High diversity and rapid spatial turnover of integron gene cassettes in soil

Discovery of cytosine deaminases enables base-resolution methylome mapping using a single enzyme

Deaminases have important uses in modification detection and genome editing. However, the range of applications is limited by the small number of characterized enzymes. To expand the toolkit of deaminases, we developed an in vitro approach that bypasses a major hurdle with their toxicity in cells. We assayed 175 putative cytosine deaminases on a variety of substrates and found a broad range of activity on double- and single-stranded DNA in various sequence contexts, including CpG-specific deaminases and enzymes without sequence preference. We also characterized enzyme selectivity across six DNA modifications and reported enzymes that do not deaminate modified cytosines. The detailed analysis of diverse deaminases opens new avenues for biotechnological and medical applications. As a demonstration, we developed SEM-seq, a non-destructive single-enzyme methylation sequencing method using a modification-sensitive double-stranded DNA deaminase. The streamlined protocol enables accurate, base-resolution methylome mapping of scarce biological material, including cell-free DNA and 10 pg input DNA.

Microbial biofilms on macroalgae harbour diverse integron gene cassettes

Integrons are genetic platforms that capture, rearrange and express mobile modules called gene cassettes. The best characterized gene cassettes encode antibiotic resistance, but the function of most integron gene cassettes remains unknown. Functional predictions suggest that many gene cassettes could encode proteins that facilitate interactions with other cells and with the extracellular environment. Because cell interactions are essential for biofilm stability, we sequenced gene cassettes from biofilms growing on the surface of the marine macroalgae Ulva australis and Sargassum linearifolium. Algal samples were obtained from coastal rock platforms around Sydney, Australia, using seawater as a control. We demonstrated that integrons in microbial biofilms did not sample genes randomly from the surrounding seawater, but harboured specific functions that potentially provided an adaptive advantage to both the bacterial cells in biofilm communities and their macroalgal host. Further, integron gene cassettes had a well-defined spatial distribution, suggesting that each bacterial biofilm acquired these genetic elements via sampling from a large but localized pool of gene cassettes. These findings suggest two forms of filtering: a selective acquisition of different integron-containing bacterial species into the distinct biofilms on Ulva and Sargassum surfaces, and a selective retention of unique populations of gene cassettes at each sampling location.

Dissecting molecular evolution of class 1 integron gene cassettes and identifying their bacterial hosts in suburban creeks via epicPCR

OBJECTIVES

Our study aimed to sequence class 1 integrons in uncultured environmental bacterial cells in freshwater from suburban creeks and uncover the taxonomy of their bacterial hosts. We also aimed to characterize integron gene cassettes with altered DNA sequences relative to those from databases or literature and identify key signatures of their molecular evolution.

METHODS

We applied a single-cell fusion PCR-based technique-emulsion, paired isolation and concatenation PCR (epicPCR)-to link class 1 integron gene cassette arrays to the phylogenetic markers of their bacterial hosts. The levels of streptomycin resistance conferred by the WT and altered aadA5 and aadA11 gene cassettes that encode aminoglycoside (3″) adenylyltransferases were experimentally quantified in an Escherichia coli host.

RESULTS

Class 1 integron gene cassette arrays were detected in Alphaproteobacteria and Gammaproteobacteria hosts. A subset of three gene cassettes displayed signatures of molecular evolution, namely the gain of a regulatory 5'-untranslated region (5'-UTR), the loss of attC recombination sites between adjacent gene cassettes, and the invasion of a 5'-UTR by an IS element. Notably, our experimental testing of a novel variant of the aadA11 gene cassette demonstrated that gaining the observed 5'-UTR contributed to a 3-fold increase in the MIC of streptomycin relative to the ancestral reference gene cassette in E. coli.

CONCLUSIONS

Dissecting the observed signatures of molecular evolution of class 1 integrons allowed us to explain their effects on antibiotic resistance phenotypes, while identifying their bacterial hosts enabled us to make better inferences on the likely origins of novel gene cassettes and IS that invade known gene cassettes.

