Biology subjects

Elena, A. X.

Publications and source records attributed to Elena, A. X..

7 recordsLinked to original sources

bioRxiv2026

Microbial community diversity predicts invasion resistance of freshwater biofilms against antibiotic-resistant bacteria

Rivers receive continuous inputs of antibiotic-resistant bacteria (ARB) from wastewater, agriculture, and other anthropogenic sources, yet it remains unclear whether the recipient ecological component and its microbial communities determine whether introduced ARB establish or disappear. Ecological invasion theory predicts that invasion success depends on biodiversity, community stability, and occupation of ecological niche space, but these mechanisms have rarely been evaluated together in natural microbial communities. Here, we challenged river biofilms collected from 20 sites in 12 European rivers across six countries with a model antibiotic-resistant Escherichia coli carrying a conjugative IncP-1 plasmid The invasion assays were carried out under standardized laboratory flume conditions. River biofilms differed markedly in their permissiveness to invasion despite identical invasion conditions. Higher bacterial diversity consistently accelerated invader loss rates, whereas communities containing more abundant and diverse close phylogenetic neighbours of the invader exhibited stronger exclusion during early biofilm establishment. Diversity loss during transition into the experimental system emerged as the strongest explanatory variable of invasion resistance prior to biofilm maturation, whereas Shannon diversity became the dominant predictor in mature communities. Integrating these complementary ecological dimensions substantially improved explanatory prediction of ARB persistence compared with individual predictors alone. Particularly invasion-resistant biofilms also exhibited distinct ecological community composition consistent with mature, structurally complex microbial assemblages. Together, our findings demonstrate that the establishment of ARB in the environment is not stochastic but can be predicted from measurable ecological properties of recipient microbiomes, highlighting microbial biodiversity and community organization as natural barriers to antimicrobial resistance dissemination.

microbiology↗

bioRxiv2026

Resistance to the conjugation inhibitor AZT reveals mating partner incompatibility during plasmid transfer

Plasmid-mediated dissemination of antibiotic resistance genes (ARGs) is a major driver of antimicrobial resistance (AMR). The nucleoside analogue zidovudine (azidothymidine, AZT) has emerged as a promising conjugation inhibitor, yet the consequences of AZT resistance for subsequent plasmid transfer remain poorly understood. Here, we investigated how AZT resistance in donor and recipient bacteria influences conjugative plasmid transfer. Independent AZT-resistant mutants arose through nonsense mutations in two distinct thymidine metabolism genes, yjjG and tdk. Consistent with previous studies, AZT suppressed plasmid transfer 10-fold between susceptible mating partners, whereas resistance in both partners restored transfer despite continued AZT exposure. Unexpectedly, plasmid transfer was markedly reduced even in the absence of AZT when only one mating partner carried a resistance mutation, declining by up to 11.5-fold regardless of whether the resistant strain was the donor or the recipient. This mixed-resistance phenotype was rescued by supplementation with dTMP, a thymidine pathway metabolite downstream of both resistance-associated mutations, thereby increasing plasmid transfer by up to 5.88-fold and restoring transfer to levels comparable to those of susceptible-susceptible matings. In contrast, excess dTMP reduced conjugation between susceptible partners, supporting a broader role for balanced nucleotide metabolism in determining conjugation efficiency. Together, our findings identify nucleotide metabolism as a previously unrecognised determinant of conjugative plasmid transfer and suggest that the long-term efficacy of conjugation inhibitors such as AZT will depend not only on the evolution of resistance, but also on how resistance reshapes the physiological compatibility of bacterial mating partners. ImportanceAntibiotic resistance spreads rapidly because conjugative plasmids transfer resistance genes between bacteria. Drugs that inhibit plasmid transfer are therefore being explored as a new strategy to limit antimicrobial resistance, but little is known about how resistance against these compounds affects subsequent gene transfer. We show that resistance to the conjugation inhibitor zidovudine (AZT) does not simply restore plasmid transfer. Instead, transfer depends on the resistance status of both mating partners. While two susceptible or two resistant bacteria transferred plasmids efficiently, mixed susceptible-resistant pairings showed markedly reduced conjugation even in the absence of AZT. Restoring thymidine metabolism rescued this phenotype, identifying balanced nucleotide metabolism as a previously unrecognised determinant of conjugative plasmid transfer. These findings suggest that the long-term performance of conjugation inhibitors will depend not only on the evolution of resistance, but also on how resistance reshapes the physiological compatibility of bacterial mating partners, providing a new framework for understanding and designing anti-conjugation strategies.

microbiology↗

bioRxiv2026

Reusable immobilised quaternary ammonium particles reduce microbial and resistome burdens without promoting resistance selection during wastewater post-treatment.

