Biology subjects

Dimitriu, T.

Publications and source records attributed to Dimitriu, T..

14 recordsLinked to original sources

bioRxiv2026

Antimicrobial resistance in a warmer world: selection and transfer of kanamycin resistance is temperature dependent in E. coli.

Climate warming consistently correlates with increased antimicrobial resistance (AMR). Understanding the biological mechanisms underpinning this relationship is important for both prediction and mitigation of the future burden of antibiotic resistance in a warmer world, especially given AMR can spread through both selection and horizontal gene transfer. Here, we experimentally measure how temperature alters susceptibility to kanamycin, selection and spread of resistance in Escherichia coli MG1655 carrying the natural plasmids R1 and RP4. We predict that susceptibility should be lowest - and plasmid transfer highest - at maximal growth rate. Thermal performance of bacterial growth peaked at 40{degrees}C and we detected a small plasmid cost - for RP4, but not R1 - in the absence of kanamycin. The thermal performance of plasmid transfer did not mirror that of bacterial growth, instead, R1 transfer peaked at 35{degrees}C with a much narrower thermal tolerance. Susceptibility to kanamycin decreased with increasing growth rate until 31{degrees}C, before increasing again as temperatures approached and exceeded optimal growth temperature. Increasing susceptibility coupled with high growth rates meant that selection was strongest at the highest measured temperature, but the shape of the relationship changed with kanamycin concentration. In mixed populations of resistant and susceptible bacteria, we found that AMR spread most where selection was strongest, irrespective of plasmid transfer. Our findings suggest increased AMR at higher temperatures is predominantly driven by higher growth rates and increased susceptibility, resulting in stronger selection. Our study provides a framework to uncover generalities across antibiotic classes, strains, species, and plasmids, laying the foundation for improved prediction of AMR selection in the environment.

microbiology↗

bioRxiv2026

Antibiotic inhibition uncouples growth from horizontal gene transfer

Conjugative plasmids often encode resistance to multiple antibiotics, allowing a single mobile genetic element to transfer across diverse selective environments. This co-selection is often invoked to explain the persistence and spread of multidrug resistance, with antibiotic resistance genes encoded on the same plasmid frequently treated as equivalent routes of plasmid maintenance. However, accumulating evidence suggests that different antibiotics can produce distinct co-selection outcomes. These differences have been interpreted through the lens of fitness and population-level selection, while the potential effects on plasmid transfer itself are largely unknown. Here, we show that different antibiotics generate significantly different transfer dynamics for the exact same multidrug-resistant plasmid. Surprisingly, much of this variation arises from continued conjugation after antibiotic exposure begins, whereby a transient residual conjugation window persists despite strong growth inhibition, allowing new transconjugants to continue forming for hours after treatment in an antibiotic dependent manner. A simple model for describing antibiotic effect on transfer competence of both donors and recipients quantitatively explains these antibiotic-specific dissemination dynamics. Moreover, different recipient genetic backgrounds exhibit distinct residual conjugation windows, demonstrating that the capacity for continued plasmid transfer during antibiotic exposure is both drug- and host-dependent. Together, our results show that antibiotics suppress plasmid dissemination on different timescales, creating drug-specific residual conjugation windows that are largely decoupled from growth inhibition. These findings identify conjugation dynamics as a previously overlooked contributor to co-selection outcomes and suggest that antibiotics that select for the same multidrug-resistant plasmid are not equivalent in their ability to promote plasmid persistence.

microbiology↗

bioRxiv2026

Maintenance of restriction-modification system diversity creates pan-immunity

Bacterial antiviral defense systems are highly diverse and unevenly distributed across populations, such that different strains carry distinct immune repertoires that together form a pan-immune system. Restriction-modification (RM) systems are the most abundant bacterial defense systems and exemplify this architecture, exhibiting remarkable diversity in structure, function, specificity, and efficacy. How and why such diversity is maintained, why weaker systems are not outcompeted, and whether diversity provides benefits beyond protection of individual cells remain unclear. Here, we experimentally tracked bacteria and phages across populations differing in RM diversity. We find no consistent evidence of a trade-off between defense strength and host fitness. Instead, we identify a trade-off between defense strength and horizontal transferability: stronger RM systems are less able to spread between strains, likely because factors that increase defense strength also increase toxicity risk upon transfer to unmethylated hosts. These weaker yet more mobile systems may therefore act as more accessible pan-immune components that bacterial populations can acquire in response to shifting parasite pressures. Furthermore, we show RM systems experience negative frequency-dependent selection, such that common specificities are more readily overcome by phages while rare ones remain protective, causing the benefits of potent systems to erode as they spread. Together, these dynamics maintain RM diversity and explain why weaker systems persist alongside stronger ones. Finally, we show that population-level RM diversity generates collective protection by constraining the emergence of RM-escaping phages and limiting the invasion of bacterial surface mutants that avoid phage adsorption, providing experimental support for the pan-immune model.

microbiology↗

bioRxiv2026

Type of conjugative pili governs transfer efficiency in liquid and affects interpretation of transfer assays.

