A high-throughput approach to the culture-based estimation of plasmid transfer rates

Horizontal gene transfer is an essential component of bacterial evolution. Quantitative information on transfer rates is particularly useful to better understand and possibly predict the spread of antimicrobial resistance. A variety of methods has been proposed to estimate the rates of plasmid-mediated gene transfer all of which require substantial labor input or financial resources. A cheap but reliable method with high-throughput capabilities is yet to be developed in order to better capture the variability of plasmid transfer rates, e.g. among strains or in response to environmental cues. We explored a new approach to the culture-based estimation of plasmid transfer rates in liquid media allowing for a large number of parallel experiments. It deviates from established approaches in the fact that it exploits data on the absence/presence of transconjugant cells in the wells of a well plate observed over time. Specifically, the binary observations are compared to the probability of transconjugant detection as predicted by a dynamic model. The bulk transfer rate is found as the best-fit value of a designated model parameter. The feasibility of the approach is demonstrated on mating experiments where the RP4 plasmid is transfered from Serratia marcescens to several Escherichia coil recipients. The methods uncertainty is explored via split sampling and virtual experiments.Peer reviewe

The spread of the plasmid RP4 in a synthetic bacterial community is dependent on the particular donor strain

The rapid spread of antibiotic resistance challenges modern medicine. So far, mechanistic and quantitative knowledge concerning the spread of resistance genes mainly relies on laboratory experiments with simplified setups, e.g. two strain communities. Thus, the transferability of the obtained process rates might be limited. To investigate the role of a diverse community concerning the dissemination of the multidrug resistance plasmid RP4, an Escherichia coli harboring RP4 invaded a microbial community consisting of 21 species. Changes in the community composition as well as plasmid uptake by community members were monitored for 22 days. Special focus was laid on the question of whether the observed changes were dependent on the actual invading donor isolate and the ambient antibiotic concentration. In our microcosm experiment, the community composition was primarily influenced by the given environmental variables and only secondarily by the particular invader E. coli. The establishment of resistance within the community, however, was directly dependent on the donor identity. The extent to which ambient conditions influence the spread of RP4 depended on the E. coli donor strain. These results emphasize that even within one species there are great differences in the ability to conquer an ecological niche and to spread antibiotic resistance.Peer reviewe

High variability of plasmid uptake rates in Escherichia coli isolated from sewage and river sediments

The horizontal transfer of plasmids is a key mechanism behind the spread of antibiotic resistance in bacteria. So far, transfer rate constants were measured for a variety of plasmids, donors and recipients. The employed strains typically had a long history in laboratories. Existing data are, therefore, not necessarily representative for real-world environments. Moreover, information on the inter-strain variability of plasmid transfer rates is scarce. Using a high-throughput approach, we studied the uptake of RP4 by various Escherichia coli recipients using Serratia marcescens as the donor. The recipient strains were isolated from human-borne sewage and river sediments. The rate constants of plasmid transfer generally followed a log-normal distribution with considerable variance. The rate constants for good and poor recipients (95 and 5% quantile) differed by more than three orders of magnitude. Specifically, the inter-strain variability of the rate constant was large in comparison to alterations induced by low-level antibiotic exposure. We did not find evidence for diverging efficiencies of plasmid uptake between E. coli recipients of different origin. On average, strains isolated from river bottom sediments were equally efficient in the acquisition of RP4 as isolates extracted from sewage. We conclude that E. coli strains persisting in the aquatic environment and those of direct human origin share a similar intrinsic potential for the conjugative uptake of certain plasmids. In view of the large inter-strain variability, we propose to work towards probabilistic modeling of the environmental spread of antibiotic resistance.Peer reviewe

Sewage from Airplanes Exhibits High Abundance and Diversity of Antibiotic Resistance Genes

Airplane sanitary facilities are shared by an international audience. We hypothesized the corresponding sewage to be an extraordinary source of antibiotic-resistant bacteria (ARB) and resistance genes (ARG) in terms of diversity and quantity. Accordingly, we analyzed ARG and ARB in airplane-borne sewage using complementary approaches: metagenomics, quantitative polymerase chain reaction (qPCR), and cultivation. For the purpose of comparison, we also quantified ARG and ARB in the inlets of municipal treatment plants with and without connection to airports. As expected, airplane sewage contained an extraordinarily rich set of mobile ARG, and the relative abundances of genes were mostly increased compared to typical raw sewage of municipal origin. Moreover, combined resistance against third-generation cephalosporins, fluorochinolones, and aminoglycosides was unusually common (28.9%) among Escherichia coli isolated from airplane sewage. This percentage exceeds the one reported for German clinical isolates by a factor of 8. Our findings suggest that airplane-borne sewage can effectively contribute to the fast and global spread of antibiotic resistance.Peer reviewe

High variability of plasmid uptake rates in Escherichia coli isolated from sewage and river sediments

