Prevalence of sulfonamide-resistant bacteria, resistance genes and integron-associated horizontal gene transfer in natural water bodies and soils adjacent to a swine feedlot in northern Taiwan

In vivo fitness of sul gene-dependent sulfonamide-resistant Escherichia coli in the mammalian gut

The widespread sulfonamide resistance genes sul1, sul2, and sul3 in food and gut bacteria have attracted considerable attention. In this study, we assessed the in vivo fitness of sul gene-dependent sulfonamide-resistant Escherichia coli, using a murine model. High fitness costs were incurred for sul1 and sul3 gene-dependent E. coli strains in vivo. A fitness advantage was found in three of the eight mice after intragastric administration of sul2 gene-dependent E. coli strains. We isolated three compensatory mutant strains (CMSs) independently from three mice that outcompeted the parent strain P2 in vivo. Whole-genome sequencing revealed seven identical single nucleotide polymorphism (SNP) mutations in the three CMSs compared with strain P2, an additional SNP mutation in strain S2-2, and two additional SNP mutations in strain S2-3. Furthermore, tandem mass tag-based quantitative proteomic analysis revealed abundant differentially expressed proteins (DEPs) in the CMSs compared with P2. Of these, seven key fitness-related DEPs distributed in two-component systems, galactose and tryptophan metabolism pathways, were verified using parallel reaction monitoring analysis. The DEPs in the CMSs influenced bacterial motility, environmental stress tolerance, colonization ability, carbohydrate utilization, cell morphology maintenance, and chemotaxis to restore fitness costs and adapt to the mammalian gut environment.IMPORTANCESulfonamides are traditional synthetic antimicrobial agents used in clinical and veterinary medical settings. Their long-term excessive overuse has resulted in widespread microbial resistance, limiting their application for medical interventions. Resistance to sulfonamides is primarily conferred by the alternative genes sul1, sul2, and sul3 encoding dihydropteroate synthase in bacteria. Studying the potential fitness cost of these sul genes is crucial for understanding the evolution and transmission of sulfonamide-resistant bacteria. In vitro studies have been conducted on the fitness cost of sul genes in bacteria. In this study, we provide critical insights into bacterial adaptation and transmission using an in vivo approach.

Response characteristics and functional predictions of soil microorganisms to heavy metals, antibiotics, and their resistance genes originating from different animal farms amended with Herbaspirillum huttiense

Current understanding is limited regarding technologies that use biochar and microorganisms to simultaneously treat soils contaminated with both veterinary antibiotics (VAs) and heavy metals (HMs) from different animal farms. The contributions of the keystone taxa and their similarities from different animal farms under VA and HM stresses before and after soil remediation should be further investigated as well. An innovative treatment of Herbaspirillum huttiense (HHS1) inoculated waste fungus chaff-based (WFCB) biochar was designed for immobilization of copper (Cu) and zinc (Zn), and the removal of oxytetracycline (OTC), enrofloxacin (ENR), and a subsequent reduction in their resistance genes in soils from pig, cow, and chicken farms. Roles of indigenous microorganisms which can treat soils contaminated with VAs and HMs were summarized. Results showed that available Cu and Zn were reduced by 19.5% and 28.1%, respectively, while 49.8% of OTC and 85.1% of ENR were removed by WFCB-HHS1. The decrease in ENR improved overall microbial community diversity, and the increases in genera HHS1, Pedobacter, Flavobacterium and Aequorivita, along with the decreases of genera Bacillus, Methylobacter, and Fermentimonas were indirectly favorable to treat HMs and VAs in soils from different animal farms. Bacterial communities in different animal farm soils were predominantly influenced by stochastic processes. The regulations of functional genes associated with metabolism and environmental information processing, which contribute to HM and VA defense, were altered when using WFCB-HHS1. Furthermore, the spread of their antibiotic resistance genes was restricted.

Identification of sulfamethazine degraders in swine farm-impacted river and farmland: A comparative study of aerobic and anaerobic environments

Sulfonamides (SAs) are extensively used antibiotics in the prevention and treatment of animal diseases, leading to significant SAs pollution in surrounding environments. Microbial degradation has been proposed as a crucial mechanism for removing SAs, but the taxonomic identification of microbial functional guilds responsible for SAs degradation in nature remain largely unexplored. Here, we employed 13C-sulfamethazine (SMZ)-based DNA-stable isotope probing (SIP) and metagenomic sequencing to investigate SMZ degraders in three distinct swine farm wastewater-receiving environments within an agricultural ecosystem. These environments include the aerobic riparian wetland soil, agricultural soil, and anaerobic river sediment. SMZ mineralization activities exhibited significant variation, with the highest rate observed in aerobic riparian wetland soil. SMZ had a substantial impact on the microbial community compositions across all samples. DNA-SIP analysis demonstrated that Thiobacillus, Auicella, Sphingomonas, and Rhodobacter were dominant active SMZ degraders in the wetland soil, whereas Ellin6067, Ilumatobacter, Dongia, and Steroidobacter predominated in the agricultural soil. The genus MND1 and family Vicinamibacteraceae were identified as SMZ degrader in both soils. In contrast, anaerobic SMZ degradation in the river sediment was mainly performed by genera Microvirga, Flavobacterium, Dechlorobacter, Atopostipes, and families Nocardioidaceae, Micrococcaceae, Anaerolineaceae. Metagenomic analysis of 13C-DNA identified key SAs degradation genes (sadA and sadC), and various of dioxygenases, and aromatic hydrocarbon degradation-related functional genes, indicating their involvement in degradation of SMZ and its intermediate products. These findings highlight the variations of indigenous SAs oxidizers in complex natural habitats and emphasize the consideration of applying these naturally active degraders in future antibiotic bioremediation.

Removal of selected sulfonamides and sulfonamide resistance genes from wastewater in full-scale constructed wetlands

Sulfonamides are high-consumption antibiotics that reach the aquatic environment. The threat related to their presence in wastewater and the environment is not only associated with their antibacterial properties, but also with risk of the spread of drug resistance in bacteria. Therefore, the aim of this work was to evaluate the occurrence of eight commonly used sulfonamides, sulfonamide resistance genes (sul1-3) and integrase genes intI1-3 in five full-scale constructed wetlands (CWs) differing in design (including hybrid systems) and in the source of wastewater (agricultural drainage, domestic sewage/surface runoff, and animal runs runoff in a zoo). The CWs were located in low-urbanized areas in Poland and in Czechia. No sulfonamides were detected in the CW treating agricultural tile drainage water. In the other four systems, four sulfonamide compounds were detected. Sulfamethoxazole exhibited the highest concentration in those four CWs and its highest was 12,603.23 ± 1000.66 ng/L in a CW treating a mixture of domestic sewage and surface runoff. Despite the high removal efficiencies of sulfamethoxazole in the tested CWs (86 %-99 %), it was still detected in the treated wastewater. The sul1 genes occurred in all samples of raw and treated wastewater and their abundance did not change significantly after the treatment process and it was, predominantly, at the level 105 gene copies numbers/mL. Noteworthy, sul2 genes were only found in the influents, and sul3 were not detected. The sulfonamides can be removed in CWs, but their elimination is not complete. However, hybrid CWs treating sewage were superior in decreasing the relative abundance of genes and the concentration of SMX. CWs may play a role in the dissemination of sulfonamide resistance genes of the sul1 type and other determinants of drug resistance, such as the intI1 gene, in the environment, however, the magnitude of this phenomenon is a matter of further research.

