Widespread dissemination of class 1 integron components in soils and related ecosystems as revealed by cultivation-independent analysis

Mobile genetic elements profiling, gene flow, and antimicrobial susceptibility profiles, among Pseudomonas aeruginosa isolates, isolated from Al Muthanna hospitals' wound and burn units in Iraq

The prevalence assessment of integrons among multidrug-resistant strains of Pseudomonas aeruginosa receives much-needed attention from this study, as we achieved our desired objective by conducting a thorough analysis on one hundred swabs obtained from burn and clinical cases at the hospitals present in Al Muthanna governorate during November of the year 2021 through to March of the year 2022. By implementing various methodologies encompassing the scrutiny of growth traits and cellular composition as well as executing biochemical assays, a total of 55 isolates were determined to exhibit the existence of P. aeruginosa. When cultured in Hifluoro agar media, Pseudomonas aeruginosa produced diverse hues; particularly noticeable was its blue-green colour. It was discovered through investigation that there were no intI2 and inti3 genes present in those isolated. Findings from this research disclosed that about one-fifth, or precisely twelve out of fifty-five P. aeruginosa strains screened, had an actively expressed Integrase I gene. The association between elevated rates of resistance to multiple antimicrobial agents and the existence of integrons is worth mentioning. Furthermore, the assemblage of isolates that were efficacious in the presence of integrons demonstrated an augmented resistance towards several frequently employed antibiotics like rifampicin and ceftazidime. In conclusion, it can be stated with confidence that a considerable occurrence of integrons can be observed in Pseudomonas aeruginosa strains that display resistance to numerous pharmaceutical agents. Additionally, the discovery of the intI1 gene in a considerable proportion of isolates underscores the effectiveness of integrons in conferring resistance to a variety of antimicrobial agents. These revelations supplement our insight into antibiotic-resistant mechanisms while also underscoring the necessity for viable strategies aimed at halting and preventing bacterial drug resistance.

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

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

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

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

Effect of composted pig manure, biochar, and their combination on antibiotic resistome dissipation in swine wastewater-treated soil

The prevalence of antibiotic resistance genes (ARGs), owing to irrigation using untreated swine wastewater, in vegetable-cultivated soils around swine farms poses severe threats to human health. Furthermore, at the field scale, the remediation of such soils is still challenging. Therefore, here, we performed field-scale experiments involving the cultivation of Brassica pekinensis in a swine wastewater-treated soil amended with composted pig manure, biochar, or their combination. Specifically, the ARG and mobile genetic element (MGE) profiles of bulk soil (BS), rhizosphere soil (RS), and root endophyte (RE) samples were examined using high-throughput quantitative polymerase chain reaction. In total, 117 ARGs and 22 MGEs were detected. Moreover, we observed that soil amendment using composted pig manure, biochar, or their combination decreased the absolute abundance of ARGs in BS and RE after 90 days of treatment. However, the decrease in the abundance of ARGs in RS was not significant. We also observed that the manure and biochar co-application showed a minimal synergistic effect. To clarify this observation, we performed network and Spearman correlation analyses and used structure equation models to explore the correlations among ARGs, MGEs, bacterial composition, and soil properties. The results revealed that the soil amendments reduced the abundances of MGEs and potential ARG-carrying bacteria. Additionally, weakened horizontal gene transfer was responsible for the dissipation of ARGs. Thus, our results indicate that composted manure application, with or without biochar, is a useful strategy for soil nutrient supplementation and alleviating farmland ARG pollution, providing a justification for using an alternative to the common agricultural practice of treating the soil using only untreated swine wastewater. Additionally, our results are important in the context of soil health for sustainable agriculture.

Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology

Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.

Fate of Horizontal-Gene-Transfer Markers and Beta-Lactamase Genes during Thermophilic Composting of Human Excreta

Thermophilic composting is a suitable treatment for the recycling of organic wastes for agriculture. However, using human excreta as feedstock for composting raises concerns about antibiotic resistances. We analyzed samples from the start and end of a thermophilic composting trial of human excreta, together with green cuttings and straw, with and without biochar. Beta-lactamase genes bla_CTX-M, bla_IMP, and bla_TEM conferring resistance to broad-spectrum beta-lactam antibiotics, as well as horizontal gene transfer marker genes, intI1 and korB, were quantified using qPCR. We found low concentrations of the beta-lactamase genes in all samples, with non-significant mean decreases in bla_CTX-M and bla_TEM copy numbers and a mean increase in bla_IMP copy numbers. The decrease in both intI1 and korB genes from start to end of composting indicated that thermophilic composting can decrease the horizontal spread of resistance genes. Thus, thermophilic composting can be a suitable treatment for the recycling of human excreta.

Influence of sewage sludge stabilization method on microbial community and the abundance of antibiotic resistance genes

Municipal sewage sludge (MSS) and other biosolids are of high interest for agriculture. These nutrient-rich organic materials can potentially serve as organic fertilizers. Besides an increase of organic matter in soil, other positive effects were shown after their application. Especially the positive influence on circular economy increased the attention paid to management of MSS in recent years. Unfortunately, the use of sewage sludge has some drawbacks. Biosolids are frequently polluted with heavy metals, xenobiotic organic compounds and industrial chemicals, which may be hazardous for the environment and humans. Here, we investigated the influence of stabilization method and the size of wastewater treatment plant on the structure of microbial communities as well as the abundance of antibiotic resistance genes (ARG) and mobile genetic elements (MGE). All tested ARG and MGE were detectable in almost all of the samples. Interestingly, the presence of MGE as well as particular heavy metals correlated positively with the presence of several ARG. We conclude that the distribution of ARG and MGE in biosolids originated from municipal wastewater treatment plants, cannot be explained by the size of the facility or the applied stabilization method. Moreover, we postulate that the presence of pollutants and long-term impacts should be assessed prior to a possible use of sewage sludge as fertilizer.

