Gene cassettes and cassette arrays in mobile resistance integrons

Resistance to Antibiotics in Thermophilic Campylobacters

Campylobacter jejuni (C. jejuni) is one of the most frequent causes of bacterial enterocolitis globally. The disease in human is usually self-limiting, but when complications arise antibiotic therapy is required at a time when resistance to antibiotics is increasing worldwide. Mechanisms of antibiotic resistance in bacteria are diverse depending on antibiotic type and usage and include: enzymatic destruction or drug inactivation; alteration of the target enzyme; alteration of cell membrane permeability; alteration of ribosome structure and alteration of the metabolic pathway(s). Resistance of Campylobacter spp. to antibiotics, especially fluoroquinolones is now a major public health problem in developed and developing countries. In this review the mechanisms of resistance to fluoroquinolones, macrolides, tetracycline, aminoglycoside and the role of integrons in resistance of Campylobacter (especially at the molecular level) are discussed, as well as the mechanisms of resistance to β-lactam antibiotics, sulphonamides and trimethoprim. Multiple drug resistance is an increasing problem for treatment of campylobacter infections and emergence of resistant strains and resistance are important One Health issues.

Prevalence and characterization of antibiotic resistance genes and integrons in Escherichia coli isolates from captive non-human primates of 13 zoos in China

Antimicrobial resistance (AMR) has become a public health concern; but antibiotic resistance genes (ARGs) and integrons that link to AMR of Escherichia coli from non-human primates remain largely unknown. This study aimed to investigate antibiotic resistance, emerging environmental pollutants ARGs, and integrons factors (intI1, intI2 and intI3) in 995 E. coli isolates obtained from 50 species of captive non-human primates of 13 zoos in China. Our result showed 83.62% of the E. coli isolates were resistant to at least one antibiotic and 47.94% isolates showed multiple drug resistances (MDR). The E. coli isolates mainly showed resistance to tetracycline (tetracycline 62.71%, doxycycline 61.11%), β-lactams (ampicillin 54.27%, amoxicillin 52.36%), and sulfonamide (trimethoprim-sulfamethoxazole 36.78%). A total of 423 antibiotic resistance patterns were observed, of which DOX/TET (49 isolates, 4.92%) was the most common pattern. Antibiotic resistance rates among 13 zoos had a significant difference (P < 0.01). We further detected 22 ARGs in the 995 E. coli isolates, of which tetA had the highest occurrence (70.55%). The presence of integrons class 1 and 2 were 24.22% and 1.71%, respectively, while no class 3 integron was found. Significant positive associations were observed among integrons and antibiotics, of which the strongest association was observed for integrons / Gentamicin (OR, 2.642) and integrons / Cefotaxime (OR, 2.512). In addition, cassette arrays were detected in 64 strains of class 1 integron-positive isolates (26.56%) and 10 strains of class 2 integron-positive isolates (58.82%). Eighteen cassette arrays were found within 64 class 1 integron isolates, while 3 cassette arrays were identified within 10 class 2 integron isolates. Our results indicate a high diversity of antibiotic resistance phenotypes in non-human primate E. coli isolates, which carry multiple ARGs and integrons. Corresponding preventive measures should be taken to prevent the spread of integron-mediated ARGs in non-human primates and their living environments in zoos.

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.

Antibiotic resistance and class 1 integron genes distribution in irrigation water-soil-crop continuum as a function of irrigation water sources

The increasing demand for fresh water coupled with the need to recycle water and nutrients has witnessed a global increase in wastewater irrigation. However, the development of antibiotic resistance hotspots in different environmental compartments, as a result of wastewater reuse is becoming a global health concern. The effect of irrigation water sources (wastewater, surface water, fresh water) on the presence and abundance of antibiotic resistance genes (ARGs) (bla_CTX-m-32, tet-W, sul1, cml-A, and erm-B) and class 1 integrons (intI1) were investigated in the irrigation water-soil-crop continuum using quantitative real-time PCR (qPCR). Sul1 and bla_CTX-m-32 were the most and least abundant ARGs in three environments, respectively. The abundance of ARGs and intI1 significantly decreased from wastewater to surface water and then fresh water. However, irrigation water sources had no significant effect on the abundance of ARGs and intI1 in soil and crop samples. Principal component analysis (PCA) showed that UV index and air temperature attenuate the abundance of ARGs and intI1 in crop samples whereas the air humidity and soil electrical conductivity (EC) promotes the ARGs and intI1. So that the climate condition of semi-arid regions significantly affects the abundance of ARGs and intI1 in crop samples. The results suggest that treated wastewater might be safely reused in agricultural practice in semi-arid regions without a significant increase of potential health risks associated with ARGs transfer to the food chain. However, further research is needed for understanding and managing ARGs transfer from the agricultural ecosystem to humans through the food chain.

Dynamics of integron structures across a wastewater network - Implications to resistance gene transfer

Class 1 and other integrons are common in wastewater networks, often being associated with antibiotic resistance genes (ARGs). However, the importance of different integron structures in ARG transfer within wastewater systems has only been implied, especially between community and hospital sources, among wastewater treatment plant compartments, and in receiving waters. This uncertainty is partly because current clinical class 1 integron qPCR assays (i.e., that target human-impacted structures, i.e., clintI1) poorly delineate clintI1 from non-impacted class 1 integron structures. They also say nothing about their ARG content. To fill these technical gaps, new real-time qPCR assays were developed for "impacted" class 1 structures (called aint1; i.e., anthropogenic class 1 integrons) and empty aint1 structures (i.e., carry no ARGs; called eaint1). The new assays and other integron assays then were used to examine integron dynamics across a wastewater network. 16S metagenomic sequencing also was performed to characterise associated microbiomes. aint1 abundances per bacterial cell were about 10 times greater in hospital wastewaters compared with other compartments, suggesting aint1 enrichment with ARGs in hospital sources. Conversely, the relative abundance of eaint1 structures were over double in recycled activated sludge compared with other compartments, except receiving waters (RAS; ∼30% of RAS class 1 structures did not carry ARGs). Microbiome analysis showed that human-associated bacterial taxa with mobile integrons also differed in RAS and river sediments. Further, class 1 integrons in RAS bacteria appear to have released ARGs, whereas hospital bacteria have accumulated ARGs. Results show that quantifying integron dynamics can help explain where ARG transfer occurs in wastewater networks, and should be considered in future studies on antibiotic resistance in the environment.

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.

Key factors driving the fate of antibiotic resistance genes and controlling strategies during aerobic composting of animal manure: A review

Occurrence of antibiotic resistance genes (ARGs) in animal manure impedes the reutilization of manure resources. Aerobic composting is potentially effective method for resource disposal of animal manure, but the fate of ARGs during composting is complicated due to the various material sources and different operating conditions. This review concentrates on the biotic and abiotic factors influencing the variation of ARGs in composting and their potential mechanisms. The dynamic variations of biotic factors, including bacterial community, mobile genetic elements (MGEs) and existence forms of ARGs, are the direct driving factors of the fate of ARGs during composting. However, most key abiotic indicators, including pH, moisture content, antibiotics and heavy metals, interfere with the richness of ARGs indirectly by influencing the succession of bacterial community and abundance of MGEs. The effect of temperature on ARGs depends on whether the ARGs are intracellular or extracellular, which should be paid more attention. The emergence of various controlling strategies renders the composting products safer. Four potential removal mechanisms of ARGs in different controlling strategies have been concluded, encompassing the attenuation of selective/co-selective pressure on ARGs, killing the potential host bacteria of ARGs, reshaping the structure of bacterial community and reducing the cell-to-cell contact of bacteria. With the effective control of ARGs, aerobic composting is suggested to be a sustainable and promising approach to treat animal manure.

Integrons, a predictive biomarker for antibiotic resistance in acute sepsis: the IRIS study

BACKGROUND

Considering the increase in MDR Gram-negative bacteria (GNB), the choice of empirical antibiotic therapy is challenging. In parallel, use of broad-spectrum antibiotics should be avoided to decrease antibiotic selection pressure. Accordingly, clinicians need rapid diagnostic tools to narrow antibiotic therapy. Class 1-3 integrons, identified by intI1-3 genes, are genetic elements that play a major role in antibiotic resistance in GNB.