Occurrence and influencing factors of antibiotics and antibiotic resistance genes in sediments of the largest multi-habitat lakes in Northern China

Baiyangdian Lake is a typical and largest multi-habitat lake in the North plain of China. To understand the generation and transmission of antibiotics resistance genes (ARGs) in multi-habitat lakes, the contents of nutrients (TC, TOC, TN, TP and TS), heavy metals (Zn, Cr, Ni, Cu, Pb, As, Cd and Hg), 22 antibiotics, 16S-rRNA(16S), Class I integron (intI1) and 20 ARGs were determined. Samples were taken from the Fuhe river, river estuaries, reed marshes, living area, fish ponds and open water of Baiyangdian Lake. The results showed that quinolones were the main pollutants in six habitats, and the content range was ND-104.94 ng/g. Thereinto, aac (6') -IB, blaTEM-1, ermF, qnrA, qnrD, tetG, sul1, sul2 and tetM were detected in all the analyzed samples. The absolute abundance of sul1 was the highest (5.25 × 10⁵ copies/g-6.21 × 10⁷ copies/g) in most of the samples. In these different habitats, the abundance of antibiotics and ARGs in river estuary was the highest, and that in reed marshes was the lowest. There was a significant positive correlation between the abundance of heavy metals (Cu, Pb, Zn, Ni, Cd, Hg) and the absolute abundance of 11 ARGs (P < 0.01). Redundancy analysis showed that Cu, Zn, intI1, TP and macrolides were the important factors affecting the distribution of ARGs. Our finding provides a more likely driving and influencing factor for the transmission of ARGs in lakes with complex and diverse habitats.

Effects of functional modules and bacterial clusters response on transmission performance of antibiotic resistance genes under antibiotic stress during anaerobic digestion of livestock wastewater

The formation and transmission of antibiotic resistance genes (ARGs) have attracted increasing attention. It is unclear whether the internal mechanisms by which antibiotics affect horizontal gene transfer (HGT) of ARGs during anaerobic digestion (AD) were influenced by dose and type. We investigated the effects of two major antibiotics (oxytetracycline, OTC, and sulfamethoxazole, SMX) on ARGs during AD according to antibiotic concentration in livestock wastewater influent. The low-dose antibiotic (0.5 mg/L) increased ROS and SOS responses, promoting the formation of ARGs. Meanwhile, low-dose antibiotics could also promote the spread of ARGs by promoting pili, communication responses, and the type IV secretion system (T4SS). However, different types and doses of antibiotics would lead to changes in the above functional modules and then affect the enrichment of ARGs. With the increasing dose of SMX, the advantages of pili and communication responses would gradually change. In the OTC system, low-dose has the strongest promoting ability in both pili and communication responses. Similarly, an increase in the dose of SMX would change T4SS from facilitation to inhibition, while OTC completely inhibits T4SS. Microbial and network analysis also revealed that low-dose antibiotics were more favorable for the growth of host bacteria.

Biotic Interactions in Soil are Underestimated Drivers of Microbial Carbon Use Efficiency

Microbial carbon use efficiency (CUE)-the balance between microbial growth and respiration-strongly impacts microbial mediated soil carbon storage and is sensitive to many well-studied abiotic environmental factors. However, surprisingly, little work has examined how biotic interactions in soil may impact CUE. Here, we review the theoretical and empirical lines of evidence exploring how biotic interactions affect CUE through the lens of life history strategies. Fundamentally, the CUE of a microbial population is constrained by population density and carrying capacity, which, when reached, causes species to grow more quickly and less efficiently. When microbes engage in interspecific competition, they accelerate growth rates to acquire limited resources and release secondary chemicals toxic to competitors. Such processes are not anabolic and thus constrain CUE. In turn, antagonists may activate one of a number of stress responses that also do not involve biomass production, potentially further reducing CUE. In contrast, facilitation can increase CUE by expanding species realized niches, mitigating environmental stress and reducing production costs of extracellular enzymes. Microbial interactions at higher trophic levels also influence CUE. For instance, predation on microbes can positively or negatively impact CUE by changing microbial density and the outcomes of interspecific competition. Finally, we discuss how plants select for more or less efficient microbes under different contexts. In short, this review demonstrates the potential for biotic interactions to be a strong regulator of microbial CUE and additionally provides a blueprint for future research to address key knowledge gaps of ecological and applied importance for carbon sequestration.

Distribution Patterns of Antibiotic Resistance Genes and Their Bacterial Hosts in a Manure Lagoon of a Large-Scale Swine Finishing Facility

The spread of antibiotic resistance genes (ARGs) that are present in livestock manures, which are discharged into the environment, is a severe threat to human and animal health. Here, we used 16S rRNA gene profiling and metagenomic analysis to characterize microbial community composition and antibiotic resistance in a manure storage lagoon from a large-scale swine finishing facility. Manure samples were collected at intervals of two years. Both the prokaryotic community and the resistome were dominated by the Firmicutes, Proteobacteria and Bacteroidota. Metagenomic analysis of two samples revealed 726 and 641 ARGs classified into 59 and 46 AMR gene families. Besides multidrug efflux pumps, the predominating ARGs potentially encoded resistance to tetracyclines, macrolide-lincosamide-streptogramin, aminoglycosides, peptide antibiotics, rifamycin, chloramphenicol, and beta-lactams. Genes from all predominant AMR gene families were found in both samples indicating overall long-term stability of the resistome. Antibiotic efflux pumps were the primary type of ARGs in the Proteobacteria, while antibiotic target alteration or protection was the main mechanism of resistance in the Firmicutes, Actinobacteriota and Bacteroidota. Metagenome-assembled genomes (MAG) of four multidrug-resistant strains were assembled. The first MAG, assigned to Escherichia flexneri, contained 46 ARGs, including multidrug efflux pumps, modified porins, beta-lactamases, and genes conferring resistance to peptide antibiotics. The second MAG, assigned to the family Alcaligenaceae, contained 18 ARGs encoding resistance to macrolide-lincosamide-streptogramin, tetracyclines, aminoglycosides and diaminopyrimidins. Two other MAGs representing the genera Atopostipes and Prevotella, contained four and seven ARGs, respectively. All these MAGs represented minor community members and accounted for less than 0.3% of the whole metagenome. Overall, a few lineages originated from the gut but relatively rare in the manure storage lagoon, are the main source of ARGs and some of them carry multiple resistance determinants.

Sub-lethal concentration of sulfamethoxazole affects the growth performance of milkfish (Chanos chanos), the microbial composition of antibiotic-resistant bacteria and the prevalence of sulfonamide-resistance genes in mariculture

To investigate the impacts of sub-lethal concentrations of antibiotic agents in mariculture, culturable approach and DNA based detection were employed to isolate and analyse resistant bacteria and resistant genes in this study. Milkfish (Chanos chanos), the target rearing animal was exposed to sulfamethoxazole (SMX; 2 mg/L) for 8 weeks and resulted in reduced survival rate and weight gain to 61.9 % and 28.4 %, respectively compared to control milkfish (p < 0.001). The composition of SMX-resistant bacteria isolated from the culture water and the gastrointestinal tracts of milkfish underwent changes in response to SMX treatment with a reduced diversity. The prevalence of SMX resistant genes sul in bacterial isolates was elevated from 2.8 % of control to 100 % of SMX-administrated water. Exposure to SMX at a sub-lethal dosage enhanced the prevalence of resistance genes sul1 and sul2 in resistant bacteria, thus implying high frequency of resistance dissemination in the marine environment and surrounding ecosystems.