Insights into antibiotic resistance-related changes in microbial communities, resistome and mobilome in paddy irrigated with reclaimed wastewater

Reclaimed wastewater (reclaimed wastewater, RWW) from municipal wastewater treatment plants for paddy irrigation is a well-established practice to alleviate water scarcity. However, the reuse may result in the persistent exposure of the paddy to residual antibiotics in RWW. Continuous presence of even low-level antibiotics can exert selective pressure on microbiota, resulting in the proliferation and dissemination of antibiotic resistance genes (ARGs) in paddy. In this study, metagenomic analysis was applied to firstly deciphered the effects of residual antibiotics on microbiome and resistome in constructed mesocosm-scale paddy soils. The diversity and abundance of ARG have remarkably risen with the increasing antibiotic concentration in RWW. Network analysis revealed that 28 genera belonging to six phyla were considered as the potential ARG hosts, and their abundances were enhanced with increasing antibiotic concentrations. A partial least-squares path model indicated that the microbial community was the principal direct driver of the ARG abundance and the resistome alteration in paddy soil under long-term RWW irrigation. Microbes may acquire ARGs via horizontal gene transfer. IntI1 could play an essential role in the propagation and spread of ARGs. Functional analysis suggested that enhanced SOS response and T4SSs (Type IV secretion systems) modules could stimulate horizontal transfer potential and promote the ARG abundance. The obtained results provide a scientific decision for assessing the ecological risk of RWW application.

Functional enrichment of integrons: Facilitators of antimicrobial resistance and niche adaptation

Integrons are genetic elements, found among diverse bacteria and archaea, that capture and rearrange gene cassettes to rapidly generate genetic diversity and drive adaptation. Despite their broad taxonomic and geographic prevalence, and their role in microbial adaptation, the functions of gene cassettes remain poorly characterized. Here, using a combination of bioinformatic and experimental analyses, we examined the functional diversity of gene cassettes from different environments. We find that cassettes encode diverse antimicrobial resistance (AMR) determinants, including those conferring resistance to antibiotics currently in the developmental pipeline. Further, we find a subset of cassette functions is universally enriched relative to their broader metagenomes. These are largely involved in (a)biotic interactions, including AMR, phage defense, virulence, biodegradation, and stress tolerance. The remainder of functions are sample-specific, suggesting that they confer localised functions relevant to their microenvironment. Together, they comprise functional profiles different from bulk metagenomes, representing niche-adaptive components of the prokaryotic pangenome.

Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments

Many human activities contaminate terrestrial and aquatic environments with numerous chemical pollutants that not only directly alter the environment but also affect microbial communities in ways that are potentially concerning to human health, such as selecting for the spread of antibiotic-resistance genes (ARGs) through horizontal gene transfer. In the present study, metagenomes available in the public domain from polluted (with antibiotics, with petroleum, with metal mining, or with coal-mining effluents) and unpolluted terrestrial and aquatic environments were compared to examine whether pollution has influenced the abundance and composition of ARGs and mobile elements, with specific focus on IS26 and class 1 integrons (intI1). When aggregated together, polluted environments had a greater relative abundance of ARGs than unpolluted environments and a greater relative abundance of IS26 and intI1. In general, chemical pollution, notably with petroleum, was associated with an increase in the prevalence of ARGs linked to multidrug efflux pumps. Included in the suite of efflux pumps were mexK, mexB, mexF, and mexW that are polyspecific and whose substrate ranges include multiple classes of critically important antibiotics. Also, in some instances, β-lactam resistance (TEM181 and OXA-541) genes increased, and genes associated with rifampicin resistance (RNA polymerases subunits rpoB and rpoB2) decreased in relative abundance. This meta-analysis suggests that different types of chemical pollution can enrich populations that carry efflux pump systems associated with resistance to multiple classes of medically critical antibiotics.IMPORTANCEThe United Nations has identified chemical pollution as being one of the three greatest threats to environmental health, through which the evolution of antimicrobial resistance, a seminally important public health challenge, may be favored. While this is a very plausible outcome of continued chemical pollution, there is little evidence or research evaluating this risk. The objective of the present study was to examine existing metagenomes from chemically polluted environments and evaluate whether there is evidence that pollution increases the relative abundance of genes and mobile genetic elements that are associated with antibiotic resistance. The key finding is that for some types of pollution, particularly in environments exposed to petroleum, efflux pumps are enriched, and these efflux pumps can confer resistance to multiple classes of medically important antibiotics that are typically associated with Pseudomonas spp. or other Gram-negative bacteria. This finding makes clear the need for more investigation on the impact of chemical pollution on the environmental reservoir of ARGs and their association with mobile genetic elements that can contribute to horizontal gene transfer events.

