Biology subjects

Rendueles, O.

Publications and source records attributed to Rendueles, O..

11 recordsLinked to original sources

bioRxiv2026

Within-host evolution of Klebsiella spp. from intestinal carriage to bacteremia

Gut colonization by the Gram-negative bacillus Klebsiella pneumoniae is a significant risk factor for extra-intestinal infections. However, the mechanisms by which this opportunistic pathogen causes disseminated infections remain poorly understood. To investigate this phenomenon, 22 strain pairs of Klebsiella spp. were sequentially isolated from rectal swabs and blood samples of ICU patients. All strains adhered to intestinal epithelial cells in vitro, but failed to invade or disrupt epithelial barrier integrity. Few phenotypic differences between strains of the same pair were observed regarding their biofilm-forming capacities and ampicillin resistance. Whole genome sequencing of five pairs showed diverse sequence types, the presence of numerous antibiotics resistance genes but few virulence genes. Pairwise comparison of genomic sequences of blood and fecal isolates evidenced a few single nucleotide polymorphisms and small insertions-deletions, mostly affecting genes involved in biosynthesis of surface structures (such as capsules, pili). Most genetic changes were driven by horizontal gene transfer events, with the notable acquisition of a plasmid that enhanced bacterial fitness by eliminating competitors. In addition, some blood isolates had reduced the number of antibiotic resistance genes, underscoring the high plasticity of the Klebsiella resistome. Finally, one bloodstream isolate carried a mutS mutation, conferring a hypermutator phenotype that could increase evolvability despite the fitness burden. Together, these findings indicate that within-host genetic adaptations, rather than the acquisition of virulence traits, can enhance the colonization, competitiveness and ultimately the ability of K. pneumoniae to cause invasive infections. ImportanceKlebsiella commonly colonizes the human gut, and this carriage can progress to infections, particularly in intensive care unit (ICU) patients. To better understand the in vivo evolution, genetically associated Klebsiella strains isolated from the feces and blood of ICU patients were analyzed. Although strains were able to adhere to intestinal cells, none could invade or damage the intestinal barrier. Genomic comparisons of pairs strains showed limited genetic differences, mostly mutations affecting surface structures. Frequent horizontal gene transfer events were observed, which could improve bacterial competitiveness and permits a remarkably flexible resistome. Overall, this study shows that within-host evolution, rather than the gain of virulence traits, can enhance the ability of Klebsiella to persist, outcompete other bacteria, and ultimately cause infections.

microbiology↗

bioRxiv2025

Environment-dependent evolution drives divergent adaptive strategies and parasite dynamics in a minimal community

Prophages, phage genomes integrated into bacterial chromosomes, are widespread, yet, the extent to which these resident parasites contribute to host fitness and shape evolutionary trajectories, particularly in polymicrobial environments, remains unclear. Here, we use an experimental evolution approach in which a polylysogenic bacterial strain carrying phages on both its chromosome and plasmids evolves under environmental conditions that modulate the costs and benefits of prophage carriage. By tracking bacterial growth and phage production over time, we uncover divergent, environment-dependent adaptive strategies among lysogens. Some populations evolve dramatically increased phage production, with titers rising over 1,000-fold, whereas in environments where phages impose strong fitness costs, prophages are either purged or domesticated. Across all evolved populations, adaptation is accompanied by defects in cellular segmentation arising from mutations in the divisome and Tat translocation pathways. Whole-genome sequencing revealed shifts in lysate composition, suggesting altered interactions among co-occurring prophages, alongside the loss of plasmid- encoded prophage antibiotic resistance genes and reduced resistance to two distinct antibiotic classes. Together, our results demonstrate that prophages are dynamic evolutionary players whose interactions with host genomes and ecological context jointly shape bacterial adaptation, in complex communities, with implications for exploiting phage-antibiotic trade-offs in therapeutic design.

