Horizontal Gene Transfer of an IncP1 Plasmid to Soil Bacterial Community Introduced by Escherichia coli through Manure Amendment in Soil Microcosms

Dissemination mechanisms of unique antibiotic resistance genes from flowback water to soil revealed by combined Illumina and Nanopore sequencing

As a byproduct of shale gas extraction, flowback water (FW) is produced in large quantities globally. Due to the unique interactions between pollutants and microorganisms, FW always harbor multiple antibiotic resistance genes (ARGs) that have been confirmed in our previous findings, potentially serving as a point source for ARGs released into the environment. However, whether ARGs in FW can disseminate or integrate into the environmental resistome remains unclear. In this study, unique ARGs from FW were identified, and the ARG profiles in soil and FW-spiked soil were compared using a combination of Illumina and Nanopore sequencing. The results indicated that the total abundance of the soil resistome increased by 30.8 % in soil contaminated with FW. Of this increase, 11.1 % was attributable to the integration of exogenous ARGs from FW into the soil resistome. Sequence alignment at the gene level further confirmed the successful integration of 20 unique ARG sequences classified as multidrug and vancomycin resistance genes into the soil resistome. These 20 ARG sequences were detected only in the FW. Multiple lines of evidence indicated that horizontal gene transfer dominated ARG dissemination in soil contaminated by FW. This conclusion is supported by the discrepancy between changes in mobile ARGs and host abundance, the upregulation of oxidative stress-related genes (SOD1 and SOD2) and the SOS response (lexA and recA), as well as the upregulation of genes related to quorum sensing (virD4, virB9, and virB3) and naked DNA uptake (pilD, pilT, and pilQ).

Detection of rare plasmid hosts using a targeted Hi-C approach

Despite the significant role plasmids play in microbial evolution, there is limited knowledge of their ecology, evolution, and transfer in microbial communities. This is partly due to the limitations of current methods in associating a plasmid with its host in microbiomes. To address this knowledge gap, we developed and implemented a novel approach to identify rare plasmid hosts by combining Hi-C, a proximity ligation method, with enrichment for plasmid-specific DNA. We hereafter refer to this approach as Hi-C+. We applied Hi-C and Hi-C+ to soil microbial communities in which we mimicked increasingly rare transfer of an antimicrobial resistance plasmid from a donor to a recipient. This was achieved by inoculating agricultural soil with mixtures of known plasmid-containing and plasmid-free cells at different proportions. We demonstrated that Hi-C can link a plasmid to its host in soil when the relative abundance of that plasmid-host pair is as low as 0.001%. Hi-C+ further improved the detection limit of Hi-C 100-fold and allowed the identification of plasmid hosts at the genus level. As a culture-independent approach, Hi-C+ will significantly improve our understanding of the range and frequency of spread of antibiotic resistance and other genes that are introduced into soil and other microbiomes.

Mechanisms and influencing factors of horizontal gene transfer in composting system: A review

Organic solid wastes such as livestock manure and sewage sludge are important sources and repositories of antibiotic resistance genes (ARGs). Composting, a solid waste treatment technology, has demonstrated efficacy in degrading various antibiotics and reducing ARGs. However, some recalcitrant ARGs (e.g., sul1, sul2) will enrich during the composting maturation period. These ARGs persist in compost products and spread through horizontal gene transfer (HGT). We analyzed the reasons behind the increase of ARGs during the maturation phase. It was found that the proliferation of ARG-host bacteria and HGT process play an important role. This article revealed that microbial physiological responses, environmental factors, pollutants, and quorum sensing (QS) can all influence the HGT process in composting systems. We examined the influence of these factors on HGT in the compost system and summarized potential mechanisms by analyzing the alterations in microbial communities. We comprehensively summarized the HGT hazards that these factors may present in composting systems. Finally, we summarized methods to inhibit HGT in compost, such as using additives, quorum sensing inhibitors (QSIs), microbial inoculation, and predicting HGT events. Overall, the HGT mechanism and driving force in complex composting systems are still insufficiently studied. In view of the current situation, using predictions to assess the risk of HGT in composting may be advisable.