Effects of the coexistence of antibiotics and heavy metals on the fate of antibiotic resistance genes in chicken manure and surrounding soils

Both heavy metals and antibiotics exert selection pressure on bacterial resistance, and as they are commonly co-contaminated in the environment, they may play a larger role in bacterial resistance. This study examined how breeding cycles affect antibiotic resistance genes (ARGs) in chicken manure and the surrounding topsoils at 20, 50, 100, 200, and 300 m from twelve typical laying hen farms in the Ningxia Hui Autonomous Region of northwest China. Six antibiotics, seven heavy metals, ten mobile genetic elements (MGEs), and microbial community affected the ARGs profile in chicken dung and soil samples. Tetracycline antibiotic residues were prevalent in chicken manure, as were relatively high content of aureomycin during each culture period. Zinc (Zn) content was highest among the seven heavy metals in chicken feces. Chicken dung also enriched aminoglycosides, MLSB, and tetracycline ARGs, notably during brooding and high production. The farm had a minimal influence on antibiotics in the surrounding soil, but its effect on ARGs and MGEs closer to the farm (50 m) was stronger, and several ARGs and MGEs increased with distance. Manure microbial composition differed dramatically throughout breeding cycles and sampling distances. ARGs were more strongly related with antibiotics and heavy metals in manure than soil, whereas MGEs were the reverse. Antibiotics, heavy metals, MGEs, and bacteria in manure accounted 12.28%, 22.25%, 0.74%, and 0.19% of ARGs composition variance, respectively, according to RDA and VPA. Bacteria (2.89%) and MGEs (2.82%) only affected soil ARGs composition. These findings showed that heavy metals and antibiotics are the main factors affecting faecal ARGs and bacteria and MGEs soil ARGs. This paper includes antibiotic resistance data for large-scale laying hen husbandry in northwest China and a theoretical framework for decreasing antibiotic resistance.

Integrons in the development of antimicrobial resistance: critical review and perspectives

Antibiotic resistance development and pathogen cross-dissemination are both considered essential risks to human health on a worldwide scale. Antimicrobial resistance genes (AMRs) are acquired, expressed, disseminated, and traded mainly through integrons, the key players capable of transferring genes from bacterial chromosomes to plasmids and their integration by integrase to the target pathogenic host. Moreover, integrons play a central role in disseminating and assembling genes connected with antibiotic resistance in pathogenic and commensal bacterial species. They exhibit a large and concealed diversity in the natural environment, raising concerns about their potential for comprehensive application in bacterial adaptation. They should be viewed as a dangerous pool of resistance determinants from the "One Health approach." Among the three documented classes of integrons reported viz., class-1, 2, and 3, class 1 has been found frequently associated with AMRs in humans and is a critical genetic element to serve as a target for therapeutics to AMRs through gene silencing or combinatorial therapies. The direct method of screening gene cassettes linked to pathogenesis and resistance harbored by integrons is a novel way to assess human health. In the last decade, they have witnessed surveying the integron-associated gene cassettes associated with increased drug tolerance and rising pathogenicity of human pathogenic microbes. Consequently, we aimed to unravel the structure and functions of integrons and their integration mechanism by understanding horizontal gene transfer from one trophic group to another. Many updates for the gene cassettes harbored by integrons related to resistance and pathogenicity are extensively explored. Additionally, an updated account of the assessment of AMRs and prevailing antibiotic resistance by integrons in humans is grossly detailed-lastly, the estimation of AMR dissemination by employing integrons as potential biomarkers are also highlighted. The current review on integrons will pave the way to clinical understanding for devising a roadmap solution to AMR and pathogenicity. Graphical AbstractThe graphical abstract displays how integron-aided AMRs to humans: Transposons capture integron gene cassettes to yield high mobility integrons that target res sites of plasmids. These plasmids, in turn, promote the mobility of acquired integrons into diverse bacterial species. The acquisitions of resistant genes are transferred to humans through horizontal gene transfer.

Tracing the Sources and Prevalence of Class 1 Integrons, Antimicrobial Resistance, and Trace Elements Using European Honey Bees

Surveillance of antimicrobial resistance is essential for an effective One Health response. This study explores the efficacy of European honey bees (Apis mellifera) for biomonitoring antimicrobial resistance (AMR) in urban areas. Class 1 integrons (intI1) are investigated as a universal AMR indicator, as well as associated cassette arrays and trace element contaminants at a city-wide scale. Class 1 integrons were found to be pervasive across the urban environment, occurring in 52% (75/144) of the honey bees assessed. The area of waterbodies within the honey bee's foraging radius was associated with intI1 prevalence, indicating an exposure pathway for future investigation to address. Trace element concentrations in honey bees reflected urban sources, supporting the application of this biomonitoring approach. As the first study of intI1 in honey bees, we provide insights into the environmental transfer of bacterial DNA to a keystone species and demonstrate how intI1 biomonitoring can support the surveillance of AMR.