Plasmid conjugation is central to plasmid maintenance and spread among bacteria. Conjugation assays in liquid or on solid media are commonly used to quantify plasmid conjugation rates. Plasmids with short, rigid conjugative pili are thought to conjugate more efficiently on surfaces, whereas plasmids encoding long, flexible pili can conjugate efficiently in liquid medium. However, this pattern has not been tested systematically. Here, we perform standardised conjugation assays on a collection of 13 conjugative plasmids belonging to families that play a key role in AMR transmission and encode different conjugative pili types. We confirm that only the plasmids encoding long flexible pili conjugate efficiently in liquid. Furthermore, most transconjugants that arise from liquid assays involving plasmids with short, rigid pili can be attributed to transfer happening after the assay itself, on the surface of selective plates. This effect is amplified when using auxotrophic rather than antibiotic resistance markers, and impacts measures of transfer and defence efficiency. Finally, most of the tested plasmids with short pili had very high conjugation rates on surfaces, suggesting their transfer is mostly limited by physical constraints.

microbiology↗

bioRxiv2025

The leading region of many conjugative plasmids is depleted in restriction-modification targets

To successfully transfer into a recipient, conjugative plasmids must overcome the new cells defense mechanisms. The leading region of many plasmids - the first part to enter the recipient - is highly enriched in anti-defense genes. Here, we investigate whether selective pressure from defense systems has also affected its sequence composition. We consider two possibilities: greater target depletion (to avoid triggering target-based defense systems) or greater codon adaptation (to more quickly express anti-defense genes). We analyse the leading region of 1,751 conjugative plasmids belonging to 13 plasmid taxonomic units (PTUs) present in the bacterial order Enterobacterales. First, we investigate GC content and possible depletion of short palindromic motifs (4-8bp) which could be a signature of selective pressure from Type II restriction-modification systems, and find evidence of depletion in certain PTUs. Then we use the codon adaptation index (CAI) to assess codon usage and find that different conjugative PTUs shown different patterns. We show that the leading region of plasmids with MOB-F and MOB-P relaxases is more adapted to optimal host codon usage, consistent with a selective pressure for translational efficiency in anti-defense genes that are transcribed while still single-stranded DNA. In particular, anti-restriction genes in the leading region have high CAI, and we use this fact to identify a single-stranded promoter in the F plasmid. Our findings uncover a new facet of plasmid evolution and emphasise the intensity of the selective pressure that plasmids face from defense systems.

microbiology↗

bioRxiv2025

Stealth plasmids: rapid evolution of deleted plasmids can displace antibiotic resistance plasmids under selection for horizontal transmission.

Conjugative plasmids carrying antimicrobial resistance (AMR) genes are critical for the spread of AMR, due to their ability to transmit horizontally between bacterial hosts. We previously observed that during experimental evolution in the presence of abundant susceptible hosts, the AMR plasmid R1 rapidly evolves variants with increased horizontal transmission due to mutations causing increased plasmid copy number. Yet AMR was progressively lost from the evolving populations. Here, we show that AMR loss was associated with evolution of stealth plasmids in which the AMR region is spontaneously deleted, making plasmid carriage undetectable by plating on selective antibiotic-containing media. These plasmids transmit both vertically and horizontally more efficiently than the ancestral AMR plasmid, driving AMR extinction in bacterial populations and effectively acting as an intrinsic defence against AMR plasmids. Our results suggest that within-host plasmid evolution could be exploited to limit the spread of AMR in natural populations of bacteria.

microbiology↗

bioRxiv2024

Various plasmid strategies limit the effect of bacterial Restriction-Modification systems against conjugation.