Distribution and transfer of antibiotic resistance genes in different soil-plant systems

The extensive application of farm manure that is contaminated with pharmaceutical antibiotics not only causes substantial soil pollution but additionally leads to the input of antibiotic resistance genes (ARGs) into the soil. These ARGs would proliferate and affect human health via the food chain. The effects of cultivated crops and wild plants on ARGs in rhizosphere soil are unclear. Therefore, we chose potted plants of cultivated crops (pakchoi, lettuce, corn) and wild plants (barnyard grass, crabgrass, dog tail), and set up test groups, i.e., treatment group, antibiotic-contaminated soil; control group, no antibiotic-contaminated soil; and a blank group without plants. The aim was to explore differences in the distribution and transfer of ARGs in the soil-plant system between cultivated crops and wild plants and at the same time to explore the influence of bacterial community evolution on ARGs in the rhizosphere soil of cultivated crops and wild plants. We concluded that under the pressure of antibiotic selection, ARGs can be transferred to the root endophytes of plants through the soil and further to the phyllosphere of plants, and cultivated crops such as pakchoi and wild plants barnyard grass have a strong ability to transport ARGs. Regardless of cultivated crops or wild plants, the abundance of ARGs in rhizosphere soil can be substantially reduced by 66.53 ~ 85.35%. Redundancy analysis and network analysis indicated that bacterial community succession is the main mechanism affecting changes of ARGs in rhizosphere soil. The reduction of Firmicutes due to the plant was the main factor responsible for the reduction of the abundance of ARGs in rhizosphere soil. The tetA, tetG, tetX, sul2, and qnrS genes are highly related to some potential pathogens, and the health risks they bring are a red flag that deserves attention.

Effect of biochar on antibiotics and antibiotic resistance genes variations during co-composting of pig manure and corn straw

Pig manure is a reservoir of antibiotics and antibiotic resistance genes (ARGs). The effect of biochar on the variations in physicochemical properties, bacterial communities, antibiotics, ARGs, and mobile genetic elements (MGEs) of compost product during co-composting of pig manure and corn straw have been investigated in this study. Compared with the control treatment (CK), biochar addition accelerated the increase in pile temperature and prolonged the high temperature period (>55°C) for 2 days. Under biochar influence, organic matter degradation, NH₄⁺-N conversion and NO₃⁻-N production was accelerated, and dissolved total organic carbon (DOC) and dissolved total nitrogen (DTN) utilization by microorganisms were enhanced. Biochar addition altered the microbial community and promoted the vital activity of Actinobacteria in the later composting stage. The antibiotics removal efficiency (except danofloxacin and enrofloxacin) was accelerated in the early composting stage (1–14 days) by biochar addition, the pile temperature had a positive effect on antibiotics removal, and the total antibiotics removal efficiency in CK and CK+Biochar treatments was 69.58% and 78.67% at the end of the composting process, respectively. The absolute abundance of most of the ARGs in the CK+Biochar treatment was lower than that in the CK treatment during composting, and the ARGs removal mainly occurred in the early (1–14 days) and later (28–50 days) stages. Biochar addition reduced the absolute abundance of MGEs (intI1, intI2) in the compost product, and most of the ARGs had a significant positive correlation with MGEs. Network analysis and redundancy analysis showed that ARGs and MGEs occurred in various host bacteria (Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Halanaerobiaeota), and that DTN and NH₄⁺-N are the main factors regulating the changes in bacterial communities, antibiotics, ARGs, and MGEs during composting. Moreover, MGEs contributed the most to the variation in ARGs. In summary, biochar addition during composting accelerated antibiotics removal and inhibited accumulation and transmission of ARGs. The results of this study could provide theoretical and technical support for biochar application for antibiotics and ARGs removal during livestock and poultry manure composting.

Spread of antimicrobial resistance genes via pig manure from organic and conventional farms in the presence or absence of antibiotic use

AIMS

Antibiotic resistant bacteria affect human and animal health. Hence, their environmental spread represents a potential hazard for mankind. Livestock farming is suspected to be a key factor for spreading antibiotic resistance; consumers expect organic farming to imply less environmental health risk. This study aimed to assess the role of manure from organic and conventional farms for spreading antimicrobial resistance (AMR) genes.

METHODS AND RESULTS

AMR-genes- namely tet(A), tet(B), tet(M), sul2, and qacE/qacEΔ1 (potentially associated with multiresistance) were quantified by qPCR. Antimicrobial use during the study period was qualitatively assessed from official records in a binary mode (yes/no). Median concentrations were between 6.44 log copy-equivalents/g for tet(A) and 7.85 for tet(M) in organic liquid manure, and between 7.48 for tet(A) and 8.3 for sul2 in organic farmyard manure. In conventional manure, median concentrations were 6.67 log copy-equivalents/g for sul2, 6.89 for tet(A), 6.77 for tet(B) and 8.36 for tet(M). Integron-associated qac-genes reached median concentrations of 7.06 log copy-equivalents/g in organic liquid manure, 7.13 in conventional manure and 8.18 in organic farmyard manure. Use of tetracyclines or sulfonamides increased concentrations of tet(A) and tet(M), or of sul2, respectively. Comparing farms that did not apply tetracyclines during the study, the relative abundance of tet(A) and tet(M) was still higher for conventional piggeries than for organic ones.

CONCLUSIONS

Relative abundances of antimicrobial resistance genes were higher in conventional farms, compared to organic ones. Antibiotic use was linked to the relative abundance of AMR-genes. However, due to the bacterial load, absolute concentrations of AMR-genes were comparable between fertilizers of organic and conventional farms.

SIGNIFICANCE AND IMPACT OF STUDY

To our knowledge, this is the first absolute quantification of AMR-genes in manure from organic farms. Our study underlines the importance of long-term-reduction in the use of antimicrobial agents in order to minimize antibiotic resistance.

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.

Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

BACKGROUND

Antimicrobial resistance (AMR) is predicted to become the leading cause of death by 2050 with antibiotic resistance being an important component. Anthropogenic pollution introduces antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) to the natural environment. Currently, there is limited empirical evidence demonstrating whether humans are exposed to environmental AMR and whether this exposure can result in measurable human health outcomes. In recent years there has been increasing interest in the role of the environment and disparate evidence on transmission of AMR to humans has been generated but there has been no systematic attempt to summarise this. We aim to create two systematic maps that will collate the evidence for (1) the transmission of antibiotic resistance from the natural environment to humans on a global scale and (2) the state of antibiotic resistance in the environment in the United Kingdom.

METHODS

Search strategies were developed for each map. Searches were undertaken in 13 bibliographic databases. Key websites were searched and experts consulted for grey literature. Search results were managed using EndNote X8. Titles and abstracts were screened, followed by the full texts. Articles were double screened at a minimum of 10% at both stages with consistency checking and discussion when disagreements arose. Data extraction occurred in Excel with bespoke forms designed. Data extracted from each selected study included: bibliographic information; study site location; exposure source; exposure route; human health outcome (Map 1); prevalence/percentage/abundance of ARB/antibiotic resistance elements (Map 2) and study design. EviAtlas was used to visualise outputs.