Wastewater treatment plants act as convergence zones for antibiotic residues, antibiotic-resistant bacteria (ARB), and antimicrobial resistance genes (ARGs), yet conventional processes are not designed to mitigate resistance dissemination from their effluents. While chemical disinfectants are generally effective, soluble quaternary ammonium compounds (QACs) can generate subinhibitory exposure gradients that promote resistance selection and co-selection both during treatment and after release into receiving waters. Here, we evaluate a contact-restricted alternative: benzyldimethyldodecyl ammonium chloride (BDMDAC) immobilised onto hydroxyapatite microparticles as a reusable and retainable post-treatment polishing strategy. Across single-strain assays, treated wastewater exposure, and experimental community evolution, immobilised BDMDAC-functionalised particles (BDMDAC-FPs) achieved concentration-dependent antimicrobial activity without detectable biocide leaching. Optimal exposure (200 mg/L, 4 h) resulted in a ~5.5 log reduction in total bacterial abundance and removal of clinically relevant ARGs. Antimicrobial efficacy was retained after one reuse cycle, supporting operational stability. Plasmid-borne QAC ARGs did not confer protection, and no enrichment of qac-associated or non-QAC ARGs was observed. Conjugation assays demonstrated suppression of horizontal gene transfer even under suboptimal exposure, and mobility-associated markers remained stable or declined during long-term community incubation. Collectively, the data support a contact-restricted mechanism in which antimicrobial pressure is spatially confined to the particle interface, generating high local lethality while limiting diffuse subinhibitory exposure. This spatial confinement decouples antimicrobial efficacy from classical disinfectant-driven resistance selection and mobility amplification. Immobilised BDMDAC-FPs therefore provide a mechanistically distinct and evolution-conscious framework for wastewater polishing technologies.

microbiology↗

bioRxiv2024

Fish are poor sentinels for surveillance of riverine AMR

Effective surveillance of antimicrobial resistance (AMR) in the environment is crucial for assessing the human and animal health risk of AMR pollution. Wastewater treatment plants (WWTPs) are one of the main sources of AMR pollutants discharged into water bodies. One important factor for assessing the risks associated with such pollution is the colonization potential of the resistant bacteria (ARB) and resistance genes (ARGs) from the environment into human or animal microbiomes upon exposure. This study explores whether fish can act as sentinels for surveillance of AMR pollution in general and specifically the human colonization potential of ARB in rivers impacted by WWTP effluents. Two riverine fish species, Brown trout, and European bullhead, were sampled up- and downstream a German WWTP. The two fish species were chosen due to their different lifestyles: Trout are mainly actively swimming in the water phase, while bullheads are sedentary and river sediment-associated. The bacterial microbiomes and resistomes of fish gills, skin, and feces were compared with those of the respective river water and sediment up- and downstream of the WWTP. Microbiomes of both fish mirrored the changes in river water and sediment downstream of the WWTP, with significant shifts in bacterial community composition, particularly an increase in Proteobacteria and Verrucomicrobia. However, increases in ARG abundances observed in water and sediment downstream of the WWTP were not reflected in any of the fish-associated resistomes. This indicates that while the fish microbiome is sensitive to environmental changes, resistomes of poikilothermic animals such as fish are less responsive to colonization by ARB originating from WWTPs and may not serve as effective sentinels for assessing AMR pollution and colonization risks in freshwater environments. This study highlights the complexity of using wildlife as indicators for environmental AMR pollution and suggests that other species are better suited for surveillance efforts. HighlightsO_LIWWTP effluent affected downstream river microbiome composition of water and sediment C_LIO_LIWWTP effluent significantly increased the level of six tested ARGs downstream C_LIO_LIChanges in environmental microbiome composition were mirrored in trout and bullhead C_LIO_LINo effect of the WWTP effluent on resistomes and individual ARG abundance in fishes C_LI