Assessing horizontal gene transfer in the rhizosphere of Brachypodium distachyon using fabricated ecosystems (EcoFABs)

Horizontal gene transfer (HGT) is a major process by which genes are transferred between microbes in the rhizosphere. However, examining HGT remains challenging due to the complexity of mimicking conditions within the rhizosphere. Fabricated ecosystems (EcoFABs) have been used to investigate several complex processes in plant-associated environments. Here we show that EcoFABs are efficient tools to examine and measure HGT frequency in the rhizosphere. We provide the first demonstration of gene transfer via a triparental conjugation system in the Brachypodium distachyon rhizosphere in an EcoFAB using Pseudomonas putida KT2440 as both donor and recipient bacterial strain with the donor containing a mobilizable and non-self-transmissible plasmid. We observed that the frequency of plasmid transfer in the rhizosphere is potentially dependent on the plant developmental stage and the composition and amount of root exudates. The frequency of plasmid transfer also increased with higher numbers of donor cells. We demonstrate the transfer of plasmid from P. putida to another B. distachyon root colonizer, Burkholderia sp. OAS925, showing HGT within a rhizosphere microbial community. Environmental stresses also influenced the rate and efficiency of HGT in the rhizosphere between different species and genera. This study provides a robust workflow to evaluate transfer of engineered plasmids in the rhizosphere when such plasmids are potentially introduced in a field or other plant-associated environments.IMPORTANCEWe report the use of EcoFABs to investigate the HGT process in a rhizosphere environment. It highlights the potential of EcoFABs in recapitulating the dynamic rhizosphere conditions as well as their versatility in studying plant-microbe interactions. This study also emphasizes the importance of studying the parameters impacting the HGT frequency. Several factors such as plant developmental stages, nutrient conditions, number of donor cells, and environmental stresses influence gene transfer within the rhizosphere microbial community. This study paves the way for future investigations into understanding the fate and movement of engineered plasmids in a field environment.

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.

Accumulation of antibiotics in the environment: Have appropriate measures been taken to protect Canadian human and ecological health?

In Canada, every day, contaminants of emerging concern (CEC) are discharged from waste treatment facilities into freshwaters. CECs such as pharmaceutical active compounds (PhACs), personal care products (PCPs), per- and polyfluoroalkyl substances (PFAS), and microplastics are legally discharged from sewage treatment plants (STPs), water reclamation plants (WRPs), hospital wastewater treatment plants (HWWTPs), or other forms of wastewater treatment facilities (WWTFs). In 2006, the Government of Canada established the Chemicals Management Plan (CMP) to classify chemicals based on a risk-priority assessment, which ranked many CECs such as PhACs as being of low urgency, therefore permitting these substances to continue being released into the environment at unmonitored rates. The problem with ranking PhACs as a low priority is that CMP's risk management assessment overlooks the long-term environmental and synergistic effects of PhAC accumulation, such as the long-term risk of antibiotic CEC accumulation in the spread of antibiotic resistance genes. The goal of this review is to specifically investigate antibiotic CEC accumulation and associated environmental risks to human and environmental health, as well as to determine whether appropriate legislative strategies are in place within Canada's governance framework. In this research, secondary data on antibiotic CEC levels in Canadian and international wastewaters, their potential to promote antibiotic-resistant residues, associated environmental short- and long-term risks, and synergistic effects were all considered. Unlike similar past reviews, this review employed an interdisciplinary approach to propose new strategies from the perspectives of science, engineering, and law.

Combined use of digestate and inorganic fertilizer alleviates the burden of class 1 integrons in perennial ryegrass rhizosphere without compromising aerial biomass production