OBJECTIVES

The objective of the IRIS study was to evaluate the negative and positive predictive values (NPVs and PPVs, respectively) of intI1-3 as markers of antibiotic resistance.

METHODS

The IRIS study was an observational cross-sectional multicentre study that enrolled adult subjects with suspected urinary tract or intra-abdominal infections. intI1-3 were detected directly from routinely collected biological samples (blood, urine or intra-abdominal fluid) using real-time PCR. A patient was considered 'MDR positive' if at least one GNB, expressing acquired resistance to at least two antibiotic families among β-lactams, aminoglycosides, fluoroquinolones and/or co-trimoxazole, was isolated from at least one biological sample.

RESULTS

Over a 2 year period, 513 subjects were enrolled and 409 had GNB documentation, mostly Enterobacterales. intI1 and/or intI2 were detected in 31.8% of patients and 24.4% of patients were considered 'MDR positive'. The NPV of intI1 and/or intI2 as a marker of acquired antibiotic resistances was estimated at 92.8% (89.1%-95.5%). The NPVs for first-line antibiotics were all above 92%, notably >96% for resistance to third-generation cephalosporins.

CONCLUSIONS

The IRIS study strongly suggests that the absence of intI1 and intI2 in biological samples from patients with GNB-related infections is predictive of the absence of acquired resistances.

Biocide-tolerance and antibiotic-resistance in community environments and risk of direct transfers to humans: Unintended consequences of community-wide surface disinfecting during COVID-19?

During the current pandemic, chemical disinfectants are ubiquitously and routinely used in community environments, especially on common touch surfaces in public settings, as a means of controlling the virus spread. An underappreciated risk in current regulatory guidelines and scholarly discussions, however, is that the persisting input of chemical disinfectants can exacerbate the growth of biocide-tolerant and antibiotic-resistant bacteria on those surfaces and allow their direct transfers to humans. For COVID-19, the most commonly used disinfecting agents are quaternary ammonium compounds, hydrogen peroxide, sodium hypochlorite, and ethanol, which account for two-thirds of the active ingredients in current EPA-approved disinfectant products for the novel coronavirus. Tolerance to each of these compounds, which can be either intrinsic or acquired, has been observed on various bacterial pathogens. Of those, mutations and horizontal gene transfer, upregulation of efflux pumps, membrane alteration, and biofilm formation are the common mechanisms conferring biocide tolerance in bacteria. Further, the linkage between disinfectant use and antibiotic resistance was suggested in laboratory and real-life settings. Evidence showed that substantial bacterial transfers to hands could effectuate from short contacts with surrounding surfaces and further from fingers to lips. While current literature on disinfectant-induced antimicrobial resistance predominantly focuses on municipal wastes and the natural environments, in reality the community and public settings are most severely impacted by intensive and regular chemical disinfecting during COVID-19 and, due to their proximity to humans, biocide-tolerant and antibiotic-resistant bacteria emerged in these environments may pose risks of direct transfers to humans, particularly in densely populated urban communities. Here we highlight these risk factors by reviewing the most pertinent and up-to-date evidence, and provide several feasible strategies to mitigate these risks in the scenario of a prolonging pandemic.

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.

Mobilisation of plasmid-mediated blaVEB-1 gene cassette into distinct genomic islands of Proteus mirabilis after ceftazidime exposure

OBJECTIVES

We sought to integrate a VEB-1-encoding gene cassette into the integron of the MDR region of genomic islands (GIs) harboured by Proteus mirabilis strains after antibiotic exposure.

METHODS

An IncP1 plasmid from Achromobacter xylosoxidans carrying the cassette array dfrA14-bla_VEB-1-aadB was introduced by conjugation into five strains of P. mirabilis: PmBRI, PmABB, PmSCO and Pm2CHAMA harbouring Salmonella GI 1 and PmESC harbouring Proteus GI 1. Circular intermediates of the cassettes were amplified by PCR. bla_VEB-harbouring P. mirabilis were exposed to increasing concentrations of ceftazidime each day. Presence of bla_VEB-1 in the GI was assessed by PCR. The complete MDR regions were mapped and sequenced in positive clones.

RESULTS

Circular intermediates were detected for dfrA14 and bla_VEB-1-aadB and dfrA14-bla_VEB-1-aadB cassettes arrays in A. xylosoxidans, and for aadA2 in P. mirabilis. Insertion of bla_VEB-1 into the GIs occurred under ceftazidime pressure. In all cases, the three cassettes from IncP1 were integrated. They replaced the cassette array of PmBRI, PmABB and PmSCO in which floRc, tet(A)G and bla_PSE-1 were conserved, whereas they replaced an integron and the IS26-flanked region in Pm2CHAMA. In PmESC, they only replaced aadB, with aadA2 being conserved. bla_VEB-1 integration occurred just after conjugation for Pm2CHAMA but required ceftazidime exposure for the other strains.

CONCLUSION

Homologous recombination of gene cassettes conferring resistance to clinically important antibiotics may occur under antibiotic pressure between an integron located on a plasmid and a co-resident GI. This feature participates in the acquisition, maintenance and spread of antibiotic resistance genes.

dfrA trimethoprim resistance genes found in Gram-negative bacteria: compilation and unambiguous numbering

To track the spread of antibiotic resistance genes, accurate identification of individual genes is essential. Acquired trimethoprim resistance genes encoding trimethoprim-insensitive homologues of the sensitive dihydrofolate reductases encoded by the folA genes of bacteria are increasingly found in genome sequences. However, naming and numbering in publicly available records (journal publications or entries in the GenBank non-redundant DNA database) has not always been unambiguous. In addition, the nomenclature has evolved over time. Here, the changes in nomenclature and the most commonly encountered problems and pitfalls affecting dfrA gene identification arising from historically incorrect or inaccurate numbering are explained. The complete set of dfrA genes/DfrA proteins found in Gram-negative bacteria for which readily searchable sequence information is currently available has been compiled using less than 98% identity for both the gene and the derived protein sequence as the criteria for assignment of a new number. In most cases, trimethoprim resistance has been demonstrated. The gene context, predominantly in a gene cassette or near the ori end of CR1 or CR2, is also covered. The RefSeq database that underpins the programs used to automatically identify resistance genes in genome data sets has been curated to assign all sequences listed to the correct number. This led to the assignment of corrected or new gene numbers to several mis-assigned sequences. The unique numbers assigned for the dfrA/DfrA set are now listed in the RefSeq database, which we propose provides a way forward that should end future duplication of numbers and the confusion that causes.

Reversing Antibiotic Resistance Caused by Mobile Resistance Genes of High Fitness Cost

The reversibility of antibiotic resistance is theoretically attractive due to the prospect of restoring the clinical potency of antibiotics. It is important to find out the factors that affect the reversibility of antibiotic resistance. Here, an mcr-1-positive multidrug-resistant (MDR) environmental Escherichia coli isolate was successively passaged under four antibiotic-free culture conditions. The relative abundances of multiple antibiotic resistance genes (ARGs) kept decreasing during the successive passages. The linear correlations between abundances of ARGs on the same MDR plasmid reflected that the decay of antibiotic resistance during the passage was mainly due to the elimination of the MDR plasmid (pMCR_W5-6). Colistin-susceptible strains were isolated at the end of the passage. The whole-genome sequencing of two susceptible isolates detected the elimination of the MDR plasmid and deletion of the mcr-1 gene. Deletions of DNA fragments from chromosome and plasmid were closely related to a variety of insertion sequences (ISs). The results of coculture of resistant and susceptible strains at different antibiotic concentrations indicated that the high fitness cost led to the poor stability of mobile ARGs. Strict control of the use of antibiotics can at least reverse the severe antibiotic resistance caused by mobile ARGs of high fitness cost.