RESULTS

For Map 1, 40 articles were included, from 11,016 unique articles identified in searches, which investigated transmission of AMR from the environment to humans. Results from Map 1 showed that consumption/ingestion was the most studied transmission route. Exposure (n = 17), infection (n = 16) and colonisation (n = 11) being studied as an outcome a similar number of times, with mortality studied infrequently (n = 2). In addition, E. coli was the most highly studied bacterium (n = 16). For Map 2, we included 62 studies quantifying ARB or resistance elements in the environment in the UK, from 6874 unique articles were identified in the searches. The most highly researched species was mixed communities (n = 32). The most common methodology employed in this research question was phenotypic testing (n = 37). The most commonly reported outcome was the characterisation of ARBs (n = 40), followed by characterisation of ARGs (n = 35). Other genetic elements, such as screening for intI1 (n = 15) (which encodes a Class 1 integron which is used as a proxy for environmental ARGs) and point mutations (n = 1) were less frequently reported. Both maps showed that research was focused towards aquatic environments.

CONCLUSIONS

Both maps can be used by policy makers to show the global (Map 1) and UK (Map 2) research landscapes and provide an overview of the state of AMR in the environment and human health impacts of interacting with the environment. We have also identified (1) clusters of research which may be used to perform meta-analyses and (2) gaps in the evidence base where future primary research should focus.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s13750-022-00262-2.

Sequencing Depth Has a Stronger Effect than DNA Extraction on Soil Bacterial Richness Discovery

Although Next-Generation Sequencing techniques have increased our access to the soil microbiome, each step of soil metagenomics presents inherent biases that prevent the accurate definition of the soil microbiome and its ecosystem function. In this study, we compared the effects of DNA extraction and sequencing depth on bacterial richness discovery from two soil samples. Four DNA extraction methods were used, and sequencing duplicates were generated for each DNA sample. The V3–V4 region of the 16S rRNA gene was sequenced to determine the taxonomical richness measured by each method at the amplicon sequence variant (ASV) level. Both the overall functional richness and antibiotic resistance gene (ARG) richness were evaluated by metagenomics sequencing. Despite variable DNA extraction methods, sequencing depth had a greater influence on bacterial richness discovery at both the taxonomical and functional levels. Sequencing duplicates from the same sample provided access to different portions of bacterial richness, and this was related to differences in the sequencing depth. Thus, the sequencing depth introduced biases in the comparison of DNA extraction methods. An optimisation of the soil metagenomics workflow is needed in order to sequence at a sufficient and equal depth. This would improve the accuracy of metagenomic comparisons and soil microbiome profiles.

Effects of mineral additives on antibiotic resistance genes and related mechanisms during chicken manure composting

In this study, two typical minerals (diatomite and bentonite) were applied during composting, and their influences on antibiotics, antibiotic resistance genes (ARGs), intI1 and the bacterial communities were investigated. The relative abundance of total ARGs decreased by 53.72% and 59.54% in diatomite and bentonite addition compared with control on day 42. The minerals addition also reduced the relative abundance of intI1, as much as 41.41% and 59.81% in diatomite and bentonite treatments. Proteobacteria and Firmicutes were the dominant candidate hosts of the major ARGs. There was a significant correlation between total ARGs and intI1 during the composting. Structural equation models further demonstrated that intI1 and antibiotics were the predominant direct factors responsible for ARG variations, and composting properties and bacterial community composition also shifted the variation of ARG profiles by influencing intI1. Overall, these findings suggest that diatomite and bentonite could decrease the potential proliferation of ARGs in chicken manure.

Distribution and Molecular Characterization of Functional Class 2 Integrons in Clinical Proteus mirabilis Isolates

Background

Integrons are the main mode of horizontal transmission of drug-resistance genes and are closely related to drug resistance in clinical bacteria. In this study, the distributions of class 1, 2, and 3 integron gene cassettes were investigated in 150 Proteus mirabilis (P. mirabilis) isolates from patients, and molecular characterization of functional class 2 integrons was further analyzed.

Methods

Class 1, 2, and 3 integrons were screened by polymerase chain reaction (PCR) in 150 clinical P. mirabilis isolates. The variable regions of the integrons were determined by restriction analysis and sequencing. Internal stop codons mutations in class 2 integrons and their common promoters were also determined by sequencing. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) was used to analyze the phylogenetic relations of class 2 integron-positive isolates.

Results

Class 1 integrons were detected in 69 (46%) of 150 P. mirabilis isolates, and six different gene cassette arrays were detected, with the most prevalent being dfrA32-aadA2. Class 2 integrons were detected in 61 (40.7%) of 150 P. mirabilis isolates, and three different gene cassette arrays were detected, including sat2-aadA1, which was detected for the first time in a class 2 integron. Nearly similar ERIC-PCR fingerprinting patterns were detected in 45 (73.8%) of 61 class 2 integron-positive isolates. The functional class 2 integron was detected in three P. mirabilis isolates having the same gene cassette, dfrA1-sat2-aadA1, in the variable region and four novel open reading frames with unknown functions. Same PintI2 and Pc promoters were detected in these three functional class 2 integron isolates, as was found in other class 2 integron isolates. However, these three strains did not totally show identical homology and drug sensitivity.

Conclusion

Although functional class 2 integrons have low distribution and relatively conserved molecular characteristics, they can still form clinical dissemination and drug resistance expression.

Reduction of the resistome risk from cow slurry and manure microbiomes to soil and vegetable microbiomes

In cow farms, the interaction between animal and environmental microbiomes creates hotspots for antibiotic resistance dissemination. A shotgun metagenomic approach was used to survey the resistome risk in five dairy cow farms. To this purpose, 10 environmental compartments were sampled: 3 of them linked to productive cows (fresh slurry, stored slurry, slurry-amended pasture soil); 6 of them to non-productive heifers and dry cows (faeces, fresh manure, aged manure, aged manure-amended orchard soil, vegetables-lettuces and grazed soil); and, finally, unamended control soil. The resistome risk was assessed using MetaCompare, a computational pipeline which scores the resistome risk according to possible links between antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and human pathogens. The resistome risk decreased from slurry and manure microbiomes to soil and vegetable microbiomes. In total (sum of all the compartments), 18,157 ARGs were detected: 24% related to ansamycins, 21% to multidrugs, 14% to aminoglycosides, 12% to tetracyclines, 9% to β-lactams, and 9% to macrolide-lincosamide-streptogramin B. All but two of the MGE-associated ARGs were only found in the animal dejections (not in soil or vegetable samples). Several ARGs with potential as resistome risk markers (based on their presence in hubs of co-occurrence networks and high dissemination potential) were identified. As a precautionary principle, improved management of livestock dejections is necessary to minimize the risk of antibiotic resistance.