Antimicrobial resistance (AMR) is one of the main global health challenges. Anaerobic digestion (AD) can significantly reduce the burden of antibiotic resistance genes (ARGs) in animal manures. However, the reduction is often incomplete. The agronomic use of digestates requires assessments of their effects on soil ARGs. The objective of this study was to assess the effect of digestate on the abundance of ARGs and mobile genetic elements (MGEs) in the rhizosphere of ryegrass (Lolium perenne L.) and to determine whether half-dose replacement of digestate with urea (combined fertilizer) can be implemented as a safer approach while maintaining a similar biomass production. A greenhouse assay was conducted during 190 days under a completely randomized design with two experimental factors: fertilizer type (unfertilized control and fertilized treatments with equal N dose: digestate, urea and combined fertilizer) and sampling date (16 and 148 days after the last application). The results indicated that the digestate significantly increased the abundance of clinical class 1 integrons (intI1 gene) relative to the unfertilized control at both sampling dates (P < 0.05), while the combined fertilizer only increased them at the first sampling. Sixteen days after completing the fertilization scheme only the combined fertilizer and urea significantly increased the biomass production relative to the control (P < 0.05). Additionally, by the end of the assay, the combined fertilizer showed significantly lower levels of the macrolide-resistance gene ermB than digestate and a cumulative biomass similar to urea or digestate. Overall, the combined fertilizer can alleviate the burden of integrons and ermB while simultaneously improving biomass production.

Low-frequency transmission and persistence of antimicrobial-resistant bacteria and genes from livestock to agricultural soil and crops through compost application

Livestock excrement is composted and applied to agricultural soils. If composts contain antimicrobial-resistant bacteria (ARB), they may spread to the soil and contaminate cultivated crops. Therefore, we investigated the degree of transmission of ARB and related antimicrobial resistance genes (ARGs) and, as well as clonal transmission of ARB from livestock to soil and crops through composting. This study was conducted at Rakuno Gakuen University farm in Hokkaido, Japan. Samples of cattle feces, solid and liquid composts, agricultural soil, and crops were collected. The abundance of Escherichia coli, coliforms, β-lactam-resistant E. coli, and β-lactam-resistant coliforms, as well as the copy numbers of ARG (specifically the bla gene related to β-lactam-resistant bacteria), were assessed using qPCR through colony counts on CHROMagar ECC with or without ampicillin, respectively, 160 days after compost application. After the application of the compost to the soil, there was an initial increase in E. coli and coliform numbers, followed by a subsequent decrease over time. This trend was also observed in the copy numbers of the bla gene. In the soil, 5.0 CFU g-1 E. coli was detected on day 0 (the day post-compost application), and then, E. coli was not quantified on 60 days post-application. Through phylogenetic analysis involving single nucleotide polymorphisms (SNPs) and using whole-genome sequencing, it was discovered that clonal blaCTX-M-positive E. coli and blaTEM-positive Escherichia fergusonii were present in cattle feces, liquid compost, and soil on day 0 as well as 7 days post-application. This showed that livestock-derived ARB were transmitted from compost to soil and persisted for at least 7 days in soil. These findings indicate a potential low-level transmission of livestock-associated bacteria to agricultural soil through composts was observed at low frequency, dissemination was detected. Therefore, decreasing ARB abundance during composting is important for public health.

Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent, plasmid transmission study

BACKGROUND

The global spread of plasmid-borne carbapenem resistance is an ongoing public health challenge; however, the nature of such horizontal gene transfer events among complex bacterial communities remains poorly understood. We examined the in-situ transfer of the globally dominant New Delhi metallo-β-lactamase (NDM)-5-positive IncX3 plasmid (denoted pX3_NDM-5) in hospital wastewater to simulate a real-world, One Health antimicrobial resistance context.

METHODS

For this transmission study, we tagged pX3_NDM-5 with the green fluorescent protein gene, gfp, using a CRISPR-based method and transferred the plasmid to a donor Escherichia coli strain. Bacteria were extracted from a hospital wastewater treatment plant (Fujian Provincial Maternity and Children's Hospital, Fuzhou, China) as the bacterial recipient community. We mixed this recipient community with the E coli donor strain carrying the gfp-tagged plasmid, both with and without sodium hypochlorite (NaClO) as an environmental stressor, and conducted several culture-based and culture-independent conjugation assays. The conjugation events were observed microscopically and quantified by fluorescence-activated cell sorting. We analysed the taxonomic composition of the sorted transconjugal pool by 16S rRNA gene amplicon sequencing and assessed the stability of the plasmid in the isolated transconjugants and its ability to transfer back to E coli.