microbiology↗

bioRxiv2025

Serotype swapping in Klebsiella spp. by plug-and-play

Understanding how complex, multi-gene systems evolve and function across genetic backgrounds is a central question in molecular evolution. While such systems often impose costs through epistatic interactions, some may behave as modular, "plug-and-play" units that retain function with minimal disruption. We used the polysaccharide capsule locus of Klebsiella pneumoniae, a highly exchangeable and fast-evolving locus, as a model. We genetically engineered capsule exchanges (swaps) across diverse genetic backgrounds and combined transcriptomics, fitness assays, and evolution experiments, to show that capsule exchange has negligible effects on global expression and only marginal fitness costs, regardless of serotype. Adaptation to capsule-costly environments consistently reduced capsule production, regardless of serotype, revealing shared adaptive trajectories rather than serotype-specific pathways. Moreover, serotype-specific traits involved in bacterial virulence, such as biofilm formation and hypermucoviscosity, were conserved across genetic backgrounds. This reveals that capsule swapping can directly shape host-pathogen interactions and influence within-patient evolution. Our findings provide strong evidence that capsule loci display plug-and-play dynamics: they are transferable, functional across contexts, and minimally disruptive to the host genome. This allows capsules to be seamlessly swapped, and help explain the evolutionary success, ecological versatility, and pervasive exchangeability of capsules in K. pneumoniae.

evolutionary biology↗

bioRxiv2023

Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola

Klebsiella variicola is an emergent human pathogen causing diverse infections, including in the urinary tract. However, little is known about the evolution and maintenance of genetic diversity in this species, the molecular mechanisms and their population dynamics. Here, we characterized the emergence of a novel rdar-like morphotype which is contingent both on the genetic background and the environment. We show that mutations in either the nitrogen assimilation control gene (nac) or the type III fimbriae regulator, mrkH, suffice to generate rdar-like colonies. These morphotypes are primarily selected for the reduced inter-cellular aggregation as a result of loss-of-function yielding reduced fimbriae expression. Additionally, these clones also display increased growth rate and reduced biofilm formation. Direct competitions between rdar and wild type clone show that mutations in mrkH provide large fitness advantages. In artificial urine, the morphotype is under strong negative frequency-dependent selection and is able to socially exploit wild type strains. An exhaustive search for mrkH mutants in public databases revealed that ca 8% of natural isolates analysed had truncated MrkH proteins many of which were due to insertions of IS elements, including a reported clinical isolate with rdar morphology. These strains were all isolated from human, mostly from urine. The decreased aggregation of these mutants could have important clinical implications as such clones could better disperse within the host allowing colonisation of other body sites and leading to systemic infections. One-sentence SummaryReport of the emergence of a novel non-aggregative colony morphology in K. variicola and the first example of social exploitation in the Klebsiella genus.

microbiology↗

bioRxiv2023

Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency

Bacterial evolution is affected by mobile genetic elements such as phages and conjugative plasmids, which may provide novel adaptive traits but also incur in fitness costs. Infection by these elements is affected by the bacterial capsule. Yet, its importance has been difficult to quantify and characterise because of the high diversity of bacterial genomes regarding confounding mechanisms such as anti-viral systems. We swapped capsule loci between Klebsiella pneumoniae strains to quantify their effect on transfer of conjugative plasmids and phages independently of the genetic background. Capsule swaps systematically invert phage susceptibility, demonstrating that serotypes are key determinants of phage infection. Capsule types also affect conjugation efficiency in both donor and recipient cells depending on the serotype, a mechanism shaped by the capsule volume and depending on the structure of the conjugative pilus. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The pili least sensitive to capsules (F-like) are also the most frequent in the species plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how the traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/536574v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@157bc4eorg.highwire.dtl.DTLVardef@10bc979org.highwire.dtl.DTLVardef@d85080org.highwire.dtl.DTLVardef@18d331e_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Latent evolution of biofilm formation depends on life-history and genetic background