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.

Antibiotic Resistance in Agricultural Soil and Crops Associated to the Application of Cow Manure-Derived Amendments From Conventional and Organic Livestock Farms

The application of organic amendments to agricultural soil can enhance crop yield, while improving the physicochemical and biological properties of the recipient soils. However, the use of manure-derived amendments as fertilizers entails environmental risks, such as the contamination of soil and crops with antibiotic residues, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). In order to delve into these risks, we applied dairy cow manure-derived amendments (slurry, fresh manure, aged manure), obtained from a conventional and an organic farm, to soil. Subsequently, lettuce and wheat plants were grown in the amended soils. After harvest, the abundance of 95 ARGs and MGE-genes from the amended soils and plants were determined by high-throughput qPCR. The structure of soil prokaryotic communities was determined by 16S rRNA amplicon sequencing and qPCR. The absolute abundance of ARGs and MGE-genes differed between treatments (amended vs. unamended), origins of amendment (conventional vs. organic), and types of amendment (slurry vs. fresh manure vs. aged manure). Regarding ARG-absolute abundances in the amendments themselves, higher values were usually found in slurry vs. fresh or aged manure. These abundances were generally higher in soil than in plant samples, and higher in wheat grain than in lettuce plants. Lettuce plants fertilized with conventional amendments showed higher absolute abundances of tetracycline resistance genes, compared to those amended with organic amendments. No single treatment could be identified as the best or worst treatment regarding the risk of antibiotic resistance in soil and plant samples. Within the same treatment, the resistome risk differed between the amendment, the amended soil and, finally, the crop. In other words, according to our data, the resistome risk in manure-amended crops cannot be directly inferred from the analysis of the amendments themselves. We concluded that, depending on the specific question under study, the analysis of the resistome risk should specifically focus on the amendment, the amended soil or the crop.

Dairy manure as a potential source of crop nutrients and environmental contaminants

Although animal manure is applied to agricultural fields for its nutrient value, it may also contain potential contaminants. To determine the variability in such contaminants as well as in valuable nutrients, nine uncomposted manure samples from Idaho dairies collected during 2.5 years were analyzed for macro- and micro-nutrients, hormones, phytoestrogens, antibiotics, veterinary drugs, antibiotic resistance genes, and genetic elements involved in the spread of antibiotic resistance. Total N ranged from 6.8 to 30.7 (C:N of 10 to 21), P from 2.4 to 9.0, and K from 10.2 to 47.7 g/kg manure. Zn (103 - 348 mg/kg) was more abundant than Cu (56 - 127 mg/kg) in all samples. Phytoestrogens were the most prevalent contaminants detected, with concentrations fluctuating over time, reflecting animal diets. This is the first study to document the presence of flunixin, a non-steroidal anti-inflammatory drug, in solid stacked manure from regular dairy operations. Monensin was the most frequently detected antibiotic. Progesterones and sulfonamides were regularly detected. We also investigated the relative abundance of several types of plasmids involved in the spread of antibiotic resistance in clinical settings. Plasmids belonging to the IncI, IncP, and IncQ1 incompatibility groups were found in almost all manure samples. IncQ1 plasmids, class 1 integrons, and sulfonamide resistance genes were the most widespread and abundant genetic element surveyed, emphasizing their potential role in the spread of antibiotic resistance. The benefits associated with amending agricultural soils with dairy manure must be carefully weighed against the potential negative consequences of any manure contaminants.

Impacts of cadmium addition on the alteration of microbial community and transport of antibiotic resistance genes in oxytetracycline contaminated soil

The large-scale development in livestock feed industry has increased the chances of antibiotics and heavy metals contamination in the soil. The fate of antibiotic resistance genes (ARGs) and microbial community in heavy metals and antibiotic contaminated soil is still unclear. In this study, we investigated the effect of cadmium (Cd) addition on the transport of ARGs, microbial community and human pathogenic bacteria in oxytetracycline (OTC) contaminated soil. Results showed that the addition of OTC significantly increased the abundance of ARGs and intI1 in the soil and lettuce tissues. The addition of Cd to OTC treated soil further increased the abundance and translocation of ARGs and intI1. Moreover, Cd promoted the transfer of potential human pathogenic bacteria (HPB) into lettuce tissues. Compared with O10 treatment, the addition of Cd decreased the concentration of OTC in soil and lettuce tissue, but slightly increased the fresh weight of lettuce tissues. Redundancy analysis indicated that bacterial community succession is a major factor in ARGs variation. Network analysis indicated that the main host bacteria of ARGs were mainly derived from Proteobacteria. Correlation analysis showed that intI1 was significantly correlated with tetG, tetC, sul1, sul2, ermX, and ermQ. Meanwhile, potential HPB (Clostridium, and Burkholderia) was significantly correlated with intI1 and eight ARGs (tetG, tetC, tetW, tetX, sul1, sul2, ermX, and ermQ.). The findings of this study suggest that the addition of heavy metals to agricultural fields must be considered in order to reduce the transfer of ARGs in the soil and crops.