FINDINGS

We show that the plasmid pX3_NDM-5 has a broad host range and can transfer across various bacterial phyla, including between Gram-negative and Gram-positive bacteria. Although environmental stress with NaClO did not affect the overall plasmid transfer frequency, it reduced the breadth of the transconjugant pool. The taxonomic composition of the transconjugal pool was distinct from that of the recipient communities, and environmental stress modulated the permissiveness of some operational taxonomic units towards the acquisition of pX3_NDM-5. Notably, pX3_NDM-5 transconjugants included the Gram-positive pathogen Enterococcus faecalis, and the plasmid could subsequently be reconjugated back to E coli. These findings suggest that E faecalis could act as a natural shuttle vector for the wide dissemination of pX3_NDM-5 plasmids.

INTERPRETATION

Our culture-independent conjugation model simulates natural environmental conditions and challenges the established theory that Gram-negative and Gram-positive bacteria rarely exchange clinically important plasmids. The data show that plasmids disseminate more widely across genera and phyla than previously thought. These findings have substantial implications when considering the spread of antimicrobial resistance across One Health sectors.

FUNDING

The Laboratory of Lingnan Modern Agriculture Project, the National Natural Science Foundation of China, the Natural Science Foundation of Fujian Province of China, and the Outstanding Young Research Talents Program of Fujian Agriculture and Forestry University.

Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era

Antimicrobial resistance (AMR) poses a substantial threat to human health. The widespread prevalence of AMR is, in part, due to the horizontal transfer of antibiotic resistance genes (ARGs), typically mediated by plasmids. Many of the plasmid-mediated resistance genes in pathogens originate from environmental, animal or human habitats. Despite evidence that plasmids mobilize ARGs between these habitats, we have a limited understanding of the ecological and evolutionary trajectories that facilitate the emergence of multidrug resistance (MDR) plasmids in clinical pathogens. One Health, a holistic framework, enables exploration of these knowledge gaps. In this Review, we provide an overview of how plasmids drive local and global AMR spread and link different habitats. We explore some of the emerging studies integrating an eco-evolutionary perspective, opening up a discussion about the factors that affect the ecology and evolution of plasmids in complex microbial communities. Specifically, we discuss how the emergence and persistence of MDR plasmids can be affected by varying selective conditions, spatial structure, environmental heterogeneity, temporal variation and coexistence with other members of the microbiome. These factors, along with others yet to be investigated, collectively determine the emergence and transfer of plasmid-mediated AMR within and between habitats at the local and global scale.

Development of a high-throughput platform to measure plasmid transfer frequency

Antibiotic resistance represents one of the greatest threats to global health. The spread of antibiotic resistance genes among bacteria occurs mostly through horizontal gene transfer via conjugation mediated by plasmids. This process implies a direct contact between a donor and a recipient bacterium which acquires the antibiotic resistance genes encoded by the plasmid and, concomitantly, the capacity to transfer the acquired plasmid to a new recipient. Classical assays for the measurement of plasmid transfer frequency (i.e., conjugation frequency) are often characterized by a high variability and, hence, they require many biological and technical replicates to reduce such variability and the accompanying uncertainty. In addition, classical conjugation assays are commonly tedious and time-consuming because they typically involve counting colonies on a large number of plates for the quantification of donors, recipients, and transconjugants (i.e., the bacteria that have received the genetic material by conjugation). Due to the magnitude of the antibiotic resistance problem, it is critical to develop reliable and rapid methods for the quantification of plasmid transfer frequency that allow the simultaneous analysis of many samples. Here, we present the development of a high-throughput, reliable, quick, easy, and cost-effective method to simultaneously accomplish and measure multiple conjugation events in 96-well plates, in which the quantification of donors, recipients, and transconjugants is estimated from the time required to reach a specific threshold value (OD600 value) in the bacterial growth curves. Our method successfully discriminates different plasmid transfer frequencies, yielding results that are equivalent to those obtained by a classical conjugation assay.