Class 1 integron and related antimicrobial resistance gene dynamics along a complex freshwater system affected by different anthropogenic pressures

The risk for human health posed by polluted aquatic environments, and especially those carrying antibiotic resistance genes (ARGs) of clinical interest, is still debated. This is because of our limited knowledge of the dynamics of antimicrobial resistance in the environment, the selection mechanisms underlying the spread of ARGs, and the ecological factors potentially favoring their return to humans. The Class 1 integron is one of the most effective platforms for the dissemination of ARGs. In this study we investigated a freshwater system consisting of a lake-river-lake continuum, determining the abundance of class 1 integrons and their associated ARGs by a modulated metagenomic approach. Bacterial abundance and community composition were used to identify the potential carriers of class 1 integrons and their associated ARGs over a period of six months. Class 1 integrons and their ARG cargoes were significantly more abundant in riverine sampling sites receiving treated wastewater. Further, class 1 integrons carried ARGs ranked at the highest risk for human health (e.g., catB genes), in particular, genes encoding resistance to aminoglycosides. Genera of potential pathogens, such as Pseudomonas and Escherichia-Shigella, were correlated with class 1 integrons. The lake-river-lake system demonstrated a clear relationship between the integrase gene of class 1 integrons (intI1) and anthropogenic impact, but also a strong environmental filtering that favored the elimination of intI1 once the human derived stressors were reduced. Overall, the results of this study underline the role class 1 integrons as proxy of anthropogenic pollution and suggest this genetic platform as an important driver of aminoglycoside resistance genes, including high risk ARGs, of potential concern for human health.

Uncovering the diversity and contents of gene cassettes in class 1 integrons from the endophytes of raw vegetables

Rapid spread of antibiotic resistance genes (ARGs) in pathogens is threatening human health. Integrons allow bacteria to integrate and express foreign genes, facilitating horizontal transfer of ARGs in environments. Consumption of raw vegetables represents a pathway for human exposure to environmental ARGs. However, few studies have focused on integron-associated ARGs in the endophytes of raw vegetables. Here, based on the approach of qPCR and clone library, we quantified the abundance of integrase genes and analyzed the diversity and contents of resistance gene cassettes in class 1 integrons from the endophytes of six common raw vegetables. The results revealed that integrase genes for class 1 integron were most prevalent compared with class 2 and class 3 integron integrase genes (1-2 order magnitude, P < 0.05). The cucumber endophytes harbored a higher absolute abundance of integrase genes than other vegetables, while the highest bacterial abundance was detected in cabbage and cucumber endophytes. Thirty-two unique resistance gene cassettes were detected, the majority of which were associated with the genes encoding resistance to beta-lactam and aminoglycoside. Antibiotic resistance gene cassettes accounted for 52.5 % of the functionally annotated gene cassettes, and bla_TEM-157 and aadA2 were the most frequently detected resistance cassettes. Additionally, carrot endophytes harbored the highest proportion of antibiotic resistance gene cassettes in the class 1 integrons. Collectively, these results provide an in-depth view of acquired resistance genes by integrons in the raw vegetable endophytes and highlight the potential health risk of the transmission of ARGs via the food chain.

Discovery of integrons in Archaea: Platforms for cross-domain gene transfer

Horizontal gene transfer between different domains of life is increasingly being recognized as an important evolutionary driver, with the potential to increase the pace of biochemical innovation and environmental adaptation. However, the mechanisms underlying the recruitment of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria. However, they have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here, we discover that integrons are also present in 75 archaeal metagenome-assembled genomes from nine phyla, and are particularly enriched among Asgard archaea. Furthermore, we provide experimental evidence that integrons can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a previously unknown mechanism of cross-domain gene transfer whereby bacteria can incorporate archaeal genes from their surrounding environment via integron activity. These findings have important implications for prokaryotic ecology and evolution.

Nanopore sequencing analysis of integron gene cassettes in sewages and soils

Integrons are genetic elements that can facilitate rapid spread of antibiotic resistance by insertion and removal of genes. However, knowledge about the diversity and distribution of gene cassettes embedded in class 1 integron is still limited. In this study, we sequenced integron gene cassettes using nanopore sequencing and quantified antibiotic resistance genes (ARGs) and integrase genes in the manured soils and sewages of a bioreactor. The results showed that class 1 integron integrase genes were the most abundant in soils and sewages compared with class 2 and class 3 integrase genes. Long-term manure application exacerbated the enrichment of total ARGs, integrase genes and antibiotic resistance-associated gene cassettes, while antibiotics and heavy metals showed no impact on the overall resistome profile. Sewage treatment could efficiently remove the absolute abundance of integrase genes (~3 orders of magnitude, copies/L) and antibiotic resistance gene cassettes. The resistance gene cassettes mainly carried the ARGs conferring resistance to aminoglycoside and beta-lactams in soils and sewages, some of which were persistent during the sewage treatment. This study underlined that soil and sewage were potential reservoirs for integron-mediated ARGs transfer, indicating that anthropogenic activity played a vital role in the prevalence and diversity of resistance gene cassettes in integrons.

Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities

Integrons are microbial genetic elements that can integrate mobile gene cassettes. They are mostly known for spreading antibiotic resistance cassettes among human pathogens. However, beyond clinical settings, gene cassettes encode an extraordinarily diverse range of functions important for bacterial adaptation. The recovery and sequencing of cassettes has promising applications, including: surveillance of clinically important genes, particularly antibiotic resistance determinants; investigating the functional diversity of integron-carrying bacteria; and novel enzyme discovery. Although gene cassettes can be directly recovered using PCR, there are no standardised methods for their amplification and, importantly, for validating sequences as genuine integron gene cassettes. Here, we present reproducible methods for the amplification, sequence processing, and validation of gene cassette amplicons from complex communities. We describe two different PCR assays that either amplify cassettes together with integron integrases, or gene cassettes together within cassette arrays. We compare the performance of Nanopore and Illumina sequencing, and present bioinformatic pipelines that filter sequences to ensure that they represent amplicons from genuine integrons. Using a diverse set of environmental DNAs, we show that our approach can consistently recover thousands of unique cassettes per sample and up to hundreds of different integron integrases. Recovered cassettes confer a wide range of functions, including antibiotic resistance, with as many as 300 resistance cassettes found in a single sample. In particular, we show that class one integrons are collecting and concentrating resistance genes out of the broader diversity of cassette functions. The methods described here can be applied to any environmental or clinical microbiome sample.

Environmental integrons: the dark side of the integron world

Integrons are bacterial genetic elements notorious for their role in spreading antibiotic resistance in clinical settings. In the natural environment, integrons present a wide and hidden diversity, raising questions as to their broader role in bacterial adaptation. From the One Health perspective, they must be considered a threatening pool of resistance determinants.

Genetic characterization of ESBL/pAmpC-producing Escherichia coli isolated from forest, urban park and cereal culture soils

Little is known about the role of forestland and non-fertilized agriculture soils as reservoirs of extended-spectrum beta-lactamase (ESBL) and plasmid-borne AmpC (pAmpC)-producing Escherichia coli isolates. Thus, in the present study, 210 soil samples from various origins (forest of Oued Zen (Ain Drahem), non-agriculture soils from different park gardens in Tunis City, cereal culture soils and home gardens) were investigated to characterize cefotaxime-resistant E. coli isolates. A total of 22 ESBL/pAmpC-producing E. coli were collected, and all harbored variants of the blaCTX-M gene (15 blaCTX-M-1, 5 blaCTX-M-55 and 2 blaCTX-M-15). A total of seven and two isolates harbored also blaEBC and blaDHA-like genes, respectively. Resistances to tetracycline, sulfonamides and fluoroquinolones were encoded by tetA (n = 4)/tetB (n = 12), sul1 (n = 17)/sul2 (n = 19) and aac(6')-Ib-cr (n = 2)/qnrA (n = 1)/qnrS (n = 1) genes, respectively. A total of seven isolates were able to transfer by conjugation cefotaxime-resistance in association or not with other resistance markers. PFGE showed that ten and two isolates were clonally related (pulsotypes P1 and P2). The 10 P1 isolates had been collected from forestland, cereal culture soils and an urban park garden in Tunis City, arguing for a large spread of clonal strains. Our findings highlight the occurrence of ESBL/pAmpC-E. coli isolates in soils under limited anthropogenic activities and the predominance of CTX-M enzymes that are largely disseminated in E. coli from humans and animals in Tunisia.

High Prevalence and Factors Associated With the Distribution of the Integron intI1 and intI2 Genes in Scottish Cattle Herds

