Biology subjects

Herencias, C.

Publications and source records attributed to Herencias, C..

10 recordsLinked to original sources

bioRxiv2026

Multireplicon plasmids emerge under predictable rules and drive the spread of antimicrobial resistance across bacterial hosts

Plasmids are DNA molecules that replicate independently of the bacterial chromosome and are typically associated with the spread of antimicrobial resistance (AMR) and virulence determinants, among other relevant traits. Fusion events between plasmids generate larger, complex backbones that carry two or more replication systems, known as multireplicon plasmids. Despite decades of study, we are still far from understanding how multireplicon plasmids arise, persist, and shape the evolution of AMR. Here, we analyzed 24,000 non-redundant plasmids across bacterial genera and found that more than 30% of them encoded multiple replicons. Compared to single-replicon plasmids, multireplicon plasmids were larger, were enriched in genes encoding antimicrobial, metal, and biocide resistance as well as virulence factors, and showed higher mobility and a broader host range. We also found that multireplicon assembly is not random. Some replicon pairs repeatedly merge into stable multireplicon plasmids, while other pairs rarely fuse even when they commonly coexist intracellularly. We also show that replicon pairs tend to be localized either in close proximity to one another or on opposite poles of the plasmid. We further highlight that multireplicon plasmids can be broadly classified into two groups: long-term coevolving replicon pairs and transient associations that lack a shared evolutionary history. Finally, we reveal the molecular mechanisms underlying multireplicon formation and highlight the role of insertion sequences in their formation and maintenance. Together, our work sheds light on the abundance, gene content, evolutionary patterns, and formation dynamics of multireplicon plasmids and pinpoints their relevance to bacterial evolution and human health.

microbiology↗

bioRxiv2025

Cultivation and genomic characterization of human gut-associated Bdellovibrio reveals natural predatory bacteria with specialized prey interactions

Predatory bacteria from the Bdellovibrio and Like Organisms (BALOs) group represent promising alternatives to conventional antibiotics, yet their presence in the human microbiome has remained unconfirmed through cultivation. While molecular detection methods have identified Bdellovibrionaceae DNA in human-associated environments, viable predatory bacteria had never been successfully isolated from human samples, limiting our understanding of their ecology and therapeutic potential. Here, we report the first successful isolation and characterization of viable Bdellovibrio strains from human fecal samples. Despite extremely low natural abundance requiring enrichment protocols for detection, two of five pooled samples yielded viable predators with characteristic lytic activity. Whole-genome sequencing of two isolates revealed >99% average nucleotide identity to the reference strain HD100 with only 26 total single nucleotide polymorphisms, indicating minimal genomic divergence between human-associated and environmental strains. Comparative genomic analysis of 163 publicly available Bdellovibrio genomes demonstrated that only 10.4% represented true B. bacteriovorus sensu stricto, highlighting substantial cryptic diversity within this genus. Pangenome analysis across 41 genomes revealed a highly conserved core genome ([~]2,500-2,650 genes) contrasting with an expanding accessory genome, reflecting functional constraints of obligate predation alongside ecological adaptation. Notably, human-associated isolates exhibited narrower prey ranges, including some multidrug-resistant isolates. These findings establish that predatory bacteria are naturally associated with the human intestinal environment without acquiring novel virulence factors, support their biosafety profile for therapeutic development, and reveal prey specialization that may reflect adaptation to human microbiome ecology. IMPORTANCEThis work demonstrates that bacterial predation operates as an active ecological process within the human microbiota. The successful isolation of viable Bdellovibrio establishes that predatory bacteria are viable microbiota members maintaining their predatory phenotype. Genomic conservation (>99% ANI to environmental strains) indicates that predation imposes stringent functional constraints superseding niche-specific adaptations. Our findings reframe microbiome understanding by revealing that predation (a top-down regulatory mechanism) operates in human-associated communities, potentially functioning as a keystone ecological process maintaining diversity through predator-prey dynamics. For microbiome research, this establishes a novel framework for host-microbe-microbe interactions where rare predators may exert disproportionate impacts on community assembly and dysbiosis pathogenesis. This work opens unprecedented opportunities for developing ecologically-informed therapeutics that harness natural predation to simultaneously combat multidrug-resistant infections while restoring microbiota homeostasis, positioning predatory bacteria as a cornerstone strategy for antimicrobial resistance management through ecological microbiota restoration.