Microplastic biofilm: An important microniche that may accelerate the spread of antibiotic resistance genes via natural transformation

Microplastic (MP) biofilms provide a specific microniche for microbial life and are a potential hotspot for the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Nevertheless, the acquisition of ARGs in MP biofilms via natural transformation mediated by extracellular DNA (eDNA) has been rarely explored. This study demonstrated that MP biofilms promoted the natural transformation of extracellular ARGs at the single-cell and multi-species levels, compared to natural substrate (NS) biofilms and bacterioplankton. The transformation frequency on MP biofilms was up to 1000-fold compare to that on NS. The small MPs and aged MPs enhanced the ARG transformation frequencies up to 77.16-fold and 32.05-fold, respectively, compared with the large MPs and pristine MPs. The transformation frequencies on MP biofilms were significantly positively correlated with the bacterial density and extracellular polymeric substance (EPS) content (P < 0.05). Furthermore, MPs significantly increased the expression of the biofilm formation related genes (motA and pgaA) and DNA uptake related genes (pilX and comA) compared to NS and bacterioplankton. The more transformants colonized on MPs contributed to the enhanced transformation frequencies at the community-wide level. Overall, eDNA-mediated transformation in MP biofilms may be an important path of ARG spread, which was promoted by heterogeneous biofilm.

Evaporation-induced hydrodynamics control plasmid transfer during surface-associated microbial growth

Droplet evaporation is a general process in unsaturated environments that results in micro-scale hydrodynamic flows which in turn determine the spatial distributions of microbial cells across surfaces. These spatial distributions can have significant effects on the development and functioning of surface-associated microbial communities, with consequences for important processes such as the spread of plasmids. Here, we experimentally quantified how evaporation-induced hydrodynamic processes modulate the initial deposition patterns of microbial cells (via the coffee ring effect and Marangoni convection) and how these patterns control the spread of an antibiotic resistance-encoding plasmid during surface-associated growth. We found that plasmid spread is a function of the initial density of cells deposited along the droplet periphery, which is a manifestation of the coffee ring effect. Using an individual-based model, we systematically linked how the different initial cell deposition patterns caused by the relative strengths of the coffee ring effect and Marangoni convection determine the extent of plasmid transfer during surface-associated growth. Our study demonstrates that evaporation-induced hydrodynamic processes that are common in nature can alter crucial ecological properties of surface-associated microbial communities and control the proliferation of plasmids, with consequences on the spread of antibiotic resistance and other plasmid-encoded traits.

An overview of plasmid transfer in the plant microbiome

Plant microbiomes are pivotal for healthy plant physiological development. Microbes live in complex co-association with plant hosts, and interactions within these microbial communities vary with plant genotype, plant compartment, phenological stage, and soil properties, among others. Plant microbiomes also harbor a substantial and diverse pool of mobile genes encoded on plasmids. Several plasmid functions attributed to plant-associated bacteria are relatively poorly understood. Additionally, the role of plasmids in disseminating genetic traits within plant compartments is not well known. Here, we present the current knowledge on the occurrence, diversity, function, and transfer of plasmids in plant microbiomes, emphasizing the factors that could modulate gene transfer in-planta. We also describe the role of the plant microbiome as a plasmid reservoir and the dissemination of its genetic material. We include a brief discussion on the current methodological limitations in studying plasmid transfer within plant microbiomes. This information could be useful to elucidate the dynamics of the bacterial gene pools, the adaptations different organisms have made, and variations in bacterial populations that might have never been described before, particularly in complex microbial communities associated with plants in natural and anthropogenic impacted environments.

Current and Future Flow Cytometry Applications Contributing to Antimicrobial Resistance Control

Antimicrobial resistance is a global threat to human health and welfare, food safety, and environmental health. The rapid detection and quantification of antimicrobial resistance are important for both infectious disease control and public health threat assessment. Technologies such as flow cytometry can provide clinicians with the early information, they need for appropriate antibiotic treatment. At the same time, cytometry platforms facilitate the measurement of antibiotic-resistant bacteria in environments impacted by human activities, enabling assessment of their impact on watersheds and soils. This review focuses on the latest applications of flow cytometry for the detection of pathogens and antibiotic-resistant bacteria in both clinical and environmental samples. Novel antimicrobial susceptibility testing frameworks embedding flow cytometry assays can contribute to the implementation of global antimicrobial resistance surveillance systems that are needed for science-based decisions and actions.

Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks

As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.

Field ponding water exacerbates the dissemination of manure-derived antibiotic resistance genes from paddy soil to surrounding waterbodies

Farmlands fertilized with livestock manure-derived amendments have become a hot topic in the dissemination of antibiotic resistance genes (ARGs). Field ponding water connects rice paddies with surrounding water bodies, such as reservoirs, rivers, and lakes. However, there is a knowledge gap in understanding whether and how manure-borne ARGs can be transferred from paddy soil into field ponding water. Our studies suggest that the manure-derived ARGs aadA1, bla1, catA1, cmlA1-01, cmx(A), ermB, mepA and tetPB-01 can easily be transferred into field ponding water from paddy soil. The bacterial phyla Crenarchaeota, Verrucomicrobia, Cyanobacteria, Choloroflexi, Acidobacteria, Firmicutes, Bacteroidetes, and Actinobacteria are potential hosts of ARGs. Opportunistic pathogens detected in both paddy soil and field ponding water showed robust correlations with ARGs. Network co-occurrence analysis showed that mobile genetic elements (MGEs) were strongly correlated with ARGs. Our findings highlight that manure-borne ARGs and antibiotic-resistant bacteria in paddy fields can conveniently disseminate to the surrounding waterbodies through field ponding water, posing a threat to public health. This study provides a new perspective for comprehensively assessing the risk posed by ARGs in paddy ecosystems.

IncP-type plasmids carrying genes for antibiotic resistance or for aromatic compound degradation are prevalent in sequenced Aromatoleum and Thauera strains

Self-transferable plasmids of the incompatibility group P-1 (IncP-1) are considered important carriers of genes for antibiotic resistance and other adaptive functions. In the laboratory, these plasmids have a broad host range; however, little is known about their in situ host profile. In this study, we discovered that Thauera aromatica K172^T , a facultative denitrifying microorganism capable of degrading various aromatic compounds, contains a plasmid highly similar to the IncP-1 ε archetype pKJK5. The plasmid harbours multiple antibiotic resistance genes and is maintained in strain K172^T for at least 1000 generations without selection pressure from antibiotics. In a subsequent search, we found additional nine IncP-type plasmids in a total of 40 sequenced genomes of the closely related genera Aromatoleum and Thauera. Six of these plasmids form a novel IncP-1 subgroup designated θ, four of which carry genes for anaerobic or aerobic degradation of aromatic compounds. Pentanucleotide sequence analyses (k-mer profiling) indicated that Aromatoleum spp. and Thauera spp. are among the most suitable hosts for the θ plasmids. Our results highlight the importance of IncP-1 plasmids for the genetic adaptation of these common facultative denitrifying bacteria and provide novel insights into the in situ host profile of these plasmids.

Triclosan Promotes Conjugative Transfer of Antibiotic Resistance Genes to Opportunistic Pathogens in Environmental Microbiome

Although triclosan, as a widely used antiseptic chemical, is known to promote the transmission of antibiotic resistance to diverse hosts in pure culture, it is still unclear whether and how triclosan could affect the transmission of broad-host-range plasmids among complex microbial communities. Here, bacterial culturing, fluorescence-based cell sorting, and high-throughput 16S rRNA gene amplicon sequencing were combined to investigate contributions of triclosan on the transfer rate and range of an IncP-type plasmid from a proteobacterial donor to an activated sludge microbiome. Our results demonstrate that triclosan significantly enhances the conjugative transfer of the RP4 plasmid among activated sludge communities at environmentally relevant concentrations. High-throughput 16S rRNA gene sequencing on sorted transconjugants demonstrates that triclosan not only promoted the intergenera transfer but also the intragenera transfer of the RP4 plasmid among activated sludge communities. Moreover, triclosan mediated the transfer of the RP4 plasmid to opportunistic human pathogens, for example, Legionella spp. The mechanism of triclosan-mediated conjugative transfer is primarily associated with excessive oxidative stress, followed by increased membrane permeability and provoked SOS response. Our findings offer insights into the impacts of triclosan on the dissemination of antibiotic resistance in the aquatic environmental microbiome.