In bacteria, genes conferring antibiotic resistance are mostly carried on conjugative plasmids, mobile genetic elements which spread horizontally between bacterial hosts. Bacteria carry defence systems which defend them against genetic parasites, but how effective these are against plasmid conjugation is poorly understood. Here, we study to what extent Restriction-Modification (RM) systems - by far the most prevalent bacterial defence systems - act as a barrier against plasmids. Using 10 different RM systems and 13 natural plasmids conferring antibiotic resistance in Escherichia coli, we uncovered variation in defence efficiency ranging from none to 105-fold protection. Further analysis revealed genetic features of plasmids that explain the observed variation in defence levels. First, the number of RM recognition sites present on the plasmids generally correlates with defence levels, with higher numbers of sites being associated with stronger defence. Secondly, some plasmids encode methylases that protect against restriction activity. Finally, we show that a high number of plasmids in our collection encode anti-restriction genes that provide protection against several types of RM systems. Overall, our results show that it is common for plasmids to encode anti-RM strategies, and that, as a consequence, RM systems form only a weak barrier for plasmid transfer by conjugation.

microbiology↗

bioRxiv2022

Antibiotics that affect translation can antagonize phage infectivity by interfering with the deployment of counter-defences.

It is becoming increasingly clear that antibiotics can both positively and negatively impact the infectivity of bacteriophages (phage), but the underlying mechanisms often remain unclear. Here we demonstrate that antibiotics that target the protein translation machinery can fundamentally alter the outcome of bacteria-phage interactions by interfering with the production of phage-encoded counter-defence proteins. Specifically, using Pseudomonas aeruginosa PA14 and phage DMS3vir as a model, we show that bacteria with CRISPR-Cas immune systems have elevated levels of immunity against phage that encode anti-CRISPR (acr) genes when translation inhibitors are present in the environment. CRISPR-Cas are highly prevalent defence systems that enable bacteria to detect and destroy phage genomes in a sequence-specific manner. In response, many phages encode acr genes that are expressed immediately following infection to inhibit key steps of the CRISPR-Cas immune response. Our data show that while phage carrying acr genes can amplify efficiently on bacteria with CRISPR-Cas immune systems in the absence of antibiotics, the presence of antibiotics that act on protein translation prevents phage amplification, while protecting bacteria from lysis. These results help to understand how antibiotics-phage synergy and antagonism depend on the molecular interactions that define phage infectivity and host immunity.

microbiology↗

bioRxiv2022

Re-inventing pathogen passage for social microbes

Passage experiments that sequentially infect hosts with parasites have long been used to manipulate virulence. However, in many invertebrate pathogens passage has been applied naively without a full theoretical understanding of how best to select for increased virulence. This has led to very mixed results. Understanding the evolution of virulence is complex because selection on parasites occurs across multiple spatial scales with potentially different conflicts operating on parasites with different life-histories. For example, in social microbes, strong selection on replication rate within hosts can lead to cheating and loss of virulence, because investment in public goods virulence reduces replication rate. In contrast, selection acting at a between host scale maintains virulence by selecting on parasite population size. In this study we tested how different scales of selection and varying mutation supply affect evolution of virulence against resistant hosts in the specialist insect pathogen Bacillus thuringiensis., aiming to optimize methods for strain improvement against a difficult to kill insect target. We show that selection for infectivity using competition between sub-populations in a metapopulation prevents social cheating, acts to retain key virulence plasmids and facilitates increased virulence. Increased virulence was associated with reduced efficiency of sporulation, and loss of function in putative regulatory genes but not with altered expression of known virulence factors. Selection in a metapopulation provides a broadly applicable tool for improving the efficacy of biocontrol agents. Moreover, a structured host population can facilitate artificial selection on infectivity, while selection on life history traits such as faster replication or larger population sizes can reduce virulence can reduce virulence in social microbes.

evolutionary biology↗

bioRxiv2021

Bacteriostatic antibiotics promote the evolution of CRISPR-Cas immunity

Phage therapy can be used in combination with antibiotics to combat infections with bacterial pathogens1-3. However, bacteria can rapidly evolve phage resistance via receptor mutation, or using their CRISPR-Cas adaptive immune systems4, which insert short phage-derived sequences into CRISPR loci in the bacterial genome5 to guide sequence-specific cleavage of cognate sequences6. Unlike CRISPR-Cas immunity, mutation of the phage receptor leads to attenuated virulence when the opportunistic pathogen Pseudomonas aeruginosa is infected with its phage DMS3vir7, which underscores the need to predict how phage resistance evolves under clinically relevant conditions. Here, using eight antibiotics with various modes of action, we show that bacteriostatic antibiotics (which inhibit cell growth without killing) specifically promote evolution of CRISPR-Cas immunity in P. aeruginosa by slowing down phage development and providing more time for cells to acquire phage-derived sequences and mount an immune response. Our data show that some antimicrobial treatments can contribute to the evolution of phage-resistant pathogens with high virulence.