Adaptation to one environment can often generate phenotypic and genotypic changes which impact the future ability of an organism to thrive in other environmental conditions. In the context of host-microbe interactions, biofilm formation can increase survival rates in vivo upon exposure to stresses, like the hosts immune system or antibiotic therapy. However, how the generic process of adaptation impacts the ability to form biofilm and how it may change through time has seldomly been studied. To do so, we used a previous evolution experiment with three strains of the Klebsiella pneumoniae species complex, in which we did not specifically select for biofilm formation. We observed that changes in the ability to form biofilm happened very fast at first and afterwards reverted to ancestral levels in many populations. Biofilm changes were associated to phenotypic changes in population yield and surface polysaccharide production. Genotypically, mutational targets in the tip adhesin of type III fimbriae (mrkD) or the fim switch of type I fimbriae were driven by nutrient availability during evolution, and their impact on biofilm formation was dependent on capsule production. Analyses of natural isolates revealed similar mutations in mrkD, suggesting that they also play an important role in adaptation outside the laboratory. Our work reveals that the latent evolution of biofilm formation, and its evolutionary dynamics, depend on nutrient availability, the genetic background and other intertwined phenotypic and genotypic changes. Ultimately, it suggests that small differences in the environment can alter an organisms fate in more complex niches like the host.

microbiology↗

bioRxiv2022

Competition between phage-resistance mechanisms determines the outcome of bacterial co-existence

Many bacterial species carry multiple prophages. Despite their potential cost, these elements can provide multiple fitness advantages to the host, such as the elimination of direct competitors. However, the long-term efficiency of prophage induction to displace competitors has received little attention. We experimentally coevolved a polylysogenic Klebsiella pneumoniae strain (ST14) with a phage-sensitive strain (BJ1) in several environments resulting in different phage pressures. We then followed the adaptation process and the emergence of resistance. After 30 days, population yield remained stable, and although BJ1 was present in all conditions, its frequency was higher when phage pressure was stronger. Resistance to phages emerged quickly through mutations that prevent capsule biosynthesis. In contrast to our expectation, lysogenic conversion was rare and costly because new BJ1 lysogens exhibited exacerbated death rates and were easily outcompeted. Unexpectedly, the adaptation process changed at longer time scales, where BJ1 populations adapted by fine-tuning the production of capsule, reducing the ability of phage to absorb, while remaining capsulated. These resistant clones are pan-resistant to a large panel of phages. Most intriguingly, some clones exhibited transient non-genetic resistance to phages. Our experimental and modelling results highlight the diversity, dynamics and competition between phage-resistance mechanisms during coevolution and how these are driven by phage pressure.

evolutionary biology↗

bioRxiv2021

Hidden paths to endless forms most wonderful: Ecology latently shapes evolution of multicellular development in predatory bacteria

Ecological causes of developmental-system evolution, for example from predation, remain under intense investigation. An important open question is the role of latent phenotypes in eco-evo-devo. The predatory bacterium Myxococcus xanthus undergoes aggregative multicellular development upon starvation. Here we use M. xanthus to test whether evolution in several distinct growth environments that do not induce development latently alters developmental phenotypes, including morphology and plasticity, in environments that do induce development. In the MyxoEE-3 evolution experiment, growing M. xanthus populations swarmed across agar surfaces while adapting to distinct conditions varying at factors such as surface stiffness or prey identity. All examined developmental phenotypes underwent extensive and ecologically specific latent evolution, with surface stiffness, prey presence and prey identity all strongly impacting the latent evolution of development. Evolution on hard agar allowed retention of developmental proficiency and extensive stochastic phenotypic radiation, including of reaction norms, with instances of both increased plasticity and canalization. In contrast, evolution on soft agar latently led to systematic loss of development, revealing an ecologically-contingent fitness trade-off between the growth and developmental phases of a multicellular life cycle that is likely determined by details of motility behavior. Similar contingency was observed after evolution during predatory growth in distinct prey environments, with Bacillus subtilis causing greater loss of development and lower stochastic diversification than Escherichia coli. Our results have implications for understanding evolutionary interactions among predation, development and motility in myxobacterial life cycles, and, more broadly, the importance of latent phenotypes for the diversification of developmental systems.

evolutionary biology↗

bioRxiv2020

The interplay between the bacterial capsule and mobile genetic elements determines direction and intensity of gene flux in Klebsiella pneumoniae.