Supercarriers of antibiotic resistome in a world's large river

BACKGROUND

Antibiotic resistome has been found to strongly interact with the core microbiota in the human gut, yet little is known about how antibiotic resistance genes (ARGs) correlate with certain microbes in large rivers that are regarded as "terrestrial gut."

RESULTS

By creating the integral pattern for ARGs and antibiotic-resistant microbes in water and sediment along a 4300-km continuum of the Yangtze River, we found that human pathogen bacteria (HPB) share 13.4% and 5.9% of the ARG hosts in water and sediment but contribute 64% and 46% to the total number of planktonic and sedimentary ARGs, respectively. Moreover, the planktonic HPB harbored 79 ARG combinations that are dominated by "natural" supercarriers (e.g., Rheinheimera texasensis and Noviherbaspirillum sp. Root189) in river basins.

CONCLUSIONS

We confirmed that terrestrial HPB are the major ARG hosts in the river, rather than conventional supercarriers (e.g., Enterococcus spp. and other fecal indicator bacteria) that prevail in the human gut. The discovery of HPB as natural supercarriers in a world's large river not only interprets the inconsistency between the spatial dissimilarities in ARGs and their hosts, but also highlights the top priority of controlling terrestrial HPB in the future ARG-related risk management of riverine ecosystems globally. Video Abstract.

Joint effects of bacterium and biochar in remediation of antibiotic-heavy metal contaminated soil and responses of resistance gene and microbial community

Soils containing both veterinary antibiotics (VAs) and heavy metals necessitate effective remediation approaches, and microbial and molecular levels of the results should be further examined. Here, a novel material combining waste fungus chaff-based biochar (WFCB) and Herbaspirillum huttiense (HHS1) was established to immobilize copper (Cu) and zinc (Zn) and degrade oxytetracycline (OTC) and enrofloxacin (ENR). Results showed that the combined material exhibited high immobilization of Cu (85.5%) and Zn (64.4%) and great removals of OTC (41.9%) and ENR (40.7%). Resistance genes including tet(PB), tetH, tetR, tetS, tetT, tetM, aacA/aphD, aacC, aadA9, and czcA were reduced. Abundances of potential hosts of antibiotic resistance genes (ARGs) including phylum Proteobacteria and genera Brevundimonas and Rhodanobacter were altered. Total phosphorus and pH were the factors driving the VA degrading microorganisms and potential hosts of ARGs. The combination of WFCB and HHS1 can serve as an important bioresource for immobilizing heavy metals and removing VAs in the contaminated soil.

Prevalence and characterization of antibiotic resistant bacteria in raw community sewage from diverse urban communities

Community sewage is a useful medium for antimicrobial resistance (AMR) surveillance of populations residing in urban dwellings as it provides the resolution of tracking sources of AMR from different waste streams within a community. Antibiotic resistance profiles of 4 opportunistic pathogens were compared from 3 sewage sources: raw community sewage from 2 housing estates, a foreign workers dormitory and a pet centre. Sewage was collected from receiving manholes and a culture-based method was used to quantify opportunistic pathogens Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Enterococcus spp. K. pneumoniae was the most prevalent opportunistic pathogen detected while P. aeruginosa was the least abundant across the sample. A total of 892 bacterial isolates were selected for antibiotic susceptibility testing using the VITEK^Ⓡ 2 Compact System (bioMérieux, Singapore). E. coli isolated from the pet centre exhibited higher resistance towards all 16 antibiotics tested, and P. aeruginosa showed at least 75% resistance towards the classes of antibiotics, except for carbapenems, aminoglycosides and quinolones (below 30%). For K. pneumoniae, resistance towards the classes of antibiotics was below 10%, except for penicillin and nitrofurans. Enterococcus spp. had high resistance towards gentamicin and clindamycin (both almost 100%), while resistance towards vancomycin was below 18% for all 4 locations. Multidrug resistant (MDR) P. aeruginosa and Enterococcus spp. showed the highest prevalence with percentages above 96%. MDR E. coli and MDR K. pneumoniae was lower, ranging between 9% to 54% and 8% to 23% respectively. Highest prevalence of MDR E. coli and K. pneumoniae were detected in the pet centre, with a percentage of 54% and 23% respectively. These results show that wastewater based surveillance is not only a useful method of understanding emerging trends of AMR across the community but also provides the resolution of capturing AMR data from key sewage sources based on population demographics. This information could provide a basis for devising better control measures to mitigate the spread of MDR.

Class 1 In-Tn5393c array contributed to antibiotic resistance of non-pathogenic Pseudoxanthomonas mexicana isolated from a wastewater bioreactor treating streptomycin

The emergence of antibiotic resistance in retort to environmental pollutants during wastewater treatment still remains elusive. Here, we first to investigate the emergence of antibiotic resistance in an environmental non-pathogenic bacterium, Pseudoxanthomonas mexicana isolated from a lab-scale bioreactor treating wastewater containing streptomycin. The molecular mechanism of antibiotic resistance development was evaluated in its genomic, transcriptional, and proteomic levels. The streptomycin resistant (SR) strain showed strong resistance to streptomycin (MIC > 600 μg/mL) as well to sulfamethoxazole, ampicillin, and kanamycin (≥250 μg/mL). A 13.4 kb class-1-integron array consisting of a new arrangement of gene cassette (IS6100-sul1-aadA2-catB3-aacA1-2-aadB-int1-IS256-int) linked with Tn5393c transposon was identified in the SR strain, which has only been reported in clinical pathogens so far. iTRAQ-LC-MS/MS proteomics revealed 22 up-regulated proteins in the SR strain growing under 100 mg L^-1 streptomycin, involving antibiotic resistance, toxin production, stress response, and ribosomal protein synthesis. At the mRNA level, elevated expressions of ARGs (strA, strB, and aadB) and 30S-ribosomal protein genes (rpsA and rpsU) were observed in the SR strain. The results highlighted the genomic plasticity and multifaceted regulatory mechanism employed by P. mexicana in adaptation to high-level streptomycin during biological wastewater treatment.

Antimicrobial Resistance and Transconjugants Characteristics of sul3 Positive Escherichia coli Isolated from Animals in Nanning, Guangxi Province

Sulfonamides are the second most popular antibiotic in many countries, which leads to the widespread emergence of sulfonamides resistance. sul3 is a more recent version of the gene associated with sulfonamide resistance, whose research is relatively little. In order to comprehend the prevalence of sul3 positive E. coli from animals in Nanning, a total of 146 strains of E. coli were identified from some farms and pet hospitals from 2015 to 2017. The drug resistance and prevalence of sul3 E. coli were analyzed by polymerase chain reaction (PCR) identification, multi-site sequence typing (MLST), drug sensitivity test, and drug resistance gene detection, and then the plasmid containing sul3 was conjugated with the recipient strain (C600). The effect of sul3 plasmid on the recipient was analyzed by stability, drug resistance, and competitive test. In this study, forty-six sul3 positive E. coli strains were separated. A total of 12 ST types were observed, and 1 of those was a previously unknown type. The ST350 is the most numerous type. All isolates were multidrug-resistant E. coli, with high resistant rates to penicillin, ceftriaxone sodium, streptomycin, tetracycline, ciprofloxacin, gatifloxacin, and chloramphenicol (100%, 73.9%, 82.6%, 100%, 80.4%, 71.7%, and 97.8%, respectively). They had at least three antibiotic resistance genes (ARGs) in addition to sul3. The plasmids transferred from three sul3-positive isolates to C600, most of which brought seven antimicrobial resistance (AMR) and increased ARGs to C600. The transferred sul3 gene and the plasmid carrying sul3 could be stably inherited in the recipient bacteria for at least 20 days. These plasmids had no effect on the growth of the recipient bacteria but greatly reduced the competitiveness of the strain at least 60 times in vitro. In Nanning, these sul3-positive E. coli had such strong AMR, and the plasmid carrying sul3 had the ability to transfer multiple resistance genes that long-term monitoring was necessary. Since the transferred plasmid would greatly reduce the competitiveness of the strain in vitro, we could consider limiting the spread of drug-resistant isolates in this respect.