microbiology↗

bioRxiv2024

Jellyfish blooms - an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments

Jellyfish, and gelatinous zooplankton (GZ) in general, represent an important component of marine food webs. Certain GZ species are capable of generating massive blooms of severe environmental impact. These blooms are often followed by a sudden collapse of the entire population, introducing considerable amounts of organic matter (GZ-OM) in the oceans interior. GZ-OM represents an abundant substrate to promote bacterial growth and copious colonizable surface for microbial interactions. Hence we hypothesized that this GZ-OM serves as a yet overlooked hotspot for transmitting antimicrobial resistance genes (ARGs) in marine environments. For this we experimentally evolved and analyzed marine microbial communities in microcosms in presence and absence of OM from scyphozoan Aurelia aurita s.l. and ctenophore Mnemiopsis leidyi. Communities evolved under GZ-OM exposure displayed an up to 4-fold increase in relative ARG and an up to 10-fold increase in abundance of horizontally transferable mobile genetic elements (MGEs) per 16S rRNA gene copy compared to the controls. This trait was consistent across ARG and MGE classes and independent of the GZ species, suggesting that the underlying mechanism is indeed based on the general influx of nutrients and colonizable surfaces. Potential ARG carriers included known key GZ-OM degraders, but also genera containing potential pathogens hinting towards an increased risk of ARG transfer to pathogenic strains. Here, Vibrio were pinpointed as potential key species directly associated with several significantly elevated ARGs and MGEs. Subsequent whole-genome sequencing of a Vibrio isolate from the microcosm experiment revealed the genetic potential for the mobilization and transfer of ARGs in GZ-OM degrading microbial consortia. With this study, we established the first link between two emerging issues of marine coastal zones, jellyfish blooms and AMR spread, both likely increasing in projected future ocean scenarios.

microbiology↗

bioRxiv2023

Cigarette smoking promotes the spread of antimicrobial resistance in the human lung and the environment

While immediate health risks of cigarette smoking are well-established, indirect health impacts of cigarette-derived pollutants through proliferation of antimicrobial resistance (AMR) among bacteria remain understudied. Here, exposure to cigarette smoke condensate at relevant concentrations resulted in >2-fold elevated transfer rates of a multi-drug-resistance encoding plasmid between Pseudomonas strains in artificial lung sputum medium. This effect was connected to elevated reactive oxygen species production as part of the bacterial stress response when exposed to cigarette-derived toxicants. Similar results were obtained under exposure to cigarette ash leachate in environmental medium. Further, used cigarette filters enriched in toxic residues were submerged in a wastewater stream, and colonized by altered microbial communities compared to unused filters. These communities were significantly enriched in pathogens and AMR. Hence, filters could facilitate hitchhiking of high-risk bacteria to novel environments. We demonstrate that cigarette-derived compounds can promote the spread of AMR within the human lung and natural environments.

microbiology↗

bioRxiv2022

Quantification of the mobility potential of antibiotic resistance genes through multiplexed ddPCR linkage analysis

Antibiotic resistance genes (ARGs) are widely disseminated within microbiomes of the human, animal, and environmental spheres. There is a clear need for global monitoring and risk assessment initiatives to evaluate the risks of ARGs towards human health. Therefore, not only ARG abundances within a given environment, but also their mobility, hence their ability to spread to human pathogenic bacteria needs to be quantified. Consequently, methods to accurately quantify the linkage of ARGs with mobile genetic elements are urgently needed. We developed a novel, sequencing-independent method for assessing ARG mobility by combining multiplexed droplet digital PCR (ddPCR) on DNA sheared into short fragments with statistical analysis. This allows quantifying the physical linkage between ARGs and mobile genetic elements, here demonstrated for the sulfonamide ARG sul1 and the Class1 integron integrase gene intI1. The methods efficiency is demonstrated using mixtures of model DNA fragments with either linked and unlinked target genes: Linkage of the two target genes can be accurately quantified based on high correlation coefficients between observed and expected values (R2) as well as low mean absolute errors (MAE) for both target genes, sul1 (R2=0.9997, MAE=0.71%, n=24) and intI1 (R2=0.9991, MAE=1.14%, n=24). Furthermore, we demonstrate that the chosen fragmentation length of DNA during shearing allows adjusting the rate of false positives and false negative detection of linkage. The applicability of the developed method for environmental samples is further demonstrated by assessing the mobility of sul1 across a wastewater treatment plant. The presented method allows rapidly obtaining reliable results within hours. It is labor- and costefficient and does not rely on sequencing technologies. Furthermore, it has a high potential to be scaled up to multiple targets. Consequently, it merits consideration to be included within global AMR surveillance initiatives for assessing ARG mobility. Author AbstractAntibiotic resistance represents a major problem in treating bacterial infections and endangers public health. Antibiotic resistant genes (ARGs) can spread among microbes in humans, animals, and the environment, thanks to mobile genetic elements. These are genetic structures involved in the mobility of genetic information and hence microbial traits. Methods that allow simultaneously quantifying the abundance of ARGs together with their association/linkage with mobile genetic elements are fundamental for assessing the risk they pose to human health, as mobility increases their likelihood to spread to human pathogens. Here we developed a novel method that allows to quantify the abundance and the linkage between ARGs and mobile genetic elements. The method relies on droplet digital PCR (ddPCR) technology performed on fragmented environmental DNA (of a chosen size), combined with statistical analysis. We found that the method accurately quantifies the linkage between the two targets in model and environmental DNA. The method is delivering rapid, labor- and cost-efficient results as it does not rely on technology that require prior bioinformatics knowledge and can be included in future monitoring frameworks.

microbiology↗