microbiology↗

bioRxiv2025

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate

Plasmids are autonomously replicating DNA molecules that stably coexist with chromosomes in bacterial cells. These genetic elements drive horizontal gene transfer and play a fundamental role in bacterial ecology and evolution. Theory suggests that plasmids might evolve faster than chromosomes, as the mutation rate per gene should proportionally increase with plasmid copy number. However, the segregation of plasmid copies to daughter cells is random, introducing an additional layer of genetic drift, known as segregational drift, that might delay plasmid evolution. The interplay between plasmid mutational supply and segregational drift determines the evolutionary rate of plasmid-encoded genes, yet the relative contribution of these opposite forces in plasmid evolution remains unclear. Here, we took a classical population genetics framework to devise a mathematical approximation that predicts the fate of plasmid mutations in bacterial populations. We then validate these predictions by integrating computational, experimental, and bioinformatic approaches. Our findings show that plasmid mutation rates scale logarithmically with copy number: while increasing copy number elevates the mutation rate, the effect diminishes at higher copy numbers, where additional copies yield only marginal increases. Nonetheless, the supply of new mutations consistently surpasses the impact of segregational drift across all copy number levels. These results underscore plasmids as powerful platforms for bacterial evolvability and help explain their remarkable prevalence across microbial phylogeny.

microbiology↗

bioRxiv2024

Plasmid-chromosome transcriptional crosstalk in multidrug resistant clinical enterobacteria

Conjugative plasmids promote the dissemination and evolution of antimicrobial resistance in bacterial pathogens. However, plasmid acquisition can produce physiological alterations in the bacterial host, leading to potential fitness costs that determine the clinical success of bacteria-plasmid associations. In this study, we used a transcriptomic approach to characterize the interactions between a globally disseminated carbapenem resistance plasmid, pOXA-48, and a diverse collection of multidrug resistant clinical enterobacteria. Although pOXA-48 produced mostly strain-specific transcriptional alterations, it also led to the common overexpression of a small chromosomal operon present in Klebsiella spp. and Citrobacter freundii strains. This operon included two genes coding for a pirin and an isochorismatase family proteins (pfp and ifp), and showed evidence of horizontal mobilization across Proteobacteria species. Combining genetic engineering, transcriptomics, and CRISPRi gene silencing, we showed that a pOXA-48-encoded LysR regulator is responsible for the plasmid-chromosome crosstalk. Crucially, the operon overexpression produced a fitness benefit in a pOXA-48-carrying K. pneumoniae clinical strain, suggesting that this crosstalk promotes the dissemination of carbapenem resistance in clinical settings.

microbiology↗

bioRxiv2024

Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria

Plasmids are extrachromosomal genetic elements commonly found in bacteria. Plasmids are known to fuel bacterial evolution through horizontal gene transfer (HGT), but recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond HGT remains poorly explored. In this study, we investigate the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of various multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveil that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded insertion sequence 1 (IS1) elements. Specifically, IS1-mediated gene inactivations expedite the adaptation rate of clinical strains in vitro and foster within-patient adaptation in the gut microbiota. We decipher the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings propose that plasmid-mediated IS transposition represents a crucial mechanism for swift bacterial adaptation.

microbiology↗

bioRxiv2023

Bdellovibrio's Prey-Independent Growth is Fuelled by Amino Acids as a Carbon Source