microbiology↗

bioRxiv2021

CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens

The acquisition of antibiotic resistance genes via horizontal gene transfer is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic material, and may therefore limit the acquisition of antibiotic resistance. CRISPR-Cas adaptive immune systems are one of the most prevalent defences in bacteria, found in roughly half of bacterial genomes, but it has remained unclear if and how much they contribute to restricting the spread of antibiotic resistance. We analysed ~40,000 whole genomes comprising the full RefSeq dataset for 11 species of clinically important genera of human pathogens including Enterococcus, Staphylococcus, Acinetobacter and Pseudomonas. We modelled the association between CRISPR-Cas and indicators of horizontal gene transfer, and found that pathogens with a CRISPR-Cas system were less likely to carry antibiotic resistance genes than those lacking this defence system. Analysis of the mobile genetic elements targeted by CRISPR-Cas supports a model where this host defence system blocks important vectors of antibiotic resistance. These results suggest a potential "immunocompromised" state for multidrug-resistant strains that may be exploited in tailored interventions that rely on mobile genetic elements, such as phage or phagemids, to treat infections caused by bacterial pathogens.

microbiology↗

bioRxiv2020

Increased copy number couples the evolution of plasmid horizontal transmission and antibiotic resistance.

Antimicrobial resistance (AMR) in bacteria is commonly encoded on conjugative plasmids, mobile elements which can spread horizontally between hosts. Conjugative transfer disseminates AMR in communities but it remains unclear when and how high transfer rates evolve, and with which consequences. Here we studied experimentally the evolution of two antibiotic resistance encoding plasmids when confronted to different immigration rates of susceptible, plasmid-free hosts. While plasmid RP4 did not evolve detectably, plasmid R1 rapidly evolved up to 1000-fold increased transfer rates in the presence of susceptible hosts, at a cost to its host. Unexpectedly, most evolved plasmids also conferred to their hosts the ability to grow at high concentrations of antibiotics. The most common mutations in evolved plasmids were contained within the copA gene which controls plasmid replication and copy number. Evolved copA variants had elevated copy number, leading to both higher transfer rates and AMR. Due to these pleiotropic effects, host availability and antibiotics were each sufficient to select for highly transmissible plasmids conferring high levels of antibiotic resistance.

microbiology↗

bioRxiv2018

Plasmid transfer is biased towards close kin in bacteria from natural populations.

Plasmids play a key role in microbial ecology and evolution, yet the determinants of plasmid transfer rates are poorly understood. Here we investigate the importance of genetic similarity between naturally co-occurring Escherichia coli isolates in the transfer of two plasmids (narrow-host-range R1 and broad-host-range RP4). We uncovered extensive variability, spanning over five orders of magnitude, in the ability of isolates to donate and receive plasmids. Overall, transfer was strongly biased towards clone-mates, but not correlated to genetic distance between donors and recipients. Transfer was limited by the presence of a functional restriction-modification system in recipients, thus bias towards kin might be explained by sharing of identical restriction systems. Such conjugation within lineages sets the stage for longer-term pair-wise coevolutionary interactions between plasmids and bacterial hosts.

ecology↗

bioRxiv2018

Selection of horizontal gene transfer through public good production

In bacteria, cooperative genes encoding public good molecules are preferentially located on mobile genetic elements (MGEs), and horizontal transfer of MGEs favours the maintenance of public good cooperation. The rate of horizontal transfer itself can evolve in response to selective pressures acting on both MGEs and bacterial hosts: benefits and costs of infectious spread, but also indirect effects of MGE genes to the host. We show here that carriage of public good genes on MGEs can generate another indirect selection for MGE transfer. Transfer increases public good production and, when relatedness is sufficiently high, public goods benefit preferentially genotypes with high transfer ability. Both our simulations and experiments indicate that transfer is not required to occur among kin, provided that public goods still benefit kin. Public good gene mobility thus aligns the interests of chromosomes and MGEs concerning transfer, promoting gene exchange among bacteria.

evolutionary biology↗