IMPORTANCE The dissemination of bacterial antibiotic resistance is a serious threat to human health. The development of new antibiotics faces both economic and technological challenges. The reversibility of antibiotic resistance has become an important issue causing wide concern due to the prospect of restoring the clinical potency of antibiotics. Our study suggests that the high mobility of ARGs of high fitness cost may just reflect their poor stability. Therefore, strict control of the use of antibiotics can at least reverse the severe antibiotic resistance caused by mobile ARGs of high fitness cost. This study brings hope for the possibility of curbing the dissemination of antibiotic resistance.

Expression of the qepA1 gene is induced under antibiotic exposure

Background

The qepA1 gene encodes an efflux pump that reduces susceptibility to ciprofloxacin. Little is known about the regulation of qepA1 expression.

Objectives

To assess the potential role of ciprofloxacin and other antibiotics in the regulation of qepA1 gene expression. To identify the promoter that drives qepA1 expression and other factors involved in expression regulation. To assess whether the identified features are universal among qepA alleles.

Methods

A translational qepA1-yfp fusion under the control of the qepA1 upstream region was cloned into the Escherichia coli chromosome. Expression of the fusion protein was measured in the presence of various antibiotics. Deletions within the upstream region were introduced to identify regions involved in gene expression and regulation. The qepA1 coding sequence and upstream region were compared with all available qepA sequences.

Results

Cellular stress caused by the presence of various antibiotics can induce qepA1 expression. The qepA1 gene is fused to a class I integron and gene expression is driven by the Pc promoter within the integrase gene. A segment within the integron belonging to a truncated dfrB4 gene is essential for the regulation of qepA1 expression. This genetic context is universal among all sequenced qepA alleles.

Conclusions

The fusion of the qepA1 gene to a class I integron has created a novel regulatory unit that enables qepA1 expression to be under the control of antibiotic exposure. This setup mitigates potential negative effects of QepA1 production on bacterial fitness by restricting high-level expression to environmental conditions in which QepA1 is beneficial.

Improved reduction of antibiotic resistance genes and mobile genetic elements from biowastes in dry anaerobic co-digestion

This study investigated the performance of anaerobic co-digestion (AcoD) of pig manure and food waste on the reduction of antibiotic resistomes under wet and dry AcoD conditions. High-throughput quantitative PCR technology was utilized for a comprehensive assessment of the performances of the two processes. The results show that dry AcoD with a total solids (TS) content of 20% effectively reduced total antibiotic resistance genes (ARGs) by 1.24 log copies/g wet sample, while only 0.54 log copies/g wet sample was reduced in wet AcoD with a TS content of 5%. Dry AcoD was more efficient in reduction of aminoglycosides, multidrug and sulfonamide resistance genes compared with the reduction of other classes of ARGs. Dry AcoD caused a significant reduction of ARGs with resistance mechanisms of efflux pump and antibiotic deactivation. In contrast, there was no obvious difference in reductions of ARGs with different resistance mechanisms in wet AcoD. Network analysis showed that ARGs were significantly correlated with mobile genetic elements (MGEs) (Spearman's r > 0.8, P < 0.05), as well as microbial communities. Enrichment of ARGs and MGEs was found at the early period of AcoD processes, indicating some ARGs and MGEs increased during the hydrolysis and acidogenesis stages. But after a long retention time, their abundances were effectively reduced by dry AcoD in the subsequent stages.

Solar photon-Fenton process eliminates free plasmid DNA harboring antimicrobial resistance genes from wastewater

This work aimed to assess the elimination and inactivation of resistance-conferring plasmids (RCPs) present in suspension in secondary wastewater by solar photo-Fenton as these are important vectors for the dissemination of antimicrobial resistance. Experiments were performed in synthetic secondary wastewater (SWW) and municipal wastewater treatment plant effluent (MWWTPE). Solar photo-Fenton (50 mg L-1 of H2O2 and 30 mg L-1 of Fe2+) was carried out for 60 min at neutral pH by applying the intermittent iron addition strategy. The removal of RCPs was assessed by Real-Time Polymerase Chain Reaction (qPCR). The transformation of competent non-resistant E. coli was used to evaluate the inactivation of target RCPs harboring antibiotic resistance genes (ARGs) to ampicillin (pSB1A2) or kanamycin (pSB1K3) after treatment and controls. Solar photo-Fenton completely removed RCPs initially present in both matrixes (SWW and MWWTPE), showing enhanced performance compared to the dark Fenton process. Both RCPs were inactivated after 30 min of solar photo-Fenton treatment, while 60 min were necessary to achieve the same effect for the dark Fenton reaction under similar conditions. These results indicate the potential of solar photo-Fenton to improve wastewater quality and reduce the spread of antimicrobial resistance in the environment by hampering the discharge of cell-free RCPs present in suspension in MWWTP onto environmental waters.

Horizontal gene transfer is a key determinant of antibiotic resistance genes profiles during chicken manure composting with the addition of biochar and zeolite

Livestock manure is an important reservoir of antibiotic resistance genes (ARGs). Biochar and zeolite are commonly used to improve the quality of compost, however, little is known about the impacts of these additives on the fate of ARGs during composting and the underlying mechanisms involved. In this study, zeolite (ZL), biochar (BC), or zeolite and biochar (ZB) simultaneously were added to chicken manure compost to evaluate their effects on the ARGs patterns. After composting, the abundance of ARGs reduced by 92.6% in control, while the reductions were 95.9%, 98.7% and 98.2% for ZL, BC, ZB, respectively. Co-occurrence network analysis indicated that the potential hosts for most ARGs were predominantly affiliated to Firmicutes such as Lactobacillus and Fastidiosipila. Furthermore, shifts in ARGs were significantly correlated with class 1 integrase gene (intI1), and structural equation models further revealed that intI1 gene contributed most (standardized total effect 0.92) to the ARGs-removal, which was trigged by horizontal gene transfer. Together these results suggest that the addition of zeolite and biochar mitigate the accumulation and spread of ARGs during composting, and the crucial role of horizontal gene transfer (HGT) on the behaviors of ARGs should pay more attention to in the future.

Antimicrobial Resistance and Molecular Characterization of Class 1 Integron in Salmonella Isolates Recovered from Pig Farms in Chongqing, China

Salmonella is considered one of the leading causes for foodborne diseases in humans. Pork and its products contaminated with Salmonella are increasingly recognized as an important source of human salmonellosis. The aim of this study was to investigate the antimicrobial resistance and prevalence of integrons in Salmonella isolates from pig farms. In total, 92 of 724 (12.7%) samples were Salmonella-positive, including 64 (15.0%) from fecal samples, 27 (12.6%) from floor samples, 1 (4.5%) from water samples, and 0 from feed and air samples. These isolates showed the highest resistance to tetracycline (85.9%), followed by trimethoprim (67.4%), ampicillin (60.9%), and chloramphenicol (51.1%). In addition, 51 isolates carried the complete class 1 integron, most of which (42/51) harbored antibiotic resistance cassettes. A total of six gene cassettes including orfF, est-X, dfrA1+aadA1, aadA1, dfrA12+aadA2, and sat were identified, in which the most prevalent one was orfF (29.4%). Furthermore, all 19 class 1 integron-positive isolates harboring dfr genes showed resistance to trimethoprim (SXT), suggesting that the trimethoprim resistance gene (dfr) may contribute to the emergence of SXT resistance phenotype. Therefore, considering the significance of integrons and related resistance genes for public health, special measures should be taken to control Salmonella spp. on the pig farms and to prevent spread of integrons and associated resistance genes.

Multiple antibiotic resistance and DNA methylation in Enterobacteriaceae isolates from different environments

Antibiotic resistant bacteria with diverse resistance phenotypes and genotypes are ubiquitous in the environments that have become a global health concern. The role of DNA methylation in the dissemination of antibiotic resistance among different environments is currently unclear. We recovered 646 Enterobacteriaceae (Eb) isolates from hospital, livestock manure, municipal wastewater-treatment plants, river sediment and soil for comprehensive analysis of resistance phenotypes, β-lactamase genes, integrons, integron-associated gene cassettes and the levels of DNA methylation. Antibiotic susceptibility testing revealed that approximately 87.31 % isolates were multidrug resistant Eb. The β-lactamase genes were positively detected in 473 isolates with greater diversity in human or animal sourced Eb, while its prevalence was found to be highest in the Eb isolates from the natural environments. Forty-three gene cassettes (28 different types mediated by intI1) were detected in 53 (19.63 %) isolates, with greater diversity in Eb isolates from hospital and livestock manure. The multiple antibiotic resistance index of single strain was positively correlated with the 5-methylcytosine and showed a negative correlation with 6-methylademine. We conclude that the development of antibiotic resistance could possibly be coupled with DNA methylation, which might enhance the antimicrobial resistance and survival capacity of Eb.