Soil water solutes reduce the critical micelle concentration of quaternary ammonium compounds

Quaternary alkyl ammonium compounds (QAACs) are produced in large quantities for use as surfactants and disinfectants and also found in soils, sediments, and surface waters, where they are potentially involved in the selection of antibiotic resistance genes. Micelle formation influences fate and effects of QAACs. The critical micelle concentration (CMC) of six homologs of benzylalkylammonium chlorides (BAC) was determined in deionized water, 0.01 M CaCl₂ solution, and aqueous soil extracts, using both spectrofluorometric and tensiometric methods. Additionally, eight organic model compounds were employed at concentrations of 15 mg C L^-1 as background solutes in order to test the effect of dissolved organic carbon (DOC) on CMCs. Results found CMCs decreased with an increasing length of the alkyl chain from 188 mM for BAC-C8 to 0.1 mM for BAC-C18. Both methods yielded similar results for measurements in water and CaCl₂ solution; however, the spectrofluorescence method did not work for soil extracts due to fluorescence quenching phenomena. In soil extracts, CMCs of BAC-C12 were reduced below 3.7 mM, while the CMC reduction in soil extracts was less pronounced for BAC-C16. Besides ionic strength, molecular structures of BACs and dissolved organic compounds also affected the CMC. The number of carboxyl groups and small molecular weights of the DOC model compounds reduced the CMCs of BAC-C12 and BAC-C16 at pH 6. This study highlights that CMCs can be surpassed in soil solution, pore waters of sediments, or other natural waters even at (small) concentrations of QAACs typically found in the environment.

Plant Species-Dependent Increased Abundance and Diversity of IncP-1 Plasmids in the Rhizosphere: New Insights Into Their Role and Ecology

IncP-1 plasmids, first isolated from clinical specimens (R751, RP4), are recognized as important vectors spreading antibiotic resistance genes. The abundance of IncP-1 plasmids in the environment, previously reported, suggested a correlation with anthropogenic pollution. Unexpectedly, qPCR-based detection of IncP-1 plasmids revealed also an increased relative abundance of IncP-1 plasmids in total community DNA from the rhizosphere of lettuce and tomato plants grown in non-polluted soil along with plant age. Here we report the successful isolation of IncP-1 plasmids by exploiting their ability to mobilize plasmid pSM1890. IncP-1 plasmids were captured from the rhizosphere but not from bulk soil, and a high diversity was revealed by sequencing 14 different plasmids that were assigned to IncP-1β, δ, and ε subgroups. Although backbone genes were highly conserved and mobile elements or remnants as Tn501, IS1071, Tn402, or class 1 integron were carried by 13 of the sequenced IncP-1 plasmids, no antibiotic resistance genes were found. Instead, seven plasmids had a mer operon with Tn501-like transposon and five plasmids contained putative metabolic gene clusters linked to these mobile elements. In-depth sequence comparisons with previously known plasmids indicate that the IncP-1 plasmids captured from the rhizosphere are archetypes of those found in clinical isolates. Our findings that IncP-1 plasmids do not always carry accessory genes in unpolluted rhizospheres are important to understand the ecology and role of the IncP-1 plasmids in the natural environment.

Online searching platform for the antibiotic resistome in bacterial tree of life and global habitats

Metagenomic analysis reveals that antibiotic-resistance genes (ARGs) are widely distributed in both human-associated and non-human-associated habitats. However, it is difficult to equally compare ARGs between samples without a standard method. Here, we constructed a comprehensive profile of the distribution of potential ARGs in bacterial tree of life and global habitats by investigating ARGs in 55 000 bacterial genomes, 16 000 bacterial plasmid sequences, 3000 bacterial integron sequences and 850 metagenomes using a standard pipeline. We found that >80% of all known ARGs are not carried by any plasmid or integron sequences. Among potential mobile ARGs, tetracycline and beta-lactam resistance genes (such as tetA, tetM and class A beta-lactamase gene) distribute in multiple pathogens across bacterial phyla, indicating their clinical relevance and importance. We showed that class 1 integrases (intI1) display a poor linear relationship with total ARGs in both non-human-associated and human-associated environments. Furthermore, both total ARGs and intI1 genes show little correlation with the degree of anthropogenicity. These observations highlight the need to differentiate ARGs of high clinical relevance. This profile is published on an online platform (ARGs-OSP, http://args-osp.herokuapp.com/) as a valuable resource for the most challenging topics in this field, i.e. the risk, evolution and emergence of ARGs.

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.

Linkage of antibiotic resistance genes, associated bacteria communities and metabolites in the wheat rhizosphere from chlorpyrifos-contaminated soil

Rhizosphere is a crucial site for the proliferation of antibiotic resistance genes (ARGs) in agricultural soil. Pesticide contamination is ubiquitous in soil, such as chlorpyrifos as one of the most commonly used pesticides. However, limited knowledge is reported about ARGs profiles changes and the driving mechanism of ARGs prevalence in rhizosphere soil after adding pesticide. In this study, irrespective of chlorpyrifos presence, the abundances of ARGs (tetM, tetO, tetQ, tetW, tetX, sul1 and sul2) and intI1 in rhizosphere soil of wheat were obviously higher than those in bulk soil. 20.0 mg·kg^-1 chlorpyrifos significantly increased the abundance of total ARGs and intI1 in bulk soil, respectively, at day 50 and 100, but not in rhizosphere soil. Rhizosphere influence on ARGs was far greater than chlorpyrifos. ARGs and intI1 abundances were higher at day 50 than ones at day 100. C/N ratio and NO₃^--N content, which were affected by rhizosphere and cultivation time, significantly explained the increased ARGs. Compared to bulk soil, rhizosphere shifted host bacteria of tetracycline resistance genes (TRGs), intI1 at genus level, and host bacteria of sul1, sul2 at phylum level. Rhizosphere simplified the linkage of ARGs, host bacteria and metabolites. Bacterial communities played important roles in the variation of ARGs and intI1, and the difference in the distribution of potential hosts between bulk and rhizosphere soil was related to metabolites abundance and composition. These results provide valuable information for understanding the linkage of ARGs, associated bacteria communities and metabolites in the wheat rhizosphere soil.

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.

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.

The gut and feed residue microbiota changing during the rearing of Hermetia illucens larvae

Larvae of Hermetia illucens, commonly known as black soldier fly, efficiently convert organic waste into nutrient-rich supplements for different applications. Here we performed a preliminary experiment to investigate the dynamics of the H. illucens gut microbiota and changes in the composition of the bacterial community in the residue of the larval feed during rearing. We furthermore quantified the presence of antibiotic resistance and disinfectant genes in the gut and feed microbiota during the rearing process to elucidate if rearing leads to a reduction, increase, and/or transfer of resistance genes from the feed to larvae and vice versa. We found that the gut and feed residue bacterial communities were distinct throughout the rearing process. The gut microbiome remained more stable compared to the feed residue microbiome varying in both bacterial abundance and community structure during rearing. Antibiotic-resistance genes were present in both, gut and feed residues, with a significant increase in pupae and residue samples taken at the end of the rearing process. Disinfectant-resistance genes were present in the feed residue and even increased during the rearing process but were not transferred to the gut microbiome. We conclude that H. illucens larvae have a stable gut microbiome that does not change significantly over the course of larval development, whereas bacterial communities in the feed residue are strongly affected by rearing. If the presence of antibiotics and disinfectants during rearing, can promote the spread of antibiotic/disinfectant-resistance genes among feed and larvae needs to be evaluated in further experiments.