Fate of Antibiotic Resistance Genes and Changes in Bacterial Community With Increasing Breeding Scale of Layer Manure

The use of antimicrobials in intensive poultry production is becoming increasingly common because of its high throughput of meat and egg products. However, the profile of antibiotic resistance genes (ARGs) and the underlying mechanisms in different breeding scale farms were not fully explored. The study examined the profiles of ARGs in layer manure from three free-range and 12 intensive layer farms with different scales (N500, N5000, N10000, and N20000). A quantitative PCR (qPCR) array was used to quantify ARGs, and microbial community structure was analyzed by 16S rRNA gene sequencing. A total of 48 ARGs, belonging to seven major types, were identified in the layer manure samples, with sul2, tetM-01, and ermB being the predominant ones. The abundance, diversity, and mobility potential of ARGs in layer manure changed significantly with the increasing of the breeding scale. The abundances of total ARGs had significantly positive correlations with mobile genetic elements (MGEs), suggesting the mobility potential of ARGs in layer manure samples. Bacterial abundance did not show significant differences among the five group manure samples. However, bacterial diversity showed an increasing trend along the breeding scale. Pathogenic Bacteroidetes increased in the largest-scale layer manure samples and showed significant positive correlations with most ARGs. Network analysis revealed significant co-occurrence patterns between ARGs and microbial taxa, indicating ARGs had a wide range of bacterial hosts. Proteobacteria and Firmicutes were potential hosts for tetracycline and macrolide-lincosamide-streptogramin B (MLSB) resistant genes. Our results indicated that the expansion of the breeding scale of a farm promotes the abundance, diversity, and mobility potential of ARGs in layer manure.

Mechanism for biodegradation of sulfamethazine by Bacillus cereus H38

Degradation of sulfonamides (SAs) by microorganisms has become a focus of current research. Sulfamethazine (SMZ) is a type of SA widely used in the livestock and poultry industry. However, understanding the intermediate products, degradation pathways and mechanism of SMZ biodegradation is limited at present. In this study, a SMZ degrading bacterium Bacillus cereus H38, which can use SMZ as its only carbon source, was isolated from farmland soil. The bacterium was gram-positive with rod-shaped cells. The effects of initial SMZ concentration, pH, temperature and amount of inoculation on the biodegradation of SMZ were investigated by a single factor experiment. The results showed that the maximum degradation rate of SMZ was achieved in the environmental conditions at an initial SMZ concentration of 5 mg/L, pH of 7.0, temperature of 25 °C and inoculation amount of 5%. Under these optimum degradation conditions, strain H38 can completely degrade SMZ within 3 days. The effects of intracellular enzymes, extracellular enzymes and periplasmic enzymes on the SMZ degradation process were compared. It was found that intracellular enzymes contributed the most to the biodegradation of SMZ, and the degradation rate approached 70%. Three possible intermediates were identified by LC-MS/MS, and two degradation pathways were proposed. Whole genome sequencing results showed that the genome size of strain H38 was 5,477,631 bp, including 5599 coding sequences (CDSs), and the GC content was 35.21%. In addition, functional annotation of CDSs was performed to analyze the metabolic pathways of nitrogen and sulfur in strain H38 combining genomics and bioinformatics. This study proposes new insights into the mechanism for biodegradation of SAs and will inform future research.

Systematic review and meta-analysis of environmental Vibrio species - antibiotic resistance

Adequate comprehension of the genomics of microbial resistance to an antimicrobial agent will advance knowledge on the management of associated pathologies and public health safety. However, continued emergences and reemergence of pathogens, including Vibrio species, hallmarks a potential knowledge gap. A clear understanding of the process and forecast of the next trend should be in place to nip in the bud, microbial acquisition of resistance to antibiotics. Therefore, this two-decade (1 January 2000 to 31 December 2019) systematic review and meta-analytical study articulated the prevalence and incidence of antibiotics resistance genes in Vibrio species isolated from environmental samples. Articles from the Web of Science and PubMed electronic databases was engaged. Heterogeneity of the data and bias were analyzed with random effect model meta-analysis and funnel plot. A total of 1920 Vibrio sp. were reported by the ten selected articles included in this study; out of which 32.39% of identified isolates displayed antimicrobial resistance and associated genes. The distribution of antibiotics resistance genes in Vibrio sp., reported within six countries was 21% tetracycline (tet), and 20% sulphonamide (sul) and β-lactamase (bla) respectively. The quinolone, tetracycline and sulfonamide resistance genes showed 32.97% (95% CI 0.18–0.53) prevalence while chloramphenicol, macrolides and aminoglycoside resistance genes are expressed in percentages as 28.67% (95% CI 0.15–0.47) and β-lactamase resistance genes 27.93% (95% CI 0.11–0.56) respectively. The Vibrio antibiotics resistance genes (V-ARG) distribution depicts no regular trend or pattern from the analyzed data. Consequently, more studies would be required to articulate the structure of cohesion in the distribution of the resistance determinants in microbes.

Fitness cost and compensation mechanism of sulfonamide resistance genes (sul1, sul2, and sul3) in Escherichia coli

The fitness cost of antibiotic resistance is a crucial factor to determine the evolutionary and transmission success of resistant bacteria. Exploring the fitness cost and compensation mechanism of antibiotic resistance genes (ARGs) in bacteria may effectively reduce the transmission of drug-resistant genes in the environment. Engineered bacteria with the same genetic background that carry sulfonamide resistance gene were generated to explore the fitness cost of sulfonamide resistance gene in Escherichia coli. There were significant differences in the protein expression of the two-component system pathway (fliZ, fliA, fliC and lrhA), folate biosynthesis pathway (sul1, sul2 and sul3), ABC transporter system (ugpC, rbsA and gsiA), and outer membrane pore protein OmpD through the comparative analysis of differential proteins compared to sensitive bacteria. Thus, we could speculate the possible fitness compensation mechanism. Finally, quantitative Real-time PCR (qRT-PCR) was used to verify the functions of some differential proteins at the transcriptional level. The fitness cost and compensatory evolution of antibiotic resistance are an essential part of bacterial evolution.

Antibiotic resistance gene dissipation in soil microcosms amended with antibiotics and swine manure

The use of antibiotics in animal agriculture has exacerbated the presence of both antibiotic resistance genes (ARGs) and residual antibiotics excreted in animal manure. Field application of this manure is a common practice because its nutrient rich material can benefit crop growth. However, this practice can also introduce antibiotics and ARGs into nonagricultural settings. The integration of prairie buffer strips within and at the edge of crop fields is a potential management solution to reduce concentrations of ARGs commonly transported via water runoff and infiltration. An incubation experiment was conducted to investigate the fate of ARGs in directly manured crop field soils and the surrounding affected prairie strip soils. Row crop and prairie strip soils sampled from three sites received either an antibiotic spike and swine manure addition or a control water addition. The concentrations of select ARGs were then monitored over a 72-d period. Although soil vegetation and site location were not observed to influence ARG dissipation, the select genes did display different half-lives from one another. For example, tetM demonstrated the fastest dissipation of the genes quantified (average half-life, 5.18 d). Conversely, sul1 did not conform to the first-order linear regression kinetics used to describe the other investigated genes and was highly abundant in control prairie strip soils. The quantified half-lives of these select ARGs are comparable to previous studies and can inform monitoring and mitigative efforts aimed at reducing the spread of ARGs in the environment.

