Biology subjects

Erdem, E. D.

Publications and source records attributed to Erdem, E. D..

4 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

Cycles of contamination and recovery: Combined sewer overflows drive acute but transient antimicrobial resistance exposure in an urban stream

Combined sewer overflows (CSOs) are a major pathway for untreated wastewater into urban streams, yet their role in shaping antimicrobial resistance (AMR) dynamics remains poorly understood. Here, we used high-frequency, time-resolved sampling during two storm-triggered CSO events across two monitoring locations and one stormwater-only control site in an urban stream to quantify how these disturbances affect microbial communities, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) in an urban stream. CSO events caused rapid, up to two orders of magnitude, increases in bacterial, pathogen, and ARG abundance, with multiple transient peaks occurring within single overflow episodes. However, these increases were largely proportional to the total bacterial load, and most ARGs and MGEs did not change in relative abundance, indicating that CSOs primarily act as mass-transfer events rather than drivers of in situ selection. Downstream attenuation was governed by hydrological dilution despite additional CSO inputs: Both microbial and resistance signals largely returned to baseline within short time frames. This demonstrates that CSOs function as hydrologically driven pulse disturbances that generate acute but transient AMR exposure. Because CSO events lack the sustained pressure associated with continuous wastewater discharges, rapid washout prevents the long-term establishment of sewage-derived resistance. These findings highlight that AMR risk in CSO-impacted systems is driven primarily by short-term exposure rather than by persistent ecological transformation, with important implications for urban water management under increasingly extreme rainfall conditions.

microbiology↗

bioRxiv2025

Selective spread of mobile antibiotic resistance genes in wastewater microbiomes driven by the non-antibiotic pharmaceutical carbamazepine

Carbamazepine (CBZ), a widely used anticonvulsant, is a persistent aquatic micropollutant that withstands biodegradation and accumulates in wastewater-impacted environments. While non-antibiotic pharmaceuticals, including CBZ, have been shown to stimulate horizontal gene transfer (HGT) under laboratory conditions, their effects in complex microbial communities remain poorly understood. Here, we applied an experimental evolution framework to wastewater microbiomes exposed to a gradient of environmentally relevant CBZ concentrations (0-50 {micro}g/mL) for three days. CBZ reduced growth of the community in a concentration-dependent manner. Still, community composition was largely unaffected by CBZ exposure. However, antibiotic resistance gene (ARG)- and mobile genetic element (MGE)-specific responses emerged. Among the tested 26 ARGs, four clinically relevant ones (blaCMY, blaOXA-48, blaCTX-M, dfrA1) increased in relative abundance in a dose-dependent manner, correlating with proliferation of IncP and IncW plasmids and the transposon IS26, pointing to enhanced HGT as the underlying mechanism. In contrast, only ermF abundance rose independently of MGEs, suggesting direct selection. Other ARGs and MGEs, including integron integrase intI1 and IncQ plasmids, showed no consistent CBZ response. Effects were strongest at subinhibitory concentrations (0.05-5 {micro}g/mL), matching upper levels detected in surface waters. These findings demonstrate that CBZ can selectively promote AMR dissemination through both HGT and direct selection, but in a targeted rather than community-wide manner. Our results highlight the need to consider non-antibiotic pharmaceuticals in AMR surveillance and environmental risk assessment frameworks, as they may shape the environmental resistome beyond antibiotic exposure.

microbiology↗