Integron Identification in Bacterial Genomes and Cassette Recombination Assays

Integrons are genetic elements involved in bacterial adaptation to the environment. Sedentary chromosomal integrons (SCIs) can stockpile and rearrange a myriad of different functions encoded in gene cassettes. Through their association with transposable elements and conjugative plasmids, some SCIs have acquired mobility and are now termed Mobile Integrons (MIs). MIs have reached the hospitals and are involved in the rise and spread of antibiotic resistance genes through horizontal gene transfer among numerous bacterial species. Here we aimed at describing methods for the detection of integrons in sequenced bacterial genomes as well as for the experimental characterization of the activity of their different components: the integrase and the recombination sites.

Comment on "Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection" by A.N. Zhang et al

An article published in Microbiome in July 2018 uses incorrect definitions of integron integrase IntI1 and of class 1 integrons that affect the interpretation of the data.

Into the sea: Antimicrobial resistance determinants in the microbiota of little penguins (Eudyptula minor)

Terrestrial and aquatic birds have been proposed as sentinels for the spread of antimicrobial resistant bacteria, but few species have been investigated specifically in the context of AMR in the marine ecosystem. This study contrasts the occurrence of class 1 integrons and associated antimicrobial resistance genes in wild and captive little penguins (Eudyptula minor), an Australian seabird with local population declines. PCR screening of faecal samples (n = 448) revealed a significant difference in the prevalence of class 1 integrons in wild and captive groups, 3.2% and 44.7% respectively, with genes that confer resistance to streptomycin, spectinomycin, trimethoprim and multidrug efflux pumps detected. Class 1 integrons were not detected in two clinically relevant bacterial species, Klebsiella pneumoniae or Escherichia coli, isolated from penguin faeces. The presence of class 1 integrons in the little penguin supports the use of marine birds as sentinels of AMR in marine environments.

Tn6603, a Carrier of Tn5053 Family Transposons, Occurs in the Chromosome and in a Genomic Island of Pseudomonas aeruginosa Clinical Strains

Transposons of the Pseudomonasaeruginosa accessory gene pool contribute to phenotype and to genome plasticity. We studied local P. aeruginosa strains to ascertain the encroachment of mer-type res site hunter transposons into clinical settings and their associations with other functional modules. Five different Tn5053 family transposons were detected, all chromosomal. Some were solitary elements; one was in res of Tn1013^#, a relative of a reported carrier of int-type res site hunters (class 1 integrons), but most were in res of Tn6603, a new Tn501-related transposon of unknown phenotype. Most of the Tn6603::Tn elements, and some Tn6603 and Tn6603::Tn elements found in GenBank sequences, were at identical sites in an hypothetical gene of P. aeruginosa genomic island PAGI-5v. The island in clonally differing strains was at either of two tRNA^Lys loci, suggesting lateral transfer to these sites. This observation is consistent with the membership of the prototype PAGI-5 island to the ICE family of mobile genetic elements. Additionally, the res site hunters in the nested transposons occupied different positions in the Tn6603 carrier. This suggested independent insertion events on five occasions at least. Tn5053 family members that were mer-/tni-defective were found in Tn6603- and Tn501-like carriers in GenBank sequences of non-clinical Pseudomonas spp. The transposition events in these cases presumably utilized tni functions in trans, as can occur with class 1 integrons. We suggest that in the clinical context, P. aeruginosa strains that carry Tn6603 alone or in PAGI-5v can serve to disseminate functional res site hunters; these in turn can provide the requisite trans-acting tni functions to assist in the dissemination of class 1 integrons, and hence of their associated antibiotic resistance determinants.

Pyrolyzed biowastes deactivated potentially toxic metals and eliminated antibiotic resistant genes for healthy vegetable production

Potentially toxic metals (PTEs) and antibiotic resistance genes (ARGs) present in bio-wastes were the major environmental and health risks for soil use. If pyrolyzing bio-wastes into biochar could minimize such risks had not been elucidated. This study evaluated PTE pools, microbial and ARGs abundances of wheat straw (WS), swine manure (SM) and sewage sludge (SS) before and after pyrolysis, which were again tested for soil amendment at a 2% dosage in a pot experiment with a vegetable crop of pak choi (Brassica campestris L.). Pyrolysis led to PTEs concentration in biochars but reduced greatly their mobility, availability and migration potential, as revealed respectively by leaching, CaCl₂ extraction and risk assessment coding. In SM and SS after pyrolysis, gene abundance was removed by 4-5 orders for bacterial, by 2-3 orders for fungi and by 3-5 orders for total ARGs. With these material amended, PTEs available pool decreased by 25%-85% while all ARGs eliminated to background in the pot soil. Unlike a >50% yield decrease and a >30% quality decline with unpyrolyzed SM and SS, their biochars significantly increased biomass production and overall quality of pak choi grown in the amended soil. Comparatively, amendment of the biochars decreased plant PTEs content by 23-57% and greatly reduced health risk of pak choi, with total target hazard quotient values well below the guideline limit for subsistence diet by adult. Furthermore, biochar soil amendment enabled a synergic improvement on soil fertility, product quality, and biomass production as well as metal stabilization in the soil-plant system. Thus, biowastes pyrolysis and reuse in vegetable production could help build up a closed loop of production-waste-biochar-production, addressing not only circular economy but healthy food and climate nexus also and contributing to achieving the United Nations sustainable development goals.

Integron mediated antimicrobial resistance in diarrheagenic Escherichia coli in children: in vitro and in silico analysis

The exchange of genes between bacterial chromosome and plasmid(s) and their integration into integrons are mainly responsible for acquisition and dissemination of antibiotic resistance. We investigated the role of integrons and their underlying molecular mechanisms leading to development of adaptability in E. coli and eventual resistance to antimicrobials. Escherichia coli isolates (n = 120); including 40 diarrheagenic isolates, an even number of isolates from cases other than diarrhea, and equal number of isolates from healthy children recovered from fresh stool samples were used for identification of integron genes and gene cassettes. The association of integrons with antibiotic resistance was assayed before phylogenetic analysis. DNA sequence analysis revealed class 1 and 2 integrons in 55.83% and 21.66% isolates, respectively. The integron presence was found significantly associated with the probability of antibiotic resistance in E. coli; the association being highest with class 1 integron. Modelling and molecular docking along with molecular dynamics simulation analyses found ceftriaxone and amoxicillin as potential inhibitors of dihydrofolate reductase (DHFR). The class 1 integrons of these pathogenic isolates can serve as prospective therapeutic targets using specific silencing strategies and combinational antimicrobial therapy. The findings may be useful for the development of a potent and versatile drug for DHFR inhibition.

Cyanobacterial blooms contribute to the diversity of antibiotic-resistance genes in aquatic ecosystems

Cyanobacterial blooms are a global ecological problem that directly threatens human health and crop safety. Cyanobacteria have toxic effects on aquatic microorganisms, which could drive the selection for resistance genes. The effect of cyanobacterial blooms on the dispersal and abundance of antibiotic-resistance genes (ARGs) of concern to human health remains poorly known. We herein investigated the effect of cyanobacterial blooms on ARG composition in Lake Taihu, China. The numbers and relative abundances of total ARGs increased obviously during a Planktothrix bloom. More pathogenic microorganisms were present during this bloom than during a Planktothrix bloom or during the non-bloom period. Microcosmic experiments using additional aquatic ecosystems (an urban river and Lake West) found that a coculture of Microcystis aeruginosa and Planktothrix agardhii increased the richness of the bacterial community, because its phycosphere provided a richer microniche for bacterial colonization and growth. Antibiotic-resistance bacteria were naturally in a rich position, successfully increasing the momentum for the emergence and spread of ARGs. These results demonstrate that cyanobacterial blooms are a crucial driver of ARG diffusion and enrichment in freshwater, thus providing a reference for the ecology and evolution of ARGs and ARBs and for better assessing and managing water quality.