Integrons are genetic elements that capture and express antimicrobial resistance genes within arrays, facilitating horizontal spread of multiple drug resistance in a range of bacterial species. The aim of this study was to estimate prevalence for class 1, 2, and 3 integrons in Scottish cattle and examine whether spatial, seasonal or herd management factors influenced integron herd status. We used fecal samples collected from 108 Scottish cattle herds in a national, cross-sectional survey between 2014 and 2015, and screened fecal DNA extracts by multiplex PCR for the integrase genes intI1, intI2, and intI3. Herd-level prevalence was estimated [95% confidence interval (CI)] for intI1 as 76.9% (67.8-84.0%) and intI2 as 82.4% (73.9-88.6%). We did not detect intI3 in any of the herd samples tested. A regional effect was observed for intI1, highest in the North East (OR 11.5, 95% CI: 1.0-130.9, P = 0.05) and South East (OR 8.7, 95% CI: 1.1-20.9, P = 0.04), lowest in the Highlands. A generalized linear mixed model was used to test for potential associations between herd status and cattle management, soil type and regional livestock density variables. Within the final multivariable model, factors associated with herd positivity for intI1 included spring season of the year (OR 6.3, 95% CI: 1.1-36.4, P = 0.04) and watering cattle from a natural spring source (OR 4.4, 95% CI: 1.3-14.8, P = 0.017), and cattle being housed at the time of sampling for intI2 (OR 75.0, 95% CI: 10.4-540.5, P < 0.001). This study provides baseline estimates for integron prevalence in Scottish cattle and identifies factors that may be associated with carriage that warrant future investigation.

The Natural History of Integrons

Integrons were first identified because of their central role in assembling and disseminating antibiotic resistance genes in commensal and pathogenic bacteria. However, these clinically relevant integrons represent only a small proportion of integron diversity. Integrons are now known to be ancient genetic elements that are hotspots for genomic diversity, helping to generate adaptive phenotypes. This perspective examines the diversity, functions, and activities of integrons within both natural and clinical environments. We show how the fundamental properties of integrons exquisitely pre-adapted them to respond to the selection pressures imposed by the human use of antimicrobial compounds. We then follow the extraordinary increase in abundance of one class of integrons (class 1) that has resulted from its acquisition by multiple mobile genetic elements, and subsequent colonisation of diverse bacterial species, and a wide range of animal hosts. Consequently, this class of integrons has become a significant pollutant in its own right, to the extent that it can now be detected in most ecosystems. As human activities continue to drive environmental instability, integrons will likely continue to play key roles in bacterial adaptation in both natural and clinical settings. Understanding the ecological and evolutionary dynamics of integrons can help us predict and shape these outcomes that have direct relevance to human and ecosystem health.

Metagenomic strategies identify diverse integron-integrase and antibiotic resistance genes in the Antarctic environment

The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high-throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non-Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D β-lactamase (blaOXA-205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase (aadA6), and the other is a qacG2 gene.

Microbial and chemical pollutants on the manure-crops pathway in the perspective of "One Health" holistic approach

This study determined the impact of poultry and bovine manure fertilization on the content of antibiotics, heavy metals (HMs), and the quantitative and qualitative composition of integrase and antibiotic resistance genes in soil, groundwater, and crops cultivated on manure-amended plots. Antibiotic concentration levels were analyzed using the HPLC-MS/MS, heavy metal concentration level were measured by HGAAS and ICP-OES, while the integrase genes and ARGs were quantified using Real-Time PCR (qPCR) method. Manure, soil, and crops samples contained the highest concentration of Zn (10⁴-10⁵ ng g_dm^-1) and Cu (10³-10⁵ ng g_dm^-1) of all HMs tested. Manure-supplemented soil was characterised by a high concentration of doxycycline and enrofloxacin. A high abundance of integrase genes was noted in samples of manure (10⁹-10¹⁰ copies g_dm^-1) and soil (10⁷-10⁸ copies g_dm^-1). Among all the analyzed genes, sul1, sul2, bla_TEM, and integrase genes were the most common. Results of the study demonstrate the selective character of ARGs transfer from poultry and bovine manure to plants. The only gene to occur in all studied environmental compartments was sul1 (from 10² - groundwater to 10¹¹ - poultry manure). It was also found that animal manure may cause an increase in the HMs concentration in soil and their accumulation in crops, which may influence the health of humans and animals consuming crops grown on manure-amended soil. The high abundance of integrase genes and ARGs and their reciprocal correlations with HMs pose a serious risk of the rapid spread of antibiotic resistance in the environment. Moreover, unusual dependencies between integrase genes and selected ARGs indicate the possibility of changes in the mobility nature of genetic elements.

