Biology subjects

Kneis, D.

Publications and source records attributed to Kneis, D..

3 recordsLinked to original sources

bioRxiv2023

Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance?

BackgroundIn the environment, microbial communities are constantly exposed to invasion by antimicrobial resistant bacteria (ARB) and their associated antimicrobial resistance genes (ARGs) that were enriched in the anthroposphere. A successful invader has to overcome the biotic resilience of the habitat, which is more difficult with increasing biodiversity. The capacity to exploit resources in a given habitat is enhanced when communities exhibit greater diversity, reducing opportunities for invaders, leading to a lower persistence. In the context of antimicrobial resistance (AMR) dissemination, exogenous ARB reaching a natural community may persist longer if the biodiversity of the autochthonous community is low, increasing the chance of ARGs to transfer to community members. Reciprocally, high microbial diversity could serve as a natural long-term barrier towards invasion by ARB and ARGs. ResultsTo test this hypothesis, a sampling campaign across seven European countries was carried out to obtain 172 environmental samples from sites with low anthropogenic impact. Samples were collected from contrasting environments: stationary structured forest soils, or dynamic river biofilms and sediments. Microbial diversity and relative abundance of 27 ARGs and 5 mobile genetic element marker genes were determined. In soils, higher diversity, evenness and richness were all significantly negatively correlated with the relative abundance of the majority (>85%) of ARGs. Furthermore, the number of detected ARGs per sample was inversely correlated with diversity. However, no such effects were found for the more dynamic, regularly mixed rivers. Conclusions: In conclusion, we demonstrate that diversity can serve as barrier towards AMR dissemination in the environment. This effect is mainly observed in stationary, structured environments, where long-term, diversity-based resilience against invasion can evolve. Such barrier effects can in the future be exploited to limit the environmental proliferation of AMR.

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↗

bioRxiv2021

Estimating the conjugative transfer rate of antibiotic resistance genes: Effect of model structural errors

The spread of antibiotic resistance genes (ARG) occurs widely through plasmid transfer majorly facilitated via bacterial conjugation. To assess the spread of these mobile ARG, it is necessary to develop appropriate tools to estimate plasmid transfer rates under different environmental conditions. Process-based models are widely used for the estimation of plasmid transfer rate constants. Empirical studies have repeatedly highlighted the importance of subtle processes like delayed growth, the maturation of transconjugants, the physiological cost of plasmid carriage, and the dependence of conjugation on the cultures growth stage. However, models used for estimating the transfer rates typically neglect them. We conducted virtual mating experiments to quantify the impact of these four typical structural model deficits on the estimated plasmid transfer rate constants. We found that under all conditions, the plasmid cost and the lag phase in growth must be taken into account to obtain unbiased estimates of plasmid transfer rate constants. We observed a tendency towards the underestimation of plasmid transfer rate constants when structurally deficient models were fitted to virtual mating data. This holds for all the structural deficits and mating conditions tested in our study. Our findings might explain an important component of the negative bias in model predictions known as the plasmid paradox. We also discuss other structural deficits that could lead to an overestimation of plasmid transfer rate constants and we demonstrate the impact of ill-fitted parameters on model predictions.

microbiology↗