The structural basis of promiscuity in small multidrug resistance transporters

By providing broad resistance to environmental biocides, transporters from the small multidrug resistance (SMR) family drive the spread of multidrug resistance cassettes among bacterial populations. A fundamental understanding of substrate selectivity by SMR transporters is needed to identify the types of selective pressures that contribute to this process. Using solid-supported membrane electrophysiology, we find that promiscuous transport of hydrophobic substituted cations is a general feature of SMR transporters. To understand the molecular basis for promiscuity, we solved X-ray crystal structures of a SMR transporter Gdx-Clo in complex with substrates to a maximum resolution of 2.3 Å. These structures confirm the family’s extremely rare dual topology architecture and reveal a cleft between two helices that provides accommodation in the membrane for the hydrophobic substituents of transported drug-like cations.

Gdx-Clo is a bacterial transporter from the small multidrug resistance (SMR) family. Here, the authors use solid supported membrane electrophysiology to characterize Gdx-Clo functionally and report crystal structures of Gdx-Clo which confirm the dual topology architecture and offer insight into substrate binding and transport mechanism.

Integron gene cassettes harboring novel variants of D-alanine-D-alanine ligase confer high-level resistance to D-cycloserine

Antibiotic resistance poses an increasing threat to global health. To tackle this problem, the identification of principal reservoirs of antibiotic resistance genes (ARGs) plus an understanding of drivers for their evolutionary selection are important. During a PCR-based screen of ARGs associated with integrons in saliva-derived metagenomic DNA of healthy human volunteers, two novel variants of genes encoding a d-alanine-d-alanine ligase (ddl6 and ddl7) located within gene cassettes in the first position of a reverse integron were identified. Treponema denticola was identified as the likely host of the ddl cassettes. Both ddl6 and ddl7 conferred high level resistance to d-cycloserine when expressed in Escherichia coli with ddl7 conferring four-fold higher resistance to D-cycloserine compared to ddl6. A SNP was found to be responsible for this difference in resistance phenotype between the two ddl variants. Molecular dynamics simulations were used to explain the mechanism of this phenotypic change at the atomic scale. A hypothesis for the evolutionary selection of ddl containing integron gene cassettes is proposed, based on molecular docking of plant metabolites within the ATP and d-cycloserine binding pockets of Ddl.

Co-occurrence of microplastics and triclosan inhibited nitrification function and enriched antibiotic resistance genes in nitrifying sludge

As more and more microplastics (MPs) and triclosan (TCS), which are added in consumer products, enter wastewater treatment plants with sewage, there are concerns about the impacts of the co-occurrence of MPs and TCS on biological wastewater treatment. In this study, the co-effects of four 1 mg/L MPs (polyethylene (PE), polystyrene (PS), polyvinyl chloride (PVC) and polyamide (PA)) and 0.5 mg/L TCS on nitrification were investigated in lab-scale nitrifying sequencing batch reactors (SBRs) (SBR-PE, SBR-PS, SBR-PVC and SBR-PA) relative to control which received no MPs (SBR-CK). The removal rates of NH₄⁺-N and TCS in SBR-CK were around 100% and 92%, respectively. Compared with SBR-CK, no measurable inhibition was observed on nitrification in SBR-PE and SBR-PS, however, SBR-PVC and SBR-PA rapidly lost nitrification function during 14 days, which might be due to the reducing of MLSS caused by PVC, PA and TCS co-loading. Furthermore, PS, PVC and PA decreased the removal of TCS. The co-occurrence of TCS and PS, PVC, PA increased extracellular polymeric substances, reduced microbial diversity and shifted microbial communities. Notably, the acrA-03, mexF, fabI, intI1, intI3 and IS613 genes were enriched by MPs and TCS co-loading. Therefore, the removal of MPs and TCS from wastewater should be prioritized.

Snapshot Study of Whole Genome Sequences of Escherichia coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy

Animals, humans and food are all interconnected sources of antimicrobial resistance (AMR), allowing extensive and rapid exchange of AMR bacteria and genes. Whole genome sequencing (WGS) was used to characterize 279 Escherichia coli isolates obtained from animals (livestock, companion animals, wildlife), food and humans in Italy. E. coli predominantly belonged to commensal phylogroups B1 (46.6%) and A (29%) using the original Clermont criteria. One hundred and thirty-six sequence types (STs) were observed, including different pandemic (ST69, ST95, ST131) and emerging (ST10, ST23, ST58, ST117, ST405, ST648) extraintestinal pathogenic Escherichia coli (ExPEC) lineages. Eight antimicrobial resistance genes (ARGs) and five chromosomal mutations conferring resistance to highest priority critically important antimicrobials (HP-CIAs) were identified (qnrS1, qnrB19, mcr-1, bla_CTX-M1,15,55, bla_CMY-2, gyrA/parC/parE, ampC and pmrB). Twenty-two class 1 integron arrangements in 34 strains were characterized and 11 ARGs were designated as intI1 related gene cassettes (aadA1, aadA2, aadA5, aad23, ant2_Ia, dfrA1, dfrA7, dfrA14, dfrA12, dfrA17, cmlA1). Notably, most intI1 positive strains belonged to rabbit (38%) and poultry (24%) sources. Three rabbit samples carried the mcr-1 colistin resistance gene in association with IS6 family insertion elements. Poultry meat harbored some of the most prominent ExPEC STs, including ST131, ST69, ST10, ST23, and ST117. Wildlife showed a high average number of virulence-associated genes (VAGs) (mean = 10), mostly associated with an ExPEC pathotype and some predominant ExPEC lineages (ST23, ST117, ST648) were identified.

Fate of integrons, antibiotic resistance genes and associated microbial community in food waste and its large-scale biotreatment systems

The prevalence and dissemination of antibiotic resistance genes (ARGs) have been globally gained increasing concerns. However, the fate and spread of ARGs in food waste (FW) and its large-scale biotreatment systems are seldomly understood. Here, we investigated the initial and biologically treated FW in two major FW treatment systems of aerobic fermentation (AF) and anaerobic co-digestion (AcoD) processes. The total relative abundances of integrons and ARGs significantly increased from initial FW to treated FW. Among targeted ARGs, ermB and strB were predominant ARGs, which accounted for 52.58-95.28% of total abundance across all samples. Mantel test indicated that integrons (intl1 and intl2) were positively and significantly correlated with detected ARGs (Mantel test, r = 0.24, p < 0.05), suggesting integrons display significant contributions on driving ARG alteration during FW treatment processes. RDA results indicated that bla_OXA, strB and bla_TEM were more likely to be proliferated by potential host of Firmicutes (96.55-99.77%) in initial FW, while bla_CTX-M and mefA were potentially enriched by Proteobacteria (17.12-49.82%) in AF system and ermB, sul1, aadA and tetQ were possibly enhanced by Bacteroidetes (27.43-43.71%) in AcoD system. Consideration of the higher enriched abundance of total ARGs (66.88 ± 87.34 times) and the used inoculum sludge in AcoD-treated system, the resource utilization of anaerobically digested products should draw our more attentions. These findings would deepen our understanding of prevalence and proliferation of ARGs in FW treatment systems and serve as a foundation for guiding the application of biologically treated FW.