Pharmaceutical compound removal efficiency by a small constructed wetland located in south Brazil

The fate of pharmaceuticals during the treatment of effluents is of major concern since they are not completely degraded and because of their persistence and mobility in environment. Indeed, even at low concentrations, they represent a risk to aquatic life and human health. In this work, fourteen pharmaceuticals were monitored in a constructed wetland wastewater treatment plants (WWTP) assessed in both influent and effluent samples. The basic water quality parameters were evaluated, and the removal efficiency of pharmaceutical, potential for bioaccumulation, and the impact of WWTP were assessed using Polar Organic Chemical Integrative Sampler (POCIS) and biofilms. The pharmaceutical compounds were quantified by High Performance Liquid chromatography coupled to mass spectrometry. The sampling campaign was carried out during winter (July/2018) and summer (January/2019). The WWTP performed well regarding the removal of TSS, COD, and BOD₅ and succeeded to eliminate a significant part of the organic and inorganic pollution present in domestic wastewater but has low efficiency regarding the removal of pharmaceutical compounds. Biofilms were shown to interact with pharmaceuticals and were reported to play a role in their capture from water. The antibiotics were reported to display a high risk for aquatic organisms.

Increased Antimicrobial and Multidrug Resistance Downstream of Wastewater Treatment Plants in an Urban Watershed

Development and spread of antimicrobial resistance (AMR) and multidrug resistance (MDR) through propagation of antibiotic resistance genes (ARG) in various environments is a global emerging public health concern. The role of wastewater treatment plants (WWTPs) as hot spots for the dissemination of AMR and MDR has been widely pointed out by the scientific community. In this study, we collected surface water samples from sites upstream and downstream of two WWTP discharge points in an urban watershed in the Bryan-College Station (BCS), Texas area, over a period of nine months. E. coli isolates were tested for resistance to ampicillin, tetracycline, sulfamethoxazole, ciprofloxacin, cephalothin, cefoperazone, gentamycin, and imipenem using the Kirby-Bauer disc diffusion method. Antimicrobial resistant heterotrophic bacteria were cultured on R2A media amended with ampicillin, ciprofloxacin, tetracycline, and sulfamethoxazole for analyzing heterotrophic bacteria capable of growth on antibiotic-containing media. In addition, quantitative real-time polymerase chain reaction (qPCR) method was used to measure eight ARG – tetA, tetW, aacA, ampC, mecA, ermA, blaTEM, and intI1 in the surface water collected at each time point. Significant associations (p < 0.05) were observed between the locations of sampling sites relative to WWTP discharge points and the rate of E. coli isolate resistance to tetracycline, ampicillin, cefoperazone, ciprofloxacin, and sulfamethoxazole together with an increased rate of isolate MDR. The abundance of antibiotic-resistant heterotrophs was significantly greater (p < 0.05) downstream of WWTPs compared to upstream locations for all tested antibiotics. Consistent with the results from the culture-based methods, the concentrations of all ARG were substantially higher in the downstream sites compared to the upstream sites, particularly in the site immediately downstream of the WWTP effluent discharges (except mecA). In addition, the Class I integron (intI1) genes were detected in high amounts at all sites and all sampling points, and were about ∼20 times higher in the downstream sites (2.5 × 10⁷ copies/100 mL surface water) compared to the upstream sites (1.2 × 10⁶ copies/100 mL surface water). Results suggest that the treated WWTP effluent discharges into surface waters can potentially contribute to the occurrence and prevalence of AMR in urban watersheds. In addition to detecting increased ARG in the downstream sites by qPCR, findings from this study also report an increase in viable AMR (HPC) and MDR (E. coli) in these sites. This data will benefit establishment of improved environmental regulations and practices to help manage AMR/MDR and ARG discharges into the environment, and to develop mitigation strategies and effective treatment of wastewater.

Adsorption of sulfonamides on biochars derived from waste residues and its mechanism

Waste residues have been prepared as biochar (BC) adsorbents to remove sulfonamides (SAs) at low cost, but the mechanisms of the differences in the SA adsorption performance of different BCs are not clear. Thus, the adsorption characteristics of two SAs (sulfadiazine and sulfathiazole) on three BCs derived from waste residues (sewage sludge (SB), pig manure (PB), and rice straw (RB)) were investigated. The results showed that the adsorption mechanism was chemisorption and RB was the preferred BC under the different tested conditions (pH, Ca²⁺, and humic acid), followed by PB and SB. To interpret the phenomena, FTIR, XRD, and XPS analyses were performed and results indicated that SB had the lowest C content, and there was a very significant difference in the concentrations of the two O functional groups (C˭O and C‒O) for PB and RB (P < 0.01). Density functional theory calculations revealed that the mechanisms of SA adsorption onto BCs were mainly through π-π electron donor acceptor interactions and H bonds. There was no significant difference in the π interactions between the SAs-BC containing C‒O (BC(OH)) and the SAs-BC containing C˭O (BC(C˭O)), whereas the H bond strength of SAs-BC(OH) was much stronger than that of SAs-BC(C˭O).

Antibiotic resistance contamination in four Italian municipal solid waste landfills sites spanning 34 years

Municipal solid waste landfill is now recognized as a significant reservoir of antibiotics and antibiotic resistance genes (ARGs). This study investigates the contamination of antibiotics resistance, in 10 leachate samples collected from four MSW landfills in north Italy spanning 34 years, including ARGs as well as mobile genetic element (MGEs). Antibiotics (0-434740 ng/L) and ARGs (5.56-6.85 × 10⁵copies/μL leachate) were found in leachate. Abundances of the measured ARGs were found to be clustered into two groups with different changing tendencies with landfilling age in different landfills. Even though some antibiotics were banned or limited in Italy, they were found to still occur in landfills and drive the long-term contamination of ARGs indirectly, indicating the persistence of antibiotic resistance. What's more, the complexity of antibiotic resistance in leachate was found to synthetically relate to antibiotics, metals, microbes and MGEs presenting that Mn, SMX and EFC influence positively (p < 0.01) the contamination of tetW, tetQ, tetM, tetA, ermB, and cat, contributing importantly in new leachate. This study discusses the AR pollution of leachate in Italy where antibiotics are used the most in Europe, less reported in literatures. Our results suggest that a full-scale view for landfill antibiotics resistance should be considered with history of landfills, use of antibiotics and different phase in landfills, with both "relative static" and "dynamic tracking" perspective to focus on the principal antibiotic-resistance pollutants for leachate treatment, and raise the attention for landfill post-closure care and landfill mining.

Cadmium enhances conjugative plasmid transfer to a fresh water microbial community

Co-selection of antibiotic resistance genes (ARGs) by heavy metals might facilitate the spread of ARGs in the environments. Cadmium contamination is ubiquitous, while, it remains unknown the extent to which cadmium (Cd²⁺) impact plasmid-mediated transfer of ARGs in aquatic bacterial communities. In the present study, we found that Cd²⁺ amendment at sub-inhibitory concentration significantly increased conjugation frequency of RP4 plasmid from Pseudomonas putida KT2442 to a fresh water microbial community by liquid mating method. Cd²⁺ treatment (1-100 mg/L) significantly increased the cell membrane permeability and antioxidant activities of conjugation mixtures. Amendments of 10 and 100 mg/L Cd²⁺ significantly enhanced the mRNA expression levels of mating pair formation gene (trbBp) and the DNA transfer and replication gene (trfAp) due to the repression of regulatory genes (korA, korB and trbA). Phylogenetic analysis of transconjugants indicated that Proteobacteria was the dominant recipients and high concentration of Cd²⁺ treatment resulted in expanded recipient taxa. This study suggested that sub-inhibitory Cd²⁺ contamination would facilitate plasmid conjugation and contributed to the maintenance and spread of plasmid associated ARGs, and highlighted the urgent need for effective remediation of Cd²⁺ in aquatic environments.