Predicting the taxonomic and environmental sources of integron gene cassettes using structural and sequence homology of attC sites

Integrons are bacterial genetic elements that can capture mobile gene cassettes. They are mostly known for their role in the spread of antibiotic resistance cassettes, contributing significantly to the global resistance crisis. These resistance cassettes likely originated from sedentary chromosomal integrons, having subsequently been acquired and disseminated by mobilised integrons. However, their taxonomic and environmental origins are unknown. Here, we use cassette recombination sites (attCs) to predict the origins of those resistance cassettes now spread by mobile integrons. We modelled the structure and sequence homology of 1,978 chromosomal attCs from 11 different taxa. Using these models, we show that at least 27% of resistance cassettes have attCs that are structurally conserved among one of three taxa (Xanthomonadales, Spirochaetes and Vibrionales). Indeed, we found some resistance cassettes still residing in sedentary chromosomal integrons of the predicted taxa. Further, we show that attCs cluster according to host environment rather than host phylogeny, allowing us to assign their likely environmental sources. For example, the majority of β-lactamases and aminoglycoside acetyltransferases, the two most prevalent resistance cassettes, appear to have originated from marine environments. Together, our data represent the first evidence of the taxonomic and environmental origins of resistance cassettes spread by mobile integrons.

The Antimicrobial Resistance Crisis: An Inadvertent, Unfortunate but Nevertheless Informative Experiment in Evolutionary Biology

The global rise of antimicrobial resistance (AMR) phenotypes is an exemplar for rapid evolutionary response. Resistance arises as a consequence of humanity’s widespread and largely indiscriminate use of antimicrobial compounds. However, some features of this crisis remain perplexing. The remarkably widespread and rapid rise of diverse, novel and effective resistance phenotypes is in stark contrast to the apparent paucity of antimicrobial producers in the global microbiota. From the viewpoint of evolutionary theory, it should be possible to use selection coefficients to examine these phenomena. In this work we introduce an elaboration on the selection coefficient s termed selective efficiency, considering the genetic, metabolic, ecological and evolutionary impacts that accompany selective phenotypes. We then demonstrate the utility of the selective efficiency concept using AMR and antimicrobial production phenotypes as ‘worked examples’ of the concept. In accomplishing this objective, we also put forward cogent hypotheses to explain currently puzzling aspects of the AMR crisis. Finally, we extend the selective efficiency concept into a consideration of the ongoing management of the AMR crisis.

Large-scale biogeographical patterns of antibiotic resistome in the forest soils across China

Soil is a reservoir of environmental resistomes. Information about their distribution, profiles, and driving forces in undisturbed environments is essential for understanding and managing modern antibiotic resistance genes (ARGs) in human disturbed environments. However, knowledge about the resistomes in pristine soils is limited, particularly at national scale. Here, we conducted a national-scale investigation of soil resistomes in pristine forests across China. Although the antibiotics content was low and ranged from below limit of detection (LOD) to 0.290 μg/kg, numerous detected ARGs conferring resistance to major classes of modern antibiotics were identified and indicated forest soils as a potential source of resistance traits. ARGs ranged from 6.20 × 10^-7 to 2.52 × 10^-3 copies/16S-rRNA and were predominated by those resisting aminoglycoside and encoding deactivation mechanisms. Low abundance of mobile genetic elements (MGEs) and its scarcely positive connections with ARGs suggest the low potential of horizontal gene transfer. The geographic patterns of ARGs and ARG-hosts in pristine forest soils were mainly driven by soil physiochemical variables and followed a distance-decay relationship. This work focusing on pristine soils can provide valuably new information for our understanding of the ARGs in human disturbed environments.

Exploring antibiotic resistance in environmental integron-cassettes through intI-attC amplicons deep sequencing

INTRODUCTION

Freshwater ecosystems provide propitious conditions for the acquisition and spread of antibiotic resistance genes (ARGs), and integrons play an important role in this process.

MATERIAL AND METHODS

In the present study, the diversity of putative environmental integron-cassettes, as well as their potential bacterial hosts in the Velhas River (Brazil), was explored through intI-attC and 16S rRNA amplicons deep sequencing. RESULTS AND DISCUSSION: ORFs related to different biological processes were observed, from DNA integration to oxidation-reduction. ARGs-cassettes were mainly associated with class 1 mobile integrons carried by pathogenic Gammaproteobacteria, and possibly sedentary chromosomal integrons hosted by Proteobacteria and Actinobacteria. Two putative novel ARG-cassettes homologs to fosB3 and novA were detected. Regarding 16SrRNA gene analysis, taxonomic and functional profiles unveiled Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as dominant phyla. Betaproteobacteria, Alphaproteobacteria, and Actinobacteria classes were the main contributors for KEGG orthologs associated with resistance.

CONCLUSIONS

Overall, these results provide new information about environmental integrons as a source of resistance determinants outside clinical settings and the bacterial community in the Velhas River.