Evaluation of antibiotic resistance dissemination by wastewater treatment plant effluents with different catchment areas in Germany

The study quantified the abundances of antibiotic resistance genes (ARGs) and facultative pathogenic bacteria (FPB) as well as one mobile genetic element in genomic DNA via qPCR from 23 different wastewater treatment plant (WWTP) effluents in Germany. 12 clinically relevant ARGs were categorized into frequently, intermediately, and rarely occurring genetic parameters of communal wastewaters. Taxonomic PCR quantifications of five FPB targeting Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Acinetobacter baumannii, and enterococci were performed. The WWTPs differed in their catchment areas being impacted by hospitals, food processing companies, or housing areas only. The total discharges of the analyzed ARGs and FPB were found to cluster independently of the sizes of the WWTPs with a maximum difference of two log units within one cluster. Initially, quantitative data evaluations revealed no significant difference between ARG categories and WWTP catchment areas. More distinct correlations became obvious with a Pearson correlation approach, where each single taxonomic marker is compared to each ARG target. Here, increased correlation of FPB (i.e. E. coli, K. pneumoniae, P. aeruginosa, and enterococci) with clinically relevant ARGs of the category of rarely occurring resistance genes (bla_NDM-1, vanA) was found in WWTP effluents being influenced by hospital wastewaters.

Distribution of Medically Relevant Antibiotic Resistance Genes and Mobile Genetic Elements in Soils of Temperate Forests and Grasslands Varying in Land Use

Antibiotic-resistant pathogens claim the lives of thousands of people each year and are currently considered as one of the most serious threats to public health. Apart from clinical environments, soil ecosystems also represent a major source of antibiotic resistance determinants, which can potentially disseminate across distinct microbial habitats and be acquired by human pathogens via horizontal gene transfer. Therefore, it is of global importance to retrieve comprehensive information on environmental factors, contributing to an accumulation of antibiotic resistance genes and mobile genetic elements in these ecosystems. Here, medically relevant antibiotic resistance genes, class 1 integrons and IncP-1 plasmids were quantified via real time quantitative PCR in soils derived from temperate grasslands and forests, varying in land use over a large spatial scale. The generated dataset allowed an analysis, decoupled from regional influences, and enabled the identification of land use practices and soil characteristics elevating the abundance of antibiotic resistance genes and mobile genetic elements. In grassland soils, the abundance of the macrolide resistance gene mefA as well as the sulfonamide resistance gene sul2 was positively correlated with organic fertilization and the abundance of aac(6')-lb, conferring resistance to different aminoglycosides, increased with mowing frequency. With respect to forest soils, the beta-lactam resistance gene blaIMP-12 was significantly correlated with fungal diversity which might be due to the fact that different fungal species can produce beta-lactams. Furthermore, except blaIMP-5 and blaIMP-12, the analyzed antibiotic resistance genes as well as IncP-1 plasmids and class-1 integrons were detected less frequently in forest soils than in soils derived from grassland that are commonly in closer proximity to human activities.

Detection, Isolation, and Characterization of Plasmids in the Environment

Plasmids play a major role in the bacterial adaptation to changing and stressful environmental conditions caused by antibiotics, heavy metals, and disinfectants. However, the investigation of the ecology and diversity of environmental plasmids is challenging due to their typically low abundance in soil bacterial communities and the low cultivability of their hosts. Here we discuss the potentials and limitations of cultivation-dependent and cultivation-independent approaches for detecting and quantifying plasmids in total community DNA from environmental samples. Protocols for PCR-based detection of plasmid-specific sequences in total community DNA are presented. Furthermore, protocols to obtain and characterize plasmids either from isolates (endogenous plasmid isolation) or by capturing into a recipient strain by biparental and triparental mating will be provided.

Antibiotic-manufacturing sites are hot-spots for the release and spread of antibiotic resistance genes and mobile genetic elements in receiving aquatic environments

High antibiotic releases from manufacturing facilities have been identified as a risk factor for antibiotic resistance development in bacterial pathogens. However, the role of antibiotic pollution in selection and transferability of antibiotic resistance genes (ARGs) is still limited. In this study, we analyzed effluents from azithromycin-synthesis and veterinary-drug formulation facilities as well as sediments from receiving river and creek taken at the effluent discharge sites, upstream and downstream of discharge. Culturing showed that the effluent discharge significantly increased the proportion of antibiotic resistant bacteria in exposed sediments compared to the upstream ones. Quantitative real-time PCR revealed that effluents from both industries contained high and similar relative abundances of resistance genes [sul1, sul2, qacE/qacEΔ1, tet(A)], class 1 integrons (intI1) and IncP-1 plasmids (korB). Consequently, these genes significantly increased in relative abundances in receiving sediments, with more pronounced effects being observed for river than for creek sediments due to lower background levels of the investigated genes in the river. In addition, effluent discharge considerably increased transfer frequencies of captured ARGs from exposed sediments into Escherichia coli CV601 recipient as shown by biparental mating experiments. Most plasmids exogenously captured from effluent and polluted sediments belonged to the broad host range IncP-1ε plasmid group, conferred multiple antibiotic resistance and harbored class 1 integrons. Discharge of pharmaceutical waste from antibiotic manufacturing sites thus poses a risk for development and dissemination of multi-resistant bacteria, including pathogens.