Nanotechnology as a viable alternative for the removal of antimicrobial resistance determinants from discharged municipal effluents and associated watersheds: A review

Effective and efficient utilization of antimicrobial drugs has been one of the important cornerstone of modern medicine. However, since antibiotics were first discovered by Alexander Fleming about a century ago, the time clock of antimicrobial resistance (AMR) started ticking somewhat leading to a global fear of a possible "post-antimicrobial era". Antibiotic resistance (AR) remains a serious challenge causing global outcry in both the clinical setting and the environment. The huge influence of municipal wastewater effluent discharges on the aquatic environment has made the niche a hotspot of research interest in the study of emergence and spread of AMR microbes and their resistance determinants/genes. The current review adopted a holistic approach in studying the proliferation of antibiotic resistance determinants (ARDs) as well as their impacts and fate in municipal wastewater effluents and the receiving aquatic environments. The various strategies deployed hitherto for the removal of resistance determinants in municipal effluents were carefully reviewed, while the potential for the use of nanotechnology as a viable alternative is explicitly explored. Also, highlighted in this review are the knowledge gaps to be filled in order to curtail the spread of AMR in aquatic environment and lastly, suggestions on the applicability of nanotechnology in eliminating AMR determinants in municipal wastewater treatment facilities are proffered.

Tetracycline and Sulfonamide Antibiotics in Soils: Presence, Fate and Environmental Risks

Veterinary antibiotics are widely used worldwide to treat and prevent infectious diseases, as well as (in countries where allowed) to promote growth and improve feeding efficiency of food-producing animals in livestock activities. Among the different antibiotic classes, tetracyclines and sulfonamides are two of the most used for veterinary proposals. Due to the fact that these compounds are poorly absorbed in the gut of animals, a significant proportion (up to ~90%) of them are excreted unchanged, thus reaching the environment mainly through the application of manures and slurries as fertilizers in agricultural fields. Once in the soil, antibiotics are subjected to a series of physicochemical and biological processes, which depend both on the antibiotic nature and soil characteristics. Adsorption/desorption to soil particles and degradation are the main processes that will affect the persistence, bioavailability, and environmental fate of these pollutants, thus determining their potential impacts and risks on human and ecological health. Taking all this into account, a literature review was conducted in order to shed light on the current knowledge about the occurrence of tetracycline and sulfonamide antibiotics in manures/slurries and agricultural soils, as well as on their fate in the environment. For that, the adsorption/desorption and the degradation (both abiotic and biotic) processes of these pollutants in soils were deeply discussed. Finally, the potential risks of deleterious effects on human and ecological health associated with the presence of these antibiotic residues were assessed. This review contributes to a deeper understanding of the lifecycle of tetracycline and sulfonamide antibiotics in the environment, thus facilitating decision-making for the application of preventive and mitigation measures to reduce its negative impacts and risks to public health.

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.

Experimental and theoretical study of kinetic and mechanism of hydroxyl radical-mediated degradation of sulfamethazine

Hydroxyl radical (^•OH)-based advanced oxidation technologies (AOTs) is an effective and clean way to remove sulfonamide antibiotics in water at ambient temperature and pressure. In this study, we systematically investigated the degradation kinetics of sulfamethazine (SMT) by ^•OH with a combination of experimental and theoretical approaches. The second-order rate constant (k) of SMT with ^•OH was experimentally determined to be 5.27 ± 0.06 × 10⁹ M^-1 s^-1 at pH 4.5. We also calculated the thermodynamic and kinetic behaviors for the reactions by density functional theory (DFT) using the B3LYP/6-31G*. The results revealed that ^•OH addition pathways at the methylene (C4) site on the pyridine ring and the ortho sites (C12 and C14) of the amino group on the benzene ring dominate the reaction, especially C14 site on the benzene ring accounted for 43.95% of SMT degradation kinetics. The theoretical k value which was calculated by conventional transition state theory is 3.96 × 10⁹ M^-1 s^-1, indicating that experimental observation (5.27 ± 0.06 × 10⁹) is correct. These results could further help AOTs design in treating sulfonamide during wastewater treatment processes.

Source tracking of antibiotic resistance genes in the environment - Challenges, progress, and prospects

Antibiotic resistance has become a global public health concern, rendering common infections untreatable. Given the widespread occurrence, increasing attention is being turned toward environmental pathways that potentially contribute to antibiotic resistance gene (ARG) dissemination outside the clinical realm. Studies during the past decade have clearly proved the increased ARG pollution trend along with gradient of anthropogenic interference, mainly through marker-ARG detection by PCR-based approaches. However, accurate source-tracking has been always confounded by various factors in previous studies, such as autochthonous ARG level, spatiotemporal variability and environmental resistome complexity, as well as inherent method limitation. The rapidly developed metagenomics profiles ARG occurrence within the sample-wide genomic context, opening a new avenue for source tracking of environmental ARG pollution. Coupling with machine-learning classification, it has been demonstrated the potential of metagenomic ARG profiles in unambiguously assigning source contribution. Through identifying indicator ARG and recovering ARG-host genomes, metagenomics-based analysis will further increase the resolution and accuracy of source tracking. In this review, challenges and progresses in source-tracking studies on environmental ARG pollution will be discussed, with specific focus on recent metagenomics-guide approaches. We propose an integrative metagenomics-based framework, in which coordinated efforts on experimental design and metagenomic analysis will assist in realizing the ultimate goal of robust source-tracking in environmental ARG pollution.

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.

Occurrence of Fluoroquinolones and Sulfonamides Resistance Genes in Wastewater and Sludge at Different Stages of Wastewater Treatment: A Preliminary Case Study

This study identified differences in the prevalence of antibiotic resistance genes (ARGs) between wastewater treatment plants (WWTPs) processing different proportions of hospital and municipal wastewater as well as various types of industrial wastewater. The influence of treated effluents discharged from WWTPs on the receiving water bodies (rivers) was examined. Genomic DNA was isolated from environmental samples (river water, wastewater and sewage sludge). The presence of genes encoding resistance to sulfonamides (sul1, sul2) and fluoroquinolones (qepA, aac(6′)-Ib-cr) was determined by standard polymerase chain reaction (PCR). The effect of the sampling season (summer – June, fall – November) was analyzed. Treated wastewater and sewage sludge were significant reservoirs of antibiotic resistance and contained all of the examined ARGs. All wastewater samples contained sul1 and aac(6′)-lb-cr genes, while the qepA and sul2 genes occurred less frequently. These observations suggest that the prevalence of ARGs is determined by the type of processed wastewater. The Warmia and Mazury WWTP was characterized by higher levels of the sul2 gene, which could be attributed to the fact that this WWTP processes agricultural sewage containing animal waste. However, hospital wastewater appears to be the main source of the sul1 gene. The results of this study indicate that WWTPs are significant sources of ARGs, contributing to the spread of antibiotic resistance in rivers receiving processed wastewater.