Identifying the nutritional requirements and growth conditions of microorganisms is crucial for determining their applicability in industry and understanding their role in clinical ecology. Predatory bacteria such as Bdellovibrio bacteriovorus have emerged as promising tools for combating infections by human bacterial pathogens due to their natural killing features. Bdellovibrios lifecycle occurs inside prey cells, using the cytoplasm as a source of nutrients and energy. However, this lifecycle supposes a challenge when determining the specific uptake of metabolites from the prey to complete the growth inside cells, a process that has not been completely elucidated. Here, following a model-based approach we illuminate the ability of Bdellovibrio bacteriovorus to replicate DNA, increase biomass, and generate adenosine triphosphate (ATP) in an amino acid-based rich media in the absence of prey, keeping intact its predatory capacity. In this culture, we determined the main carbon sources used and their preference, being glutamate, serine, aspartate, isoleucine, and threonine. This study offers new insights into the role of predatory bacteria in natural environments and establishes the basis for developing new Bdellovibrio applications using appropriate metabolic and physiological methodologies.

microbiology↗

bioRxiv2023

β-lactamase expression induces collateral sensitivity in Escherichia coli

Major antibiotic groups are losing effectiveness due to the uncontrollable spread of antimicrobial resistance (AMR) genes. Among these, {beta}-lactam resistance genes -encoding {beta}-lactamases- stand as the most common resistance mechanism in Enterobacterales due to their frequent association with mobile genetic elements. In this context, novel approaches that counter mobile AMR are urgently needed. Collateral sensitivity (CS) occurs when the acquisition of resistance to one antibiotic increases susceptibility to another antibiotic and can be exploited to selectively eliminate AMR. However, most CS networks described so far emerge as a consequence of chromosomal mutations and cannot be leveraged to tackle mobile AMR. Here, we dissected the CS response elicited by the acquisition of a prevalent antibiotic resistance plasmid to reveal that the expression of the {beta}-lactamase blaOXA-48 induces CS to colistin and azithromycin. We next showed that expression of other clinically relevant mobile {beta}-lactamases produces similar CS responses in multiple, phylogenetically unrelated E. coli strains. Finally, by combining experiments with surveillance data comprising thousands of antibiotic susceptibility tests, we showed that {beta}-lactamase-induced CS is pervasive within Enterobacterales. These results highlight that the physiological side-effects of {beta}-lactamases can be leveraged therapeutically, paving the way for the rational design of specific therapies to block mobile AMR or at least counteract their effects.

microbiology↗

bioRxiv2021

Predation Efficiency upon Clinical Isolates: Bdellovibrio bacteriovorus is Prey Specific and Origin Dependent

The use of predatory bacteria as live antibiotics has been proposed for managing bacterial infections, especially for those caused by antibiotic multiresistant isolates for which there are few therapeutic options. However, the current knowledge in this field is scarce, with most of the available data based on environmental isolates, with a significant lack of human clinical samples. In this study, we evaluated the predatory spectrum of the reference strain Bdellovibrio bacteriovorus 109J on 13 Serratia marcescens (5 of which were carbapenemase producers) and 78 Pseudomonas aeruginosa clinical isolates from respiratory (colonizing the lungs of patients with cystic fibrosis) or bacteremic infections, differentiated by phenotype (mucoid or not), antibiotic resistance phenotype (including multidrug-resistant isolates), and genetic lineage (frequent and rare sequence types). The source of the isolates was significantly associated with predation efficiency (100% for S. marcescens, 67% for P. aeruginosa from cystic fibrosis, and 25% for P. aeruginosa from bacteremia). In contrast, no correlation with colonial morphotype, genetic background, or antibiotic susceptibility was found. To evaluate the influence of the predator on the predation event, we employed a more aggressive B. bacteriovorus mutant 109J preying upon the same 48 bacteremic P. aeruginosa isolates. The mutants predation efficiency was higher than that of their wild-type counterpart (43% vs. 25%), pointing out that predation is specific to each prey-predator pair of isolates. Our results provide the most extensive study of clinical prey susceptibility published to date and show that the prey-predator interaction is influenced by the origin of the isolates rather than by their genetic background or their antibiotic susceptibility phenotype. IMPORTANCEThe potential usefulness of predatory bacteria in controlling human pathogens, particularly those that are multiresistant to antibiotics, is enormous. Although this possibility has long been suggested, there are still no data on predation susceptibility in clinical strains, and the possible presence of autochthonous predators of the human microbiota has not been investigated. In this study, we employed a reference predator with an environmental origin to study predation phenomena in 3 well-characterized collections of human clinical isolates. Our results demonstrated that predation is a specific consequence of each prey-predator interaction, with the origin of the strains the most relevant factor. In contrast, the genetic background, morphotype, and antibiotic resistance did not appear to influence the predation phenomenon. We also highlight the involvement of a putative polyhydroxyalkanoate depolymerase protein of B. bacteriovorus in determining prey susceptibility. To our knowledge, this study is the largest performed with strains of clinical origin, discriminating between various genera and including strains with multiresistance to antibiotics.

