogens it is crucial to learn how, where and when they are transferred and maintained in members of bacterial communities such as the gut microbiome. To gain insight into the network of plasmid-mediated antibiotic resistance sharing in the gut microbiome, we investigated the transferability and maintenance of a multi-drug resistance plasmid among the culturable bacteria of the zebrafish gut. We show that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome can depend on which species are involved, as some are important nodes in the plasmid-host network and others dead-ends. Our findings also suggest that rare gut microbiome members should not be ignored as potential reservoirs of multi-drug resistance plasmids from food.

microbiology↗

bioRxiv2018

Linking the Resistome and Plasmidome to the Microbiome

The rapid spread of antibiotic resistance is a serious human health threat. A range of environments have been identified as reservoirs of the antibiotic resistance genes (ARGs) found in pathogens. However, we lack understanding of the origins of these ARGs and their spread from environment to clinic. This is partly due to our inability to identify the bacterial hosts of ARGs and the mobile genetic elements that mediate this spread, such as plasmids and integrons. Here we demonstrated that the in vivo proximity ligation method Hi-C can determine the in situ host range of ARGs, plasmids, and integrons in a wastewater sample by physically linking them to their host chromosomes. Hi-C detected both previously known and novel associations between ARGs, mobile elements and host genomes, mostly validating this method. A better identification of the natural carriers of ARGs will aid the development of strategies to limit resistance spread to pathogens.

microbiology↗

bioRxiv2018

The transferable resistome of produce

Produce is increasingly recognized as a reservoir of human pathogens and transferable antibiotic resistance genes. This study aimed to explore methods to characterize the transferable resistome of bacteria associated with produce. Mixed salad, arugula, and cilantro purchased from supermarkets were analyzed by means of cultivation- and DNA-based methods. Before and after a nonselective enrichment step, tetracycline (tet) resistant Escherichia coli were isolated and plasmids conferring tet resistance were captured by exogenous plasmid isolation. Tet resistant E. coli isolates, transconjugants and total community (TC)-DNA from the microbial fraction detached from leaves or after enrichment were analyzed for the presence of resistance genes, class 1 integrons and various plasmids by real-time PCR and PCR-Southern blot hybridization. Real-time PCR primers were developed for IncI and IncF plasmids. Tet resistant E. coli isolated from arugula and cilantro carried IncF, IncI1, IncN, IncH11, IncU and IncX1 plasmids. Three isolates from cilantro were positive for IncN plasmids and blaCTX-M-1. From mixed salad and cilantro, IncF, Inc11, and IncP-1{beta} plasmids were captured exogenously. Importantly, whereas direct detection of IncI and IncF plasmids in TC-DNA failed, these plasmids became detectable in DNA extracted from enrichment cultures. This confirms that cultivation-independent DNA-based methods are not always sufficiently sensitive to detect the transferable resistome in the rare microbiome. In summary, this study showed that an impressive diversity of self-transmissible multiple resistance plasmids was detected in bacteria associated with produce that is consumed raw, and exogenous capturing into E. coli suggests that they could transfer to gut bacteria as well.

microbiology↗

bioRxiv2017

Emerging patterns of plasmid-host coevolution that stabilize antibiotic resistance

Multidrug resistant bacterial pathogens have become a serious global human health threat, and conjugative plasmids are important drivers of the rapid spread of resistance to last-resort antibiotics. Whereas antibiotics have been shown to select for adaptation of resistance plasmids to their new bacterial hosts, or vice versa, a general evolutionary mechanism has not yet emerged. Here we conducted an experimental evolution study aimed at determining general patterns of plasmid-bacteria evolution. Specifically, we found that a large conjugative resistance plasmid follows the same evolutionary trajectories as its non-conjugative mini-replicon in the same and other species. Furthermore, within a single host-plasmid pair three distinct patterns of adaptive evolution led to increased plasmid persistence: i) mutations in the replication protein gene (trfA1); ii) the acquisition by the resistance plasmid of a transposon from a co-residing plasmid encoding a putative toxin-antitoxin system; iii) a mutation in the hosts global transcriptional regulator gene fur. Since each of these evolutionary solutions individually have been shown to increase plasmid persistence in other plasmid-host pairs, our work points towards common mechanisms of plasmid stabilization. These could become the targets of future alternative drug therapies to slow down the spread of antibiotic resistance.

evolutionary biology↗