New parameters for the quantitative assessment of the proliferation of antibiotic resistance genes dynamic in the environment and its application: A case of sulfonamides and sulfonamide resistance genes

Antibiotic resistance genes (ARGs) have been widely detected around the world and are generally viewed as emerging pollutants with environmental persistence. The proliferation of ARGs can be easily promoted by antibiotics. However, the dynamics of ARGs in the environment are still unable to be quantified using a single parameter, which is vital to evaluating the ability of ARGs to spread by antibiotics and effectively controlling ARGs. A new parameter, termed the relative area ratio of sample to control (ΔA^R), was developed based on the quantitative features determined by ARG-time curves in soils contaminated with sulfonamides (SAs) and verified by quantitative structure-activity relationships (QSARs) models. The results showed that ΔA^R can not only be used to accurately quantify the characteristics of SAs resistance genes (Suls) over time but also be applied to reveal the relationships between the proliferation of Suls and important factors (i.e., concentrations and chemical structures). Moreover, the ΔA^R-based QSARs model indicated that bioavailability and the frequency of conjugative transfer, rather than the ability of induced mutations in bacteria, tend to be key processes of the characteristics of the proliferation of Suls. Therefore, ΔA^R is a useful parameter to perform environmental risk assessments of ARG proliferation in the environment.

Core-Shell Molecularly Imprinted Polymers on Magnetic Yeast for the Removal of Sulfamethoxazole from Water

In this work, magnetic yeast (MY) was produced through an in situ one-step method. Then, MY was used as the core and the antibiotic sulfamethoxazole (SMX) as the template to produce highly selective magnetic yeast-molecularly imprinted polymers (MY@MIPs). The physicochemical properties of MY@MIPs were assessed by Fourier-transform infrared spectroscopy (FT-IR), a vibrating sample magnetometer (VSM), X-ray diffraction (XRD), thermogravimetric analysis (TGA), specific surface area (S_BET) determination, and scanning electron microscopy (SEM). Batch adsorption experiments were carried out to compare MY@MIPs with MY and MY@NIPs (magnetic yeast-molecularly imprinted polymers without template), with MY@MIPs showing a better performance in the removal of SMX from water. Adsorption of SMX onto MY@MIPs was described by the pseudo-second-order kinetic model and the Langmuir isotherm, with maximum adsorption capacities of 77 and 24 mg g^-1 from ultrapure and wastewater, respectively. Furthermore, MY@MIPs displayed a highly selective adsorption toward SMX in the presence of other pharmaceuticals, namely diclofenac (DCF) and carbamazepine (CBZ). Finally, regeneration experiments showed that SMX adsorption decreased 21 and 34% after the first and second regeneration cycles, respectively. This work demonstrates that MY@MIPs are promising sorbent materials for the selective removal of SMX from wastewater.

Fate and driving factors of antibiotic resistance genes in an integrated swine wastewater treatment system: From wastewater to soil

Swine wastewater (SW) represents an important source of antibiotic resistance genes (ARGs) in the environment. However, few studies have assessed the occurrence and removal of ARGs in the whole wastewater treatment process followed by its farmland application. This study investigated the ARGs profiles in an integrated SW treatment system and its receiving soil, as well as their relationships with SW parameters and bacterial communities. Results revealed that sulfonamide, tetracycline and aminoglycoside resistance genes were dominant in SW. The relative abundance of total ARGs in SW was reduced by 84% after the treatments. Among the SW treatment units, anaerobic digestion, primary sedimentation and constructed wetland contributed to ARGs removal while secondary sedimentation increased the total ARGs abundance. Farmland irrigation of the treated SW resulted in enrichment of persistent ARGs in the receiving soil, which might be attributed to the propagation of potential bacterial hosts and high horizontal gene transferability. Redundancy analysis indicated that the relative abundance of total ARGs was significantly correlated with total nitrogen, total phosphorus, antibiotics and bacterial communities. The shift in bacterial community was the major driving factor for ARGs alteration during SW treatment process. Our results highlight the effect of treated SW irrigation on the antibiotic resistome in agricultural environment, and can contribute in improving SW treatment system for better antibiotic resistance control.

A critical review on antibiotics and hormones in swine wastewater: Water pollution problems and control approaches

Swine wastewater (SW) is an important source of antibiotics and hormones (A&H) in the environment due to their large-scale application in swine industry. A&H in SW can be released into the water environment through the direct discharge of SW, effluent from SW treatment plants, and runoff and leaching from farmland polluted by swine wastes. The presence of A&H in the water environment has become an increasing global concern considering their adverse effects to the aquatic organism and human. This review critically discusses: (i) the occurrence of A&H in global water environment and their potential risks to water organisms and human; (ii) the management and technical approaches for reducing the emission of A&H in SW to the water environment. The development of antibiotic alternatives and the enhanced implementation of vaccination and biosecurity are promising management approaches to cut down the consumption of antibiotics during swine production. Through the comparison of different biological treatment technologies for removing A&H in SW, membrane-based bioprocesses have relatively higher and more stable removal efficiencies. Whereas, the combined system of bioprocesses and AOPs is expected to be a promising technology for elimination and mineralization of A&H in swine wastewater. Further study on this system is therefore necessary.

Contribution of antibiotics to the fate of antibiotic resistance genes in anaerobic treatment processes of swine wastewater: A review

Antibiotic resistance genes (ARGs) in water environment have become a global health concern. Swine wastewater is widely considered to be one of the major contributors for promoting the proliferation of ARGs in water environments. This paper comprehensively reviews and discusses the occurrence and removal of ARGs in anaerobic treatment of swine wastewater, and contributions of antibiotics to the fate of ARGs. The results reveal that ARGs' removal is unstable during anaerobic processes, which negatively associated with the presence of antibiotics. The abundance of bacteria carrying ARGs increases with the addition of antibiotics and results in the spread of ARGs. The positive relationship was found between antibiotics and the abundance and transfer of ARGs in this review. However, it is necessary to understand the correlation among antibiotics, ARGs and microbial communities, and obtain more knowledge about controlling the dissemination of ARGs in the environment.

Distribution of Antibiotic Resistance Genes in Three Different Natural Water Bodies-A Lake, River and Sea

Currently, due to abuse in the use of human antibiotics and the weak regulatory control that the authorities have over sewage discharge and manure management, antibiotic resistance genes (ARGs) have become a new type of environmental pollutant. Three different natural water bodies (Poyang Lake, Haihe River and Qingdao No.1 Bathing Beach seawater) were sampled during the same periods to conduct a longitudinal comparison of distribution. The distribution and expression of 11 ARGs in 20 species were studied, and the correlations between the expression and the distribution of time and space of the ARGs in different water bodies were also analyzed. With the exception of ermA, blaNDM-1 and vanA, which were not detected in seawater, the other ARGs could be detected in all three water bodies. Tetracycline resistance genes (tetC, tetM and tetQ) in the seawater and Haihe River had even reached 100%, and sulfa ARGs (sul1 and sul2) in the seawater and Poyang Lake, as well as sul2 and sul3 in the Haihe River, had also reached 100%. The ARG pollution in Haihe River was much more serious, since 14 and 17 of 20 ARG species were significantly higher compared with seawater and Poyang Lake, respectively. Some ARGs also had a high absolute abundance. The absolute abundance of macrolide resistance genes (ermB) in seawater was as high as 8.61 × 10⁷ copies/L, and the anti-tuberculosis resistant genes (rpoB and katG) in the Haihe River Basin were highly abundant at 1.32 × 10⁶ copies/L and 1.06 × 10⁷ copies/L, respectively. This indicates that ARGs have gradually become more diverse and extensive in natural water bodies. The results of a redundancy analysis (RDA) of the three water bodies showed that although each water body is affected by different factors in space and time, overall, the presence of AGRs is closely related to the production and life of human beings and the migration of animals.