Dissemination of antibiotic resistance genes (ARGs) via integrons in Escherichia coli: A risk to human health

With the induction of various emerging environmental contaminants such as antibiotic resistance genes (ARGs), environment is considered as a key indicator for the spread of antimicrobial resistance (AMR). As such, the ARGs mediated environmental pollution raises a significant public health concern worldwide. Among various genetic mechanisms that are involved in the dissemination of ARGs, integrons play a vital role in the dissemination of ARGs. Integrons are mobile genetic elements that can capture and spread ARGs among environmental settings via transmissible plasmids and transposons. Most of the ARGs are found in Gram-negative bacteria and are primarily studied for their potential role in antibiotic resistance in clinical settings. As one of the most common microorganisms, Escherichia coli (E. coli) is widely studied as an indicator carrying drug-resistant genes, so this article aims to provide an in-depth study on the spread of ARGs via integrons associated with E. coli outside clinical settings and highlight their potential role as environmental contaminants. It also focuses on multiple but related aspects that do facilitate environmental pollution, i.e. ARGs from animal sources, water treatment plants situated at or near animal farms, agriculture fields, wild birds and animals. We believe that this updated study with summarized text, will facilitate the readers to understand the primary mechanisms as well as a variety of factors involved in the transmission and spread of ARGs among animals, humans, and the environment.

Antibiotics and Food Safety in Aquaculture

Antibiotics are widely used in aquaculture. Intensive farming drives indiscriminate use of antibiotics, which results in residues of antibiotics in cultured aquatic products and bacterial resistance. This perspective attempts to present a brief update on usage, regulations, residues, and potential human health risk of antibiotics used in aquaculture. Through the comprehensive literature review, we provide a view that the safety of aquatic products still requires further attention and more rigorous risk assessment. Finally, we make a few suggestions for future research directions: reduce the use of antibiotics to bring down the speed of resistance development and monitor resistant pathogens and genes, strictly manage the environmental sanitation of aquaculture and pay attention to the quality of water bodies introduced into aquaculture, seek international cooperation to establish an information bank of antibiotic residues and antibiotic-resistant genes, and set up a quantitative model to assess the risk of antibiotic resistance associated with the antibiotic residues.

Paper currency harbours antibiotic-resistant coliform bacteria and integron integrase

AIMS

This study was designed to analyse the prevalence of class 1 and class 2 integron integrase genes among antibiotic-resistant coliform bacteria isolated from paper currency circulating in Pakistan.

METHODS AND RESULTS

A total of 500 individual currency notes were collected from different food vending sites at Lahore, Pakistan. Bacterial population were identified by biochemical and PCR techniques. Antimicrobial susceptibility testing was performed by disc diffusion assay. The highest bacterial population on currency was found from street vendors and butcher shops. Escherichia coli was found to be the most prevalent coliform bacteria followed by Klebsiella sp. and Enterobacter sp. PCR amplification of antimicrobial resistance gene showed the presence of ampC, bla_TEM , bla_NDM-1 , qnrA, tet(A) and tet(B) genes among coliform isolates. A total of 47 integron integrase bearing strains of coliform bacteria were analysed. Sequence analysis showed the presence of dfrA1-aadA1, dfrA1, dfrA5, dfrA7, aadA1, aadA4 cassette arrays in class 1 integron and dfrA1-sat2-aadA1 in class 2 integrase genes.

CONCLUSION

Circulating currency was heavily contaminated with antimicrobial-resistant coliform bacteria bearing class 1 and class 2 integron integrase genes.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study describes a potential threat of severe bacterial infections due to improper hand hygiene and community sanitation when dealing with the currency notes.

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.

The 'SELection End points in Communities of bacTeria' (SELECT) Method: A Novel Experimental Assay to Facilitate Risk Assessment of Selection for Antimicrobial Resistance in the Environment

BACKGROUND

Antimicrobial resistance (AMR) is one of the most significant health threats to society. A growing body of research demonstrates selection for AMR likely occurs at environmental concentrations of antibiotics. However, no standardized experimental approaches for determining selective concentrations of antimicrobials currently exist, preventing appropriate environmental and human health risk assessment of AMR.

OBJECTIVES

We aimed to design a rapid, simple, and cost-effective novel experimental assay to determine selective effect concentrations of antibiotics and to generate the largest experimental data set of selective effect concentrations of antibiotics to date.

METHODS

Previously published methods and data were used to validate the assay, which determines the effect concentration based on reduction of bacterial community (wastewater) growth. Risk quotients for test antibiotics were generated to quantify risk.

RESULTS

The assay (SELection End points in Communities of bacTeria, or the SELECT method) was used to rapidly determine selective effect concentrations of antibiotics. These were in good agreement with quantitative polymerase chain reaction effect concentrations determined within the same experimental system. The SELECT method predicted no effect concentrations were minimally affected by changes in the assay temperature, growth media, or microbial community used as the inoculum. The predicted no effect concentrations for antibiotics tested ranged from 0.05μg/L for ciprofloxacin to 1,250μg/L for erythromycin.

DISCUSSION

The lack of evidence demonstrating environmental selection for AMR, and of associated human health risks, is a primary reason for the lack of action in the mitigation of release of antibiotics into the aquatic environment. We present a novel method that can reliably and rapidly fill this data gap to enable regulation and subsequent mitigation (where required) to lower the risk of selection for, and human exposure to, AMR in aquatic environments. In particular, ciprofloxacin and, to a lesser extent, azithromycin, cefotaxime, and trimethoprim all pose a significant risk for selection of AMR in the environment. https://doi.org/10.1289/EHP6635.

GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

Background

Horizontal gene transfer contributes to bacterial evolution through mobilising genes across various taxonomical boundaries. It is frequently mediated by mobile genetic elements (MGEs), which may capture, maintain, and rearrange mobile genes and co-mobilise them between bacteria, causing horizontal gene co-transfer (HGcoT). This physical linkage between mobile genes poses a great threat to public health as it facilitates dissemination and co-selection of clinically important genes amongst bacteria. Although rapid accumulation of bacterial whole-genome sequencing data since the 2000s enables study of HGcoT at the population level, results based on genetic co-occurrence counts and simple association tests are usually confounded by bacterial population structure when sampled bacteria belong to the same species, leading to spurious conclusions.

Results

We have developed a network approach to explore WGS data for evidence of intraspecies HGcoT and have implemented it in R package GeneMates (github.com/wanyuac/GeneMates). The package takes as input an allelic presence-absence matrix of interested genes and a matrix of core-genome single-nucleotide polymorphisms, performs association tests with linear mixed models controlled for population structure, produces a network of significantly associated alleles, and identifies clusters within the network as plausible co-transferred alleles. GeneMates users may choose to score consistency of allelic physical distances measured in genome assemblies using a novel approach we have developed and overlay scores to the network for further evidence of HGcoT. Validation studies of GeneMates on known acquired antimicrobial resistance genes in Escherichia coli and Salmonella Typhimurium show advantages of our network approach over simple association analysis: (1) distinguishing between allelic co-occurrence driven by HGcoT and that driven by clonal reproduction, (2) evaluating effects of population structure on allelic co-occurrence, and (3) direct links between allele clusters in the network and MGEs when physical distances are incorporated.

Conclusion

GeneMates offers an effective approach to detection of intraspecies HGcoT using WGS data.

Swine liquid manure: a hotspot of mobile genetic elements and antibiotic resistance genes

The overuse or abuse of antibiotics as veterinary medicine and growth promoters accelerates antibiotic resistance, creating a serious threat to public health in the world. Swine liquid manure as an important reservoir of antibiotic resistance genes (ARGs) has received much attention, but little information is known regarding the occurrence, persistence and fate of ARGs-associated mobile genetic elements (MGEs) in swine farms, especially their change patterns and removal in full-scale piggery wastewater treatment systems (PWWTSs). In this study, we searched the presence and distribution of MGEs and associated ARGs in swine farms, and addressed their fate and seasonal variation in full-scale PWWTSs by real-time quantitative PCR (qPCR). Our results revealed class 1 integrons, class 2 integrons and conjugative plasmids were prevalent in pig feces and piggery wastewater. A clear pattern of these MGE levels in swine liquid manure was also observed, i.e., intI1 > intI2 > traA (p < 0.01), and their absolute abundances in winter were all higher than that in summer with 0.07-2.23 logs. Notably, MGEs and ARGs prevailed through various treatment units of PWWTSs, and considerable levels of them were present in the treated effluent discharged from swine farms (up to 101-107 copies/mL for MGEs and 103-108 copies/mL for ARGs). There were significant correlations between most ARG abundance and MGE levels (p < 0.05), such as tetQ and traA (r = 0.775), sul1 and intI1 (r = 0.847), qnrS and inI2 (r = 0.859), suggesting the potential of ARGs-horizontal transfer. Thus the high prevalence and enrichment of MGEs and ARGs occurred in pig feces and piggery wastewater, also implicating that swine liquid manure could be a hotspot for horizontal transfer of ARGs.