Impact of the particulate matter from wastewater discharge on the abundance of antibiotic resistance genes and facultative pathogenic bacteria in downstream river sediments

Wastewater treatment plants (WWTPs) are point sources for both, the release of antibiotic resistance genes (ARGs) and the discharge of antibiotics (ABs) into the environment. While it is well established that ARGs emission by WWTPs leads to an ARGs increase in receiving rivers, also the role of sub-inhibitory AB concentrations in this context is being discussed. However, the results obtained in this study suggest that, at environmental concentrations, ABs do not have an effect on resistance selection. Instead, we emphasize the significance of ARG transport and, in that respect, highlight the relevance of wastewater particles and associated microorganisms. We can show that ARGs (ermB, bla_TEM,tetM, qnrS) as well as facultative pathogenic bacteria (FPB) (enterococci, Pseudomonas aeruginosa, Acinetobacter baumannii) inside the particulate fraction of WWTP effluent are very likely to remain in the riverbed of the receiving water due to sedimentation. Moreover, ARG and FPB abundances measured in the particulate fraction strongly correlated with the delta ARG and FPB abundances measured in the receiving river sediment (downstream compared to upstream) (R² = 0.93, p < 0.05). Apparently, the sheer amount of settleable ARGs and FPB from WWTP effluent is sufficient, to increase abundances in the receiving riverbed by 0.5 to 2 log units.

Application of sewage sludge to agricultural soil increases the abundance of antibiotic resistance genes without altering the composition of prokaryotic communities

The application of sewage sludge as soil amendment is a common agricultural practice. However, wastewater treatment plants, sewage sludge and sewage sludge-amended soils have been reported as hotspots for the appearance and dissemination of antibiotic resistance, driven, among other factors, by selection pressure exerted by co-exposure to antibiotics and heavy metals. To address this threat to environmental and human health, soil samples from a long-term (24 years) field experiment, carried out to study the impact of thermally dried and anaerobically digested sewage sludge (at different doses and frequencies of application) on agricultural soil quality, were investigated for the presence of genes encoding antibiotic resistance (ARGs) and mobile genetic elements (MGEs). Sewage sludge-induced changes in specific soil physicochemical and microbial properties, as indicators of soil quality, were also investigated. The application of sewage sludge increased the total concentration of copper and zinc in amended soils, but without affecting the bioavailability of these metals, possibly due to the high values of soil pH and organic matter content. Soil microbal quality, as reflected by the value of the Soil Quality Index, was higher in sewage sludge-amended soils. Similarly, the application of sewage sludge increased soil microbial activity and biomass, as well as the abundance of ARGs and MGE genes, posing a risk of dissemination of antibiotic resistance. In contrast, the composition of soil prokaryotic communities was not significantly altered by the application of sewage sludge. We found correlation between soil Cu and Zn concentrations and the abundance of ARGs and MGE genes. It was concluded that sewage sludge-derived amendments must be properly treated and managed if they are to be applied to agricultural soil.

The Transferable Resistome of Produce

Produce is increasingly recognized as a reservoir of human pathogens and transferable antibiotic resistance genes. This study aimed to explore methods to characterize the transferable resistome of bacteria associated with produce. Mixed salad, arugula, and cilantro purchased from supermarkets in Germany were analyzed by means of cultivation- and DNA-based methods. Before and after a nonselective enrichment step, tetracycline (TET)-resistant Escherichia coli were isolated and plasmids conferring TET resistance were captured by exogenous plasmid isolation. TET-resistant E. coli isolates, transconjugants, and total community DNA (TC-DNA) from the microbial fraction detached from leaves or after enrichment were analyzed for the presence of resistance genes, class 1 integrons, and various plasmids by real-time PCR and PCR-Southern blot hybridization. Real-time PCR primers were developed for IncI and IncF plasmids. TET-resistant E. coli isolated from arugula and cilantro carried IncF, IncI1, IncN, IncHI1, IncU, and IncX1 plasmids. Three isolates from cilantro were positive for IncN plasmids and blaCTX-M-1 From mixed salad and cilantro, IncF, IncI1, and IncP-1β plasmids were captured exogenously. Importantly, whereas direct detection of IncI and IncF plasmids in TC-DNA failed, these plasmids became detectable in DNA extracted from enrichment cultures. This confirms that cultivation-independent DNA-based methods are not always sufficiently sensitive to detect the transferable resistome in the rare microbiome. In summary, this study showed that an impressive diversity of self-transmissible multiple resistance plasmids was detected in bacteria associated with produce that is consumed raw, and exogenous capturing into E. coli suggests that they could transfer to gut bacteria as well.IMPORTANCE Produce is one of the most popular food commodities. Unfortunately, leafy greens can be a reservoir of transferable antibiotic resistance genes. We found that IncF and IncI plasmids were the most prevalent plasmid types in E. coli isolates from produce. This study highlights the importance of the rare microbiome associated with produce as a source of antibiotic resistance genes that might escape cultivation-independent detection, yet may be transferred to human pathogens or commensals.

Prevalence of antibiotic resistance genes in soils after continually applied with different manure for 30 years

A 30year field experiment with a wheat-soybean cropping system were performed to compare the long-term anthropogenic influence on soil ARGs. Compared with chemical fertilization, the occurrence of 38 ARGs and the abundance of seven ARGs (tetL, tetB(P), tetO, tetW, sul1, ermB, and ermF) were significantly increased by long term exposure of pig manure. However, application of wheat straw and cow manure not substantially affected the abundance of ARGs except cow manure increased the abundance of tetM and tetW to a detectable level. Relative abundance of Firmicutes, Gammaproteobacteria and Bacteroidetes and ARGs observed in the soil were significantly correlated. Integrase gene I1 (intI1) is commonly linked to genes conferring resistance to antibiotics, it was significantly increased in pig manure treated soils and showed a high positive correlation with the abundance of ARGs which were significantly affected by pig manure. Concentrations of Cu, Zn and Pb were also increased in manure treated soil and positive correlated with the relative abundance of intI1 and most of the ARGs. These results indicated that long-term animal manure application to soils has polluted the soil, especially for pig manure, and it should be scrutinized as part of future stewardship programs.

Effects of biochar on reducing the abundance of oxytetracycline, antibiotic resistance genes, and human pathogenic bacteria in soil and lettuce

Antibiotics and antibiotic resistance genes (ARGs) in soil can affect human health via the food chain. Biochar is a soil amendment but its impacts on ARGs and the microbial communities associated with soil and vegetables are unclear. Therefore, we established three lettuce pot culture experiments, i.e., O300: 300 mg/kg oxytetracycline (OTC), BO300: 300 mg/kg OTC + 2% biochar, and a control without OTC or biochar. We found that under BO300, the relative abundances of ARGs were reduced by 51.8%, 43.4%, and 44.1% in lettuce leaves, roots, and soil, respectively, compared with O300. intI1 was highly abundant in soil and lettuce, and it co-occurred with some ARGs (tetW, ermF, and sul1). Redundancy analysis and network analysis indicated that the bacterial community succession was the main mechanism that affected the variations in ARGs and intI1. The reduction of Firmicutes due to the biochar treatment of soil and lettuce was the main factor responsible for the removal of tetracycline resistance genes in leaves. Biochar application led to the disappearance of human pathogenic bacteria (HPB), which was significantly correlated with the abundances of ermF and ermX. In summary, biochar is an effective farmland amendment for reducing the abundances of antibiotics, ARGs, and HPB in order to ensure the safety of vegetables and protect human health.

