Genome-Wide Association Study Reveals Host Factors Affecting Conjugation in Escherichia coli

Plasmid-bacteria associations in the clinical context

Antimicrobial resistance (AMR) is one of the most pressing global health problems, with plasmids playing a central role in its evolution and dissemination. Over the past decades, many studies have investigated the ecoevolutionary dynamics between plasmids and their bacterial hosts. However, what drives the epidemiological success of certain plasmid-bacterium associations remains unclear. In this opinion article, we review which factors influence these associations and underline that studying plasmid-host interactions of clinical relevance is critical for understanding the evolution and spread of AMR. We also highlight the increasing importance of integrating experimental research with bioinformatics and machine learning tools to study plasmid-bacteria dynamics. This combined approach will assist researchers to dissect the molecular mechanisms underlying successful plasmid-host associations and to design strategies to prevent and predict future high-risk associations.

Conjugal plasmid transfer in the plant rhizosphere in the One Health context

Introduction

Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is one of the primary routes of antimicrobial resistance (AMR) dissemination. In the One Health context, tracking the spread of mobile genetic elements (MGEs) carrying ARGs in agri-food ecosystems is pivotal in understanding AMR diffusion and estimating potential risks for human health. So far, little attention has been devoted to plant niches; hence, this study aimed to evaluate the conjugal transfer of ARGs to the bacterial community associated with the plant rhizosphere, a hotspot for microbial abundance and activity in the soil. We simulated a source of AMR determinants that could enter the food chain via plants through irrigation.

Methods

Among the bacterial strains isolated from treated wastewater, the strain Klebsiella variicola EEF15 was selected as an ARG donor because of the relevance of Enterobacteriaceae in the AMR context and the One Health framework. The strain ability to recolonize lettuce, chosen as a model for vegetables that were consumed raw, was assessed by a rifampicin resistant mutant. K. variicola EEF15 was genetically manipulated to track the conjugal transfer of the broad host range plasmid pKJK5 containing a fluorescent marker gene to the natural rhizosphere microbiome obtained from lettuce plants. Transconjugants were sorted by fluorescent protein expression and identified through 16S rRNA gene amplicon sequencing.

Results and discussion

K. variicola EEF15 was able to colonize the lettuce rhizosphere and inhabit its leaf endosphere 7 days past bacterial administration. Fluorescence stereomicroscopy revealed plasmid transfer at a frequency of 10-3; cell sorting allowed the selection of the transconjugants. The conjugation rates and the strain's ability to colonize the plant rhizosphere and leaf endosphere make strain EEF15::lacIq-pLpp-mCherry-gmR with pKJK5::Plac::gfp an interesting candidate to study ARG spread in the agri-food ecosystem. Future studies taking advantage of additional environmental donor strains could provide a comprehensive snapshot of AMR spread in the One Health context.

The role of water matrix on antibiotic resistance genes transmission in substrate layer from stormwater bioretention cells

Recently, extensive attention has been paid to antibiotic resistance genes (ARGs) transmission. However, little available literature could be found about ARGs transmission in stormwater bioretention cells, especially the role of water matrix on ARGs transmission. Batch experiments were conducted to investigate target ARGs (blaTEM, tetR and aphA) transmission behaviors in substrate layer from stormwater bioretention cells under different water matrices, including nutrient elements (e.g., carbon, nitrogen and phosphorus), water environmental conditions (dissolved oxygen (DO), pH and salinity, etc.) and pollution factors (like heavy metals, antibiotics and disinfectants), showing that ARGs conjugation frequency increased sharply with the enhancement of water matrices (expect DO and pH), while there were obvious increasing tendencies for all ARGs transformation frequencies under only the pollution factor. The correlation between dominant bacteria and ARGs transmission implied that conjugation and transformation of ARGs were mainly determined by Firmicutes, Bacteroidota, Latescibacterota, Chloroflexi and Cyanobacteria at the phylum level, and by Sphingomonas, Ensifer, IMCC26256, Rubellimicrobium, Saccharimonadales, Vicinamibacteraceae, Nocardioides, JG30-KF-CM66 at the genus level. The mentioned dominant bacteria were responsible for intracellular reactive oxygen species (ROS) and cell membrane permeability (CMP) in the substrate layer, where the amplification of intracellular ROS variation were the largest with 144 and 147 % under the condition of TP and salinity, respectively, and the one of CMP variation were the highest more than 165 % under various pollution factors. Furthermore, both increasing DO and reducing salinity could be potential approaches for the inhibition of ARGs transmission in bioretention cells taking into account the simultaneous removal of conventional pollutants.

Word-based GWAS harnesses the rich potential of genomic data for E. coli quinolone resistance

Quinolone resistance presents a growing global health threat. We employed word-based GWAS to explore genomic data, aiming to enhance our understanding of this phenomenon. Unlike traditional variant-based GWAS analyses, this approach simultaneously captures multiple genomic factors, including single and interacting resistance mutations and genes. Analyzing a dataset of 92 genomic E. coli samples from a wastewater treatment plant in Dresden, we identified 54 DNA unitigs significantly associated with quinolone resistance. Remarkably, our analysis not only validated known mutations in gyrA and parC genes and the results of our variant-based GWAS but also revealed new (mutated) genes such as mdfA, the AcrEF-TolC multidrug efflux system, ptrB, and hisI, implicated in antibiotic resistance. Furthermore, our study identified joint mutations in 14 genes including the known gyrA gene, providing insights into potential synergistic effects contributing to quinolone resistance. These findings showcase the exceptional capabilities of word-based GWAS in unraveling the intricate genomic foundations of quinolone resistance.

Special Issue "Multidrug-Resistant Bacteria in the Environment, Their Resistance and Transfer Mechanisms"

Multidrug-resistant bacteria are an emerging issue which is not restricted to clinics and the health care sector, but is increasingly affecting the environment [...].