Diverse Gene Cassette Arrays Prevail in Commensal Escherichia coli From Intensive Farming Swine in Four Provinces of China

Multiple-drug resistance bacteria containing antimicrobial resistance genes (ARGs) are a concern for public health. Integrons are bacterial genetic elements that can capture, rearrange, and express mobile gene cassettes responsible for the spread of ARGs. Few studies link genotype and phenotype of swine-related ARGs in the context of mobile gene cassette arrays among commensal Escherichia coli (E. coli) in nonclinical livestock isolates from intensive farms. In the present study, a total of 264 isolates were obtained from 330 rectal swabs to determine the prevalence and characteristics of antibiotic-resistant gene being carried by commensal E. coli in the healthy swine from four intensive farms at Anhui, Hebei, Shanxi, and Shaanxi, in China. Antimicrobial resistance phenotypes of the recovered isolates were determined for 19 antimicrobials. The E. coli isolates were commonly nonsusceptible to doxycycline (75.8%), tetracycline (73.5%), sulfamethoxazole-trimethoprim (71.6%), amoxicillin (68.2%), sulfasalazine (67.1%), ampicillin (58.0%), florfenicol (56.1%), and streptomycin (53.0%), but all isolates were susceptible to imipenem (100%). Isolates [184 (69.7%)] exhibited multiple drug resistance with 11 patterns. Moreover, 197 isolates (74.6%) were detected carrying the integron-integrase gene (intI1) of class 1 integrons. A higher incidence of antimicrobial resistance was observed in the intI1-positive E. coli isolates than in the intI1-negative E. coli isolates. Furthermore, there were 17 kinds of gene cassette arrays in the 70 integrons as detected by sequencing amplicons of variable regions, with 66 isolates (94.3%) expressing their gene cassettes encoding for multiple drug resistance phenotypes for streptomycin, neomycin, gentamicin, kanamycin, amikacin, sulfamethoxazole-trimethoprim, sulfasalazine, and florfenicol. Notably, due to harboring multiple, hybrid, and recombination cassettes, complex cassette arrays were attributed to multiple drug resistance patterns than simple arrays. In conclusion, we demonstrated that the prevalence of multiple drug resistance and the incidence of class 1 integrons were 69.7 and 74.6% in commensal E. coli isolated from healthy swine, which were lower in frequency than that previously reported in China.

Antibiotic resistomes in drinking water sources across a large geographical scale: Multiple drivers and co-occurrence with opportunistic bacterial pathogens

Antibiotic resistance genes (ARGs) can survive the water treatment process. However, the prevalence patterns, key drivers, and relationships with opportunistic pathogens of the antibiotic resistome harbored in drinking water sources remain unclear. Herein, 53 drinking water samples collected across a large geographical scale in China were characterized based on ARGs, mobile genetic elements (MGEs), bacterial communities, antibiotics, and opportunistic bacterial pathogens. A total of 265 unique ARGs and MGEs were detected by high-throughput quantitative polymerase chain reaction (HT-qPCR), and 101 genes were shared among over 50% of samples. ARG abundance was higher in rivers than in reservoirs or groundwater, and ARG similarity showed a distance-decay relationship at the >4 000 km scale. Four out of the five detected opportunistic pathogens (i.e., Escherichia coli, Mycobacterium spp., Clostridium perfringens, and Bacillus cereus group) were potential hosts of ARGs. Based on multivariate statistics, our results demonstrated that the factors influencing the antibiotic resistome in drinking water sources were multiple and interactive. The bacterial community greatly contributed to ARG structure, and antibiotic concentrations and MGEs also affected ARG proliferation. The structural equation model indicated that geographical location and sample types (i.e., river, reservoir, and groundwater) had indirect effects on ARGs by changing the bacterial community and antibiotic concentration. Holistic consideration of natural and anthropogenic factors is recommended to understand antibiotic resistome variation in drinking water sources at a large geographical scale. Furthermore, large-scale diverse samples are suggested to minimize the potential influence of accident or stochasticity. Our findings provide insight into water quality risks induced by drinking water antibiotic resistomes.

The Peril and Promise of Integrons: Beyond Antibiotic Resistance

Integrons are bacterial genetic elements that can capture, rearrange, and express mobile gene cassettes. They are best known for their role in disseminating antibiotic-resistance genes among pathogens. Their ability to rapidly spread resistance phenotypes makes it important to consider what other integron-mediated traits might impact human health in the future, such as increased virulence, pathogenicity, or resistance to novel antimicrobial strategies. Exploring the functional diversity of cassettes and understanding their de novo creation will allow better pre-emptive management of bacterial growth, while also facilitating development of technologies that could harness integron activity. If we can control integrons and cassette formation, we could use integrons as a platform for enzyme discovery and to construct novel biochemical pathways, with applications in bioremediation or biosynthesis of industrial and therapeutic molecules. Integron activity thus holds both peril and promise for humans.