Mobile genetic elements (MGEs) drive genetic transfers between bacteria using mechanisms that are affected by the cell envelope composition, notably the capsule. Here, we show that capsules constrain phage-mediated gene flow between closely related serotypes in Klebsiella pneumoniae, a high-priority nosocomial enterobacteria. Serotype-specific phage pressure may also explain the inactivation of capsule genes, which occur frequently and recapitulate the capsule biosynthetic pathway. We show that plasmid conjugation is increased upon capsule inactivation and that capsule re-acquisition leaves long recombination tracts around the capsular locus. This suggests that capsule inactivation by phage pressure facilitates its subsequent re-acquisition by conjugation, a process re-wiring gene flow towards novel lineages whenever it leads to serotype swaps. These results reveal the basis of trade-offs between the evolution of virulence and multidrug resistance. They also caution that some alternatives to antibiotic therapy may select for capsule inactivation, thus decreasing virulence but facilitating antibiotic resistance genes acquisition.

evolutionary biology↗

bioRxiv2020

Selection for the bacterial capsule in the absence of biotic and abiotic aggressions depends on growth conditions

Extracellular capsules protect the cell against both abiotic and biotic stresses such as bacteriophages and the host immune system. Yet, it is unclear if capsules contribute to fitness in the absence of external aggressions, in spite of the cost of production. Here, we enquire if there are conditions favouring the presence of the capsule in Klebsiella, where it is a major virulence factor. We shortly experimentally evolved 19 different strains, and show that small changes in growth media have a strong impact on the maintenance of the capsule. Competitions with capsule mutants in nine different strains showed that capsules provide [~]20% of fitness advantage in nutrient-poor conditions, due to faster growth rates and higher yields. In contrast, the capsule was readily lost in nutrient-rich media. The growth environment, as well as the capsule serotype, strongly influenced the role of the capsule in major virulence traits like hypermucoviscosity and biofilm formation. Our data shows that the capsule is selected for in situations lacking abiotic, but also biotic stresses and further supports that the capsule role in virulence may be a by-product of adaptation outside the host, hinting that it may have important roles in bacterial physiology yet to be discovered. SIGNIFICANCEBacterial capsules are a wide-spread virulence factor that limits efficacy of antimicrobial therapy. Whereas most studies focus on the role of the capsule in pathogenesis, very few have addressed the conditions under which the capsule is primarily selected for. Here, we show that small changes in growth media have a strong impact in the maintenance of the capsule and the fitness advantage they confer. Our results raise the question whether conditions lacking biotic or abiotic stresses, in addition of selecting for the maintenance of the capsule, can also play a role in selecting for serotype variation. Our results further support that the role of the capsule in virulence may be a by-product of adaptation outside the host, hinting that there may be other functionalities yet to be discovered for it.

microbiology↗

bioRxiv2019

Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation

Klebsiella species are able to colonize a wide range of environments and include worrisome nosocomial pathogens. Here, we sought to determine the abundance and infectivity of prophages of Klebsiella to understand how the interactions between induced prophages and bacteria affect population dynamics and evolution. We identified many prophages in the species, placing these taxa among the top 5% of the most polylysogenic bacteria. We selected 35 representative strains of the Klebsiella pneumoniae species complex to establish a network of induced phage-bacteria interactions. This revealed that many prophages are able to enter the lytic cycle, and subsequently kill or lysogenize closely-related Klebsiella strains. Although 60% of the tested strains could produce phages that infect at least one other strain, the interaction network of all pairwise cross-infections is very sparse and mostly organized in modules corresponding to the strains capsule serotypes. Accordingly, capsule mutants remain uninfected showing that the capsule is a key factor for successful infections. Surprisingly, experiments in which bacteria are predated by their own prophages result in accelerated loss of the capsule. Our results show that phage infectiousness defines interaction modules between small subsets of phages and bacteria in function of capsule serotype. This limits the role of prophages as competitive weapons because they can infect very few strains of the species complex. This should also restrict phage-driven gene flow across the species. Finally, the accelerated loss of the capsule in bacteria being predated by their own phages, suggests that phages drive serotype switch in nature.

microbiology↗