The horizontal transfer of plasmids is a key mechanism behind the spread of antibiotic resistance in bacteria. So far, transfer rate constants were measured for a variety of plasmids, donors and recipients. The employed strains typically had a long history in laboratories. Existing data are, therefore, not necessarily representative for real-world environments. Moreover, information on the inter-strain variability of plasmid transfer rates is scarce. Using a high-throughput approach, we studied the uptake of RP4 by various Escherichia coli recipients using Serratia marcescens as the donor. The recipient strains were isolated from human-borne sewage and river sediments. The rate constants of plasmid transfer generally followed a log-normal distribution with considerable variance. The rate constants for good and poor recipients (95 and 5% quantile) differed by more than three orders of magnitude. Specifically, the inter-strain variability of the rate constant was large in comparison to alterations induced by low-level antibiotic exposure. We did not find evidence for diverging efficiencies of plasmid uptake between E. coli recipients of different origin. On average, strains isolated from river bottom sediments were equally efficient in the acquisition of RP4 as isolates extracted from sewage. We conclude that E. coli strains persisting in the aquatic environment and those of direct human origin share a similar intrinsic potential for the conjugative uptake of certain plasmids. In view of the large inter-strain variability, we propose to work towards probabilistic modeling of the environmental spread of antibiotic resistance

Exploring, exploiting and evolving diversity of aquatic ecosystem models: A community perspective

Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been developed since the 1970s. We set off to explore model diversity by making an inventory among 42 aquatic ecosystem modellers, by categorizing the resulting set of models and by analysing them for diversity. We then focus on how to exploit model diversity by comparing and combining different aspects of existing models. Finally, we discuss how model diversity came about in the past and could evolve in the future. Throughout our study, we use analogies from biodiversity research to analyse and interpret model diversity. We recommend to make models publicly available through open-source policies, to standardize documentation and technical implementation of models, and to compare models through ensemble modelling and interdisciplinary approaches. We end with our perspective on how the field of aquatic ecosystem modelling might develop in the next 5–10 years. To strive for clarity and to improve readability for non-modellers, we include a glossary

Habitat availability determines food chain length and interaction strength in food webs of a large lowland river

Many large rivers used for navigation have lost their hydromorphological heterogeneity, which has led to the widespread loss of native biodiversity and the concurrent establishment of non‐native communities. While the effects on biodiversity are well‐described, we know little about how the loss of natural habitats and the restructuring of communities cumulate into effects on riverine food webs. We constructed binary and ingestion webs for benthic macroinvertebrates and their resources in the Elbe River (Germany) and compared if food chain length, food web complexity, robustness, ingestion rates, and consumer‐resource interaction strength differ among three shoreline engineering practices. Food webs at profoundly altered shorelines were significantly less complex and had significantly shorter food chains than the food web at the semi‐natural shoreline. However, food web robustness to a simulated loss of species was comparable at all shorelines. Total ingestion rates were up to eight times lower at highly altered shorelines due to significantly lower ingestion rates by native species. Predator–prey interaction strength was comparable among shorelines due to higher shares of non‐native predators, indicating that non‐native predators can be functionally equivalent to native predators. We attributed the observed food web differences to the absence of complex habitats at profoundly altered shorelines and the accompanied absence of specialized consumers. Our study provides empirical evidence that hydromorphological modifications reduce the efficiency of food webs to control organic matter dynamics and may ultimately affect the provisioning of riverine ecosystem services

Evaluating the potential of radar-based rainfall estimates for streamflow and flood simulations in the Philippines

This case study evaluates the suitability of radar-based quantitative precipitation estimates (QPEs) for the simulation of streamflow in the Marikina River Basin (MRB), the Philippines. Hourly radar-based QPEs were produced from reflectivity that had been observed by an S-band radar located about 90 km from the MRB. Radar data processing and precipitation estimation were carried out using the open source library wradlib. To assess the added value of the radar-based QPE, we used spatially interpolated rain gauge observations (gauge-only (GO) product) as a benchmark. Rain gauge observations were also used to quantify rainfall estimation errors at the point scale. At the point scale, the radar-based QPE outperformed the GO product in 2012, while for 2013, the performance was similar. For both periods, estimation errors substantially increased from daily to the hourly accumulation intervals. Despite this fact, both rainfall estimation methods allowed for a good representation of observed streamflow when used to force a hydrological simulation model of the MRB. Furthermore, the results of the hydrological simulation were consistent with rainfall verification at the point scale: the radar-based QPE performed better than the GO product in 2012, and equivalently in 2013. Altogether, we could demonstrate that, in terms of streamflow simulation, the radar-based QPE can perform as good as or even better than the GO product – even for a basin such as the MRB which has a comparatively dense rain gauge network. This suggests good prospects for using radar-based QPE to simulate and forecast streamflow in other parts of the Philippines where rain gauge networks are not as dense