Evolution of antibiotic resistance at low antibiotic concentrations including selection below the minimal selective concentration

Determining the selective potential of antibiotics at environmental concentrations is critical for designing effective strategies to limit selection for antibiotic resistance. This study determined the minimal selective concentrations (MSCs) for macrolide and fluoroquinolone antibiotics included on the European Commissionʼs Water Framework Directive’s priority hazardous substances Watch List. The macrolides demonstrated positive selection for ermF at concentrations 1–2 orders of magnitude greater (>500 and <750 µg/L) than measured environmental concentrations (MECs). Ciprofloxacin illustrated positive selection for intI1 at concentrations similar to current MECs (>7.8 and <15.6 µg/L). This highlights the need for compound specific assessment of selective potential. In addition, a sub-MSC selective window defined by the minimal increased persistence concentration (MIPC) is described. Differential rates of negative selection (or persistence) were associated with elevated prevalence relative to the no antibiotic control below the MSC. This increased persistence leads to opportunities for further selection over time and risk of human exposure and environmental transmission.

Stanton et al. determine the minimal selective concentrations for macrolide and fluoroquinolone antibiotics and describe a selective window defined by the minimal increased persistence concentration. These assessments and thresholds allow for better assessment of potential selection for antibiotic resistance and the risks of human exposure and environmental transmission.

Antibiotic resistance gene profiling in response to antibiotic usage and environmental factors in the surface water and groundwater of Honghu Lake, China

There is an increasing concern that aquaculture has been implicated in the formation of antibiotic resistance gene (ARG) reservoirs; however, little is known about the consequences of their presence in groundwater. In this study, 22 antibiotics, including four acetylated metabolites, and 27 ARGs were analyzed in fish pond water, surface water, and groundwater of the Honghu Lake in China. Correlations between conventional parameters, ionic composition, antibiotic concentration, and relative abundance of ARGs in water samples were analyzed. Among the three different sources of water, total antibiotic levels were the highest in fish pond water and the lowest in groundwater, with moderate levels in lake water. In surface water, sulfonamides and their metabolites accounted for the highest antibiotic content, whereas tetracyclines were the most frequently found in groundwater samples. Despite the near-undetectable levels of antibiotics in groundwater, the relative abundance of ARGs in groundwater samples was even higher than that in surface waters. The magnitude and extent of ARG migration are likely to be dependent on local antibiotic contamination levels as well as on the local environmental and hydrogeological conditions, with the class 1 integrons (intI1) being essential for the dissemination of such ARGs. The effects of environmental parameters such as antibiotics, dissolved oxygen, HCO3-, and pH on ARGs were highly significant, reflecting the potential impact of these factors on the abundance of ARGs. Our findings thus highlight the need for improved control of the spread of ARGs in and from aquaculture environments.

The Role of Agriculture in the Dissemination of Class 1 Integrons, Antimicrobial Resistance, and Diversity of Their Gene Cassettes in Southern China

Integrons are hot spots for acquiring gene cassettes from the environment and play a major role in the bacterial evolution and dissemination of antimicrobial resistance (AMR), thus posing a serious threat. There are currently studies on integrons and antibiotic resistance genes; however, the presence and association of integrons in different agricultural crops and their subsequent dissemination and role in AMR have not been reported previously. This study examines the abundance of integrons, their gene cassette diversity in various crop soils, and their role in the dissemination of AMR in the southern region of China. Samples from different agri-crop soil, such as rice (R.S), sugarcane (S.S), citrus (C.S), banana (B.S), agricultural runoff (the point where the runoff of all sites meet (R.O)), and wild (non-agricultural) soil (W.S), were collected. Quantitative PCR was used to determine the abundance of integrons, and clone libraries were constructed to examine the gene cassette arrays. All the tested samples were found positive for Class-I (CL1) integrons and revealed a higher concentration and higher relative abundance of R.S than the others, with the least found at the W.S site. The W.S CL1 cassette arrays were found empty, and no putative conserved domains were found. The R.O was found to contain a high number of gene cassettes with various functions, while the smallest number of gene cassettes was found in the S.S among the crop soils. Most of the gene cassettes presented by the R.O were primarily shared with other sites, and the antibiotic-resistant genes were consistently observed to be dominant. The constructed clone libraries represented a diverse gene cassette array with 16% novel gene cassettes that play a vital role in pathogenesis, transportation, biosynthesis, and AMR. Most resistance-related gene cassettes were associated with the genes encoding resistance to quaternary ammonium compound (QAC) and aminoglycosides. This study highlights the significant differences in the abundance of integrons among various agricultural soils and offers deep insight into the pools of gene cassettes that play a key role in the dissemination of integrons and AMR.

Antimicrobial resistance gene shuffling and a three-element mobilisation system in the monophasic Salmonella typhimurium strain ST1030

In this study we describe the genetic elements and the antimicrobial resistance units (RUs) harboured by the Salmonella Typhimurium monophasic variant 1,4,[5],12:i:- strain ST1030. Of the three identified RUs two were chromosomal, RU1 (IS26-bla_TEM-1-IS26-strAB-sul2- IS26) and RU2 (IS26-tetR(B)-tetA(B)-ΔIS26), and one, RU3 (a sul3-associated class 1 integron with cassette array dfrA12-orfF-aadA2-cmlA1-aadA1), was embedded in a Tn21-derived element harboured by the conjugative I1 plasmid pST1030-1A. IS26 elements mediated the antimicrobial resistance gene (ARG) shuffling and this gave rise to pST1030-1A derivatives with different sets of ARGs. ST1030 also harboured two ColE1-like plasmids of which one, pST1030-2A, was mobilisable and the target of an intracellular translocation of the Tn21-derived element; the second (pST1030-3) was an orphan mob-associated oriT plasmid co-transferred with pST1030-1A and pST1030-2A. pST1030-2A and pST1030-3 also carried a parA gene and a type III restriction modification system, respectively. Overall analysis of our data reinforces the role played by IS26, Tn21-derived elements and non-conjugative plasmids in the spread of ARGs and supplies the first evidence, at least in Salmonella, for the identification of a natural isolate harbouring a three-element mobilisation system in the same cell.

Occurrence and distribution of antibiotic resistance genes in various rural environmental media

Antibiotic resistance genes (ARGs) in rural environments have been poorly characterized in the literature. In this study, the diversity, abundance, and distribution of ARGs in surface waters, soils, and sediments of a typical hilly rural area in the Upper Yangtze River watershed were investigated using the high-throughput quantitative polymerase chain reaction, and their relationships with chemical properties of the samples were analyzed. No significant differences in the diversity and abundance of ARGs were observed among the three medium types while the ARG distribution pattern in the sediments was obviously different from that of the surface waters. According to the co-occurrence pattern of ARGs subtypes obtained by network analysis, blaOXA10-02, blaPSE, lnuB-02, and qacEΔ1-01 can be used to estimate the relative abundance of total ARGs for the study area. It appeared that the prevalence of ARGs in the sediments was promoted by the horizontal gene transfer (HGT) and vertical gene transfer together, while their spread in the surface waters and soils were facilitated by the supply of biogenic elements and HGT, respectively. Mobile genetic elements (MGEs) were abundant and detected in all samples, and their abundance was significantly and positively correlated with that of ARGs, implying that the potential horizontal transfer of ARGs to other bacteria and pathogens in rural environments should not be overlooked.