ecology↗

bioRxiv2020

Collateral Sensitivity Associated with Antibiotic Resistance Plasmids

Collateral sensitivity (CS) is a promising alternative approach to counteract the rising problem of antibiotic resistance (ABR). CS occurs when the acquisition of resistance to one antibiotic produces increased susceptibility to a second antibiotic. For CS to be widely applicable in clinical practice, it would need to be effective against the different resistance mechanisms available to bacteria. Recent studies have focused on CS strategies designed against ABR mediated by chromosomal mutations. However, one of the main drivers of ABR in clinically relevant bacteria is the horizontal transfer of ABR genes mediated by plasmids. Here, we report the first analysis of CS associated with the acquisition of complete ABR plasmids, including the clinically important carbapenem-resistance conjugative plasmid pOXA-48. In addition, we describe the conservation of CS in clinical E. coli isolates and its application to the selective elimination of plasmid-carrying bacteria. Our results provide new insights that establish the basis for developing CS-informed treatment strategies to combat plasmid-mediated ABR.

microbiology↗

bioRxiv2020

Providing new insights on the byphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling.

In this study we analyze the growth-phase dependent metabolic states of Bdellovibrio bacteriovorus by constructing a fully compartmented, mass and charge-balanced genome-scale metabolic model of this predatory bacterium (iCH457). Considering the differences between life cycle phases driving the growth of this predator, growth-phase condition-specific models have been generated allowing the systematic study of its metabolic capabilities. Using these unprecedented computational tools, we have been able to analyze, from a system level, the dynamic metabolism of the predatory bacteria as the life cycle progresses. We provide solid computational evidences supporting potential axenic growth of B. bacteriovoruss in a rich medium based its encoded metabolic capabilities. Our systems-level analysis confirms the presence of "energy-saving" mechanisms in this predator as well as an abrupt metabolic shift between the attack and intraperiplasmic growth phases. Our results strongly suggest that predatory bacterias metabolic networks have low robustness, likely hampering their ability to tackle drastic environmental fluctuations, thus being confined to stable and predictable habitats. Overall, we present here a valuable computational testbed based on predatory bacteria activity for rational design of novel and controlled biocatalysts in biotechnological/clinical applications. AUTHOR SUMMARYBacterial predation is an interspecific relationship widely extended in nature. Among other predators, Bdellovibrio and like organism (BALOs) have received recently a great attention due to the high potential applications such as biocontrol agent in medicine, agriculture, aquaculture and water treatment. Despite the increasing interest in of this predatory bacterium its complex lifestyle and growth conditions hamper the full exploitation of their biotechnological properties. In order to overcome these important shortcomings, we provide here the first genome-scale model of a predator bacterium constructed so far. By using the model as a computational testbed, we provide solid evidences of the metabolic autonomy of this interesting bacterium in term of growth, as well as its dynamic metabolism powering the biphasic life style of this predator. We found a low metabolic robustness thus suggesting that Bdellovibrio is more niche-specific than previously thought and that the environmental conditions governing predation may be relatively uniform. Overall, we provide here a valuable computational tool largely facilitating rational design of novel and controlled predator-based biocatalysts in biotechnological/clinical applications.

systems biology↗