High Throughput Analysis of Integron Gene Cassettes in Wastewater Environments

Integrons are extensively targeted as a proxy for anthropogenic impact in the environment. We developed a novel high-throughput amplicon sequencing pipeline that enables characterization of thousands of integron gene cassette-associated reads, and applied it to acquire a comprehensive overview of gene cassette composition in effluents from wastewater treatment facilities across Europe. Between 38 100 and 172 995 reads per-sample were generated and functionally characterized by screening against nr, SEED, ARDB and β-lactamase databases. Over 75% of the reads were characterized as hypothetical, but thousands were associated with toxin-antitoxin systems, DNA repair, cell membrane function, detoxification and aminoglycoside and β-lactam resistance. Among the reads characterized as β-lactamases, the carbapenemase bla_OXA was dominant in most of the effluents, except for Cyprus and Israel where bla_GES was also abundant. Quantitative PCR assessment of bla_OXA and bla_GES genes in the European effluents revealed similar trends to those displayed in the integron amplicon sequencing pipeline described above, corroborating the robustness of this method and suggesting that these integron-associated genes may be excellent targets for source tracking of effluents in downstream environments. Further application of the above analyses revealed several order-of-magnitude reductions in effluent-associated β-lactamase genes in effluent-saturated soils, suggesting marginal persistence in the soil microbiome.

Plasmid Detection, Characterization, and Ecology

Plasmids are important vehicles for rapid adaptation of bacterial populations to changing environmental conditions. It is thought that to reduce the cost of plasmid carriage, only a fraction of a local population carries plasmids or is permissive to plasmid uptake. Plasmids provide various accessory traits which might be beneficial under particular conditions. The genetic variation generated by plasmid carriage within populations ensures the robustness toward environmental changes. Plasmid-mediated gene transfer plays an important role not only in the mobilization and dissemination of antibiotic resistance genes but also in the spread of degradative pathways and pathogenicity determinants of pathogens. Here we summarize the state-of-the-art methods to study the occurrence, abundance, and diversity of plasmids in environmental bacteria. Increasingly, cultivation-independent total-community DNA-based methods are being used to characterize and quantify the diversity and abundance of plasmids in relation to various biotic and abiotic factors. An improved understanding of the ecology of plasmids and their hosts is crucial in the development of intervention strategies for antibiotic-resistance-gene spread. We discuss the potentials and limitations of methods used to determine the host range of plasmids, as the ecology of plasmids is tightly linked to their hosts. The recent advances in sequencing technologies provide an enormous potential for plasmid classification, diversity, and evolution studies, but numerous challenges still exist.

Mathematical modelling of antimicrobial resistance in agricultural waste highlights importance of gene transfer rate

Antimicrobial resistance is of global concern. Most antimicrobial use is in agriculture; manures and slurry are especially important because they contain a mix of bacteria, including potential pathogens, antimicrobial resistance genes and antimicrobials. In many countries, manures and slurry are stored, especially over winter, before spreading onto fields as organic fertilizer. Thus, these are a potential location for gene exchange and selection for resistance. We develop and analyse a mathematical model to quantify the spread of antimicrobial resistance in stored agricultural waste. We use parameters from a slurry tank on a UK dairy farm as an exemplar. We show that the spread of resistance depends in a subtle way on the rates of gene transfer and antibiotic inflow. If the gene transfer rate is high, then its reduction controls resistance, while cutting antibiotic inflow has little impact. If the gene transfer rate is low, then reducing antibiotic inflow controls resistance. Reducing length of storage can also control spread of resistance. Bacterial growth rate, fitness costs of carrying antimicrobial resistance and proportion of resistant bacteria in animal faeces have little impact on spread of resistance. Therefore, effective treatment strategies depend critically on knowledge of gene transfer rates.

Diversification of broad host range plasmids correlates with the presence of antibiotic resistance genes

The IncP-1ε subgroup is a recently identified phylogenetic clade within IncP-1 plasmids, which plays an important role in the spread of antibiotic resistance and degradation of xenobiotic pollutants. Here, four IncP-1ε plasmids were exogenously captured from a petroleum-contaminated habitat in China and compared phylogenetically and genomically with previously reported IncP-1ε and other IncP-1 plasmids. The IncP-1ε plasmids can be clearly subdivided into two subclades, designated as ε-I and ε-II, based on phylogenetic analysis of backbone proteins TraI and TrfA. This was further supported by comparison of concatenated backbone genes. Moreover, the two subclades differed in the transposon types, phenotypes and insertion locations of the accessory elements. The accessory genes on ε-I plasmids were inserted between parA and traC, and harbored ISPa17 and Tn402-like transposon modules, typically carrying antibiotic resistance genes. In contrast, the accessory elements on ε-II plasmids were typically located between trfA and oriV, and contained IS1071, which was commonly inserted within the Tn501-like transposon, typically harboring a cluster of genes encoding mercury resistance and/or catabolic pathways. Our study is one of the first to compare IncP-1 plasmid genomes from China, expands the available collection of IncP-1ε plasmids and enhances our understanding of their diversity, biogeography and evolutionary history.

Integron diversity in marine environments

Integrons are bacterial genetic elements known to be active vectors of antibiotic resistance among clinical bacteria. They are also found in bacterial communities from natural environments. Although integrons have become especially efficient for bacterial adaptation in the particular context of antibiotic usage, their role in natural environments in other contexts is still unknown. Indeed, most studies have focused on integrons and the spread of antibiotic resistance in freshwater or soil impacted by anthropogenic activities, with only few on marine environments. Notably, integrons show a wider diversity of both gene cassettes and integrase gene in natural environments than in clinical environments, suggesting a general role of integrons in bacterial adaptation. This article reviews the current knowledge on integrons in marine environments. We also present conclusions of our studies on polluted and nonpolluted backgrounds.