A comprehensive survey of integron-associated genes present in metagenomes

Background

Integrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they maintain a large and diverse set of genes that plays an important role in adaptation and evolution. Previous studies have started to characterize the wide range of biological functions present in integrons. However, the efforts have so far mainly been limited to genomes from cultivable bacteria and amplicons generated by PCR, thus targeting only a small part of the total integron diversity. Metagenomic data, generated by direct sequencing of environmental and clinical samples, provides a more holistic and unbiased analysis of integron-associated genes. However, the fragmented nature of metagenomic data has previously made such analysis highly challenging.

Results

Here, we present a systematic survey of integron-associated genes in metagenomic data. The analysis was based on a newly developed computational method where integron-associated genes were identified by detecting their associated recombination sites. By processing contiguous sequences assembled from more than 10 terabases of metagenomic data, we were able to identify 13,397 unique integron-associated genes. Metagenomes from marine microbial communities had the highest occurrence of integron-associated genes with levels more than 100-fold higher than in the human microbiome. The identified genes had a large functional diversity spanning over several functional classes. Genes associated with defense mechanisms and mobility facilitators were most overrepresented and more than five times as common in integrons compared to other bacterial genes. As many as two thirds of the genes were found to encode proteins of unknown function. Less than 1% of the genes were associated with antibiotic resistance, of which several were novel, previously undescribed, resistance gene variants.

Conclusions

Our results highlight the large functional diversity maintained by integrons present in unculturable bacteria and significantly expands the number of described integron-associated genes.

Impacts of multi-year field exposure of agricultural soil to macrolide antibiotics on the abundance of antibiotic resistance genes and selected mobile genetic elements

Exposure of environmental bacteria to antibiotics may be increasing the global resistome. Antibiotic residues are entrained into agricultural soil through the application of animal and human wastes, and irrigation with reclaimed water. The impact of a mixture of three macrolide antibiotics on the abundance of selected genes associated with antibiotic resistance and genetic mobility were determined in a long-term field experiment undertaken in London, Canada. Replicated plots received annual applications of a mixture of erythromycin, clarithromycin and azithromycin every spring since 2010. Each antibiotic was added directly to the soil at a concentration of either 0.1 or 10 mg kg soil^-1 and all plots were cropped to soybeans. By means of qPCR, no gene targets were enriched in soil exposed to the 0.1 mg kg soil^-1 dose compared to untreated control. In contrast, the relative abundance of several gene targets including int1, sul2 and mphE increased significantly with the annual exposure to the 10 mg kg soil^-1 dose. By means of high-throughput qPCR, numerous gene targets associated with resistance to aminoglycosides, sulfonamides, trimethoprim, streptomycin, quaternary ammonium chemicals as well as mobile genetic elements (tnpA, IS26 and IS6100) were detected in soil exposed to 10 mg kg soil^-1, but not the lower dose. Overall, exposure of soil to macrolide antibiotics increased the relative abundance of numerous gene targets associated with resistance to macrolides and other antibiotics, and mobile genetic elements. This occurred at an exposure dose that is unrealistically high, but did not occur at the lower more realistic exposure dose.

Dynamics of class 1 integrons in aerobic biofilm reactors spiked with antibiotics

Class 1 integrons are strongly associated with the dissemination of antibiotic resistance in bacteria. However, little is known about whether the presence of antibiotics affects the abundance of integrons and antibiotic resistance genes during biological wastewater treatment. To explore the roles of class 1 integrons in spreading antibiotic resistance genes in environmental compartments, the dynamics of integrons were followed in biofilm reactors treating synthetic wastewater respectively spiked with streptomycin (STM) and oxytetracycline (OTC). The relative abundance of the integron-integrase gene (intI1) increased 12 or 29-fold respectively when treated with STM or OTC, under incrementally increasing dosage regimes from 0 to 50 mg L^-1. Significant increases in intI1 abundance initially occurred at an antibiotic dose of 0.1 mg L^-1. At the beginning of the experiment, 51% to 64% of integrons carried no gene cassettes. In STM and OTC spiked systems, there was a significant increase in the proportion of integrons that contained resistance gene cassettes, particularly at intermediate and higher antibiotic concentrations. Gene cassettes encoding resistance to aminoglycosides, trimethoprim, beta-lactam, erythromycin, and quaternary ammonium compounds were all detected in the treated systems. Three tetracycline resistance genes (tetA, tetC, tetG) were significantly correlated with the abundance of intI1 (p < 0.01), despite no tet resistance being present as a gene cassette. Genome sequencing of isolates showed synteny between the tet resistance genes and intI1, mediated through linkage to transposable elements including Tn3, IS26 and ISCR3. Class 1 integrons appeared to be under positive selection in the presence of antibiotics, and might have actively acquired new gene cassettes during the experiment.

Antibiotic resistance genes and bacterial community dynamics in the seawater environment of Dapeng Cove, South China

In recent years, the propagation of antibiotic resistance genes (ARGs) and increased antibiotic resistance in pathogens have gained serious attention. Numerous reports have investigated the influence of domestic sewage discharge, medical wastewater and aquaculture wastewater on rivers and lakes, while the dynamics of ARGs in seawater and the relationships between ARGs, bacterial community structure and environmental factors have been less thoroughly described. In this study, the abundance, distribution and source of ARGs, as well as the relationships between ARGs, bacterial community changes and environmental factors in the seawater environment and sediment of Dapeng Cove, were investigated. Real-time quantitative PCR and Illumina Miseq sequencing technology were applied to determine the effects of the production cycle of cage culture, tourism and seasonality on ARGs. Chloramphenicol resistance genes (floR, cmlA) and sulfonamide resistance genes (sul1) were the dominant resistance genes in water and sediment. Pearson's correlation analysis showed that the abundance of all ARGs and the integrase I gene intI1 was positively correlated with chemical oxygen demand and suspended solids. Class 1 integrons might facilitate the dissemination of ARGs, and intI1 was detected in all samples at high concentrations. In aqueous environments, Cyanobacteria, Proteobacteria and Bacteroidetes were the dominant phyla, among which Proteobacteria and Bacteroidetes were positively correlated with the concentration of target ARGs. In the sediment, Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria and Planctomycetes were the dominant phyla, among which Bacteroidetes and Planctomycetes were positively correlated with most of the target ARGs and had a significant influence on changes in the abundance of ARGs. The domestic sewage was the main source of ARGs in the seawater. Our results showed that bacterial community structure and environmental factors affected the distributional dynamics of ARGs. Anthropogenic activities played significant roles in promoting ARGs abundance in the seawater environments.

Spatial and seasonal variations of antibiotic resistance genes and antibiotics in the surface waters of Poyang Lake in China

Antibiotic resistance genes (ARGs) and antibiotics in the aquatic environment raise health concerns particularly on the dispersal and persistence of antibiotic resistance. Large lakes, which serve as catch basins of anthropogenic inputs provide an ideal environment for understanding the occurrence and accumulation of ARGs and antibiotics in freshwater environments. Here, the largest freshwater lake in China, Poyang Lake, located in the developing district of Yangtze valley was used to study the characterization of the spatial and seasonal variation of both ARGs and antibiotics. Results showed that twelve tested ARGs (sul1, sul2, sul3, tetA, tetB, tetC, tetH, tetW, tetO, tetM, qnrS, and qnrB) were detected in the surface waters of Poyang Lake, with a detection frequency ranging from 19.2% to 100%, and sul2 and tetA genes were identified as potential indicators of ARG pollution in this region. Among the 11 analyzed antibiotics, sulfonamides were the predominant antibiotics with a contribution of more than 50% to the total concentrations of tested antibiotics. The total concentrations of both ARGs and antibiotics were higher in the dry season than those in the wet season. Furthermore, ARGs and antibiotics in the surface waters also varied with sampling locations, being consistently at riverine tributaries. Positive correlations were also observed between the concentrations of ARGs and antibiotics, as well as the integron gene (intI1), indicating that antibiotics and intI1 may be playing important roles in the occurrence and dispersal of ARGs in the surface waters. Lastly, our results suggest that intensive anthropogenic activities related to antibiotic usage have substantially contributed to the occurrence and persistence of ARGs and antibiotics in Poyang Lake.