Fates of antibiotic resistance genes in a distributed swine wastewater treatment plant

This study explores the prevalence, emission, and reduction of five ARGs (sulI, tetA, mphB, qnrD, and mcr-1) and integron (intI) through a distributed swine wastewater purification facility and the effluent-receiving environment. Typical metal resistance genes (MRGs), pathogenic bacterial indicators, the bacterial community, and wastewater properties were also explored to determine their effects on the fates of ARGs. Results indicated that the purification process could hardly effectively remove ARGs' prevalence. 3.1 × 10⁴ -7.1 × 10⁸  copies/L were present after purification, and 4%-57% of them persisted in the subsequent creek and adjacent soil. 16S rRNA sequencing suggested that the discharge of wastewater significantly changed the bacterial community in receiving creek and soil. Molecular ecological networks analysis detected the wide co-occurrence among ARGs, MRGs, and PBGs, which could further facilitate the propagation of antibiotic resistance. ARG incidence and specific bacterial genera were closely correlated, suggesting an extensive hosting relationship. Redundancy analyses showed wastewater organics and nutrients showed positive correlation to most ARGs' abundance, but negatively correlated to their relative abundance. PRACTITIONER POINTS: Fate of five ARGs and intI was studied in a swine wastewater treatment system. The treatment process could not effectively reduce ARGs' abundance. ARGs and pathogens in wastewater were transferred to the receiving creek and soil. The network analysis found wide co-occurrence among ARGs, metal resistance genes, and pathogens. Wastewater nutrients positively correlated to ARG's abundance but negatively correlated to their relative abundance.

Distribution of antibiotic resistance genes in soil amended using Azolla imbricata and its driving mechanisms

The floating aquatic plant of Azolla imbricata has an outstanding purification capability for polluted river water, and it is also employed to improve soil fertility. However, the occurrence and distribution of antibiotic resistance genes (ARGs) in soil amended using A.imbricata remain unclear. In the soil amendment with A. imbricata, heavy metals, antibiotics, transposase genes, ARGs, and bacterial communities in the soil were determined in this study. The results indicated that the diversity of bacteria and ARGs increased, while the diversity of ARGs decreased under the amendment using an appropriate amount of A. imbricata. The Firmicutes, Chloroflexi, Actinobacteria, and Cyanobacteria were the main host bacteria of ARGs. The vertical gene transfer of ARGs was weak, and the horizontal gene transfer became the dominant transfer pathway of ARGs. The amendment with A. imbricata altered the distribution of heavy metals, antibiotics, transposase genes, ARGs, and dominant bacteria. The amendment using A. imbricata promoted the degradation of antibiotics, decreased the concentrations of available heavy metals, and eliminated the abundance of ARGs and transposase genes. Our findings suggested a comprehensive effect of multiple stresses on the fate of ARGs in soil amended with A. imbricata, providing an insight into the distribution and propagation of ARGs in soil amended using plant residues.

Prevalence of antibiotic resistance genes in cell culture liquid waste and the virulence assess for isolated resistant strains

Cell culture liquid waste containing antibiotic resistance genes (ARGs) and microbial community were still not received enough recognition, which pose potential risks to human health. Sixty-eight resistance genes and intl1 were detected in eight samples by Quantitative real-time PCR, while intl1 was only detected in hospital group. Meanwhile, the bacterial community was complex and diverse in each sample by 16S rRNA gene high-throughput sequencing, in addition, Morganella and Enterococcus presented a significant difference between two groups. Whole genome shotgun sequencing revealed that Morganella morganii had more resistance genes and virulence factors in hospital group, and three extended-spectrum beta-lactamase (ESBL) genotypes were found to be blaDHA-5, blaOXA-1, and blaTEM-1. This study provided a preliminary report on ARGs and resistant strains, which reminded people attention to the health risks of potential pathogens in this waste.

Fate of antibiotics and antibiotic resistance genes in a full-scale restaurant food waste treatment plant: Implications of the roles beyond heavy metals and mobile genetic elements

Is our food safe and free of the crisis of antibiotics and antibiotic resistance (AR)? And will the derived food waste (FW) impose AR risk to the environment after biological treatment? This study used restaurant FW leachates flowing through a 200 tons-waste/day biological treatment plant as a window to investigate the fate of antibiotics and antibiotic-resistance genes (ARGs) during the acceptance and treatment of FW. Sulfonamides (sulfamethazine, sulfamethoxazole) and quinolones (ciprofloxacin, enrofloxacin, ofloxacin) were detected during FW treatment, while tetracyclines, macrolides and chloramphenicols were not observable. ARGs encoding resistance to sulfonamides, tetracyclines and macrolides emerged in FW leachates. Material flow analysis illustrated that the total amount of antibiotics (except sulfamethazine) and ARGs were constant during FW treatment processes. Both the concentration and total amount of most antibiotics and ARGs fluctuated during treatment, physical processes (screening, centrifugation, solid-liquid and oil-water separation) did not decrease antibiotic or ARGs concentrations or total levels permanently; the affiliated wastewater treatment plant appeared to remove sulfonamides and most ARGs concentrations and total amount. Heavy metals Ni, Co and Cu were important for disseminating antibiotics concentrations and MGEs for distributing ARGs concentrations. Humic substances (fulvic acids, hydrophilic fractions), C-associated and N-associated contents were essential for the distribution of the total amounts of antibiotics and ARGs. Overall, this study implied that human food might not be free of antibiotics and ARGs, and FW was an underestimated AR pool with various determinants. Nonetheless, derived hazards of FW could be mitigated through biological treatment with well-planned daily operations.

Physicochemical quality of and Escherichia coli resistance profiles in urban surface waters

Aquatic ecosystems of urban rivers are contaminated through waste disposal, which poses a public health problem. The objective of this research was to evaluate the quality of water used for recreation and public supply of six rivers in the city of Cascavel - Paraná, including Cascavel, Quati, Bezerra, Antas, Clarito and Amambay. Samples were collected every 4 months in 2017, and their physicochemical and microbiological parameters, as well as resistance profiles of strains of Escherichia coli to antimicrobials distributed by pharmacies of the primary healthcare network, were evaluated. Parameters such as water temperature, turbidity, total nitrogen, total phosphorus, total coliforms and thermotolerant coliforms showed significant differences. The allowed limit for thermotolerant coliforms, which was set by National Environment Council, Resolution 357/2005, was exceeded in all of the six analyzed rivers. It was determined that 48.1% of E. coli strains showed resistance to nine antimicrobial tested. The highest levels of resistance were found for ampicillin (27.7%), tetracycline (27.7%) and amoxicillin (24.0%). The results of this study contribute to the understanding of the hazards associated with the contamination of springs in urban centers with wastewater containing resistant bacteria. Therefore, recovery work is necessary in these areas because of the importance of these water sources for the entire western region of Paraná state.

Anthropogenic impacts on sulfonamide residues and sulfonamide resistant bacteria and genes in Larut and Sangga Besar River, Perak

The environmental reservoirs of sulfonamide (SA) resistome are still poorly understood. We investigated the potential sources and reservoir of SA resistance (SR) in Larut River and Sangga Besar River by measuring the SA residues, sulfamethoxazole resistant (SMX^r) in bacteria and their resistance genes (SRGs). The SA residues measured ranged from lower than quantification limits (LOQ) to 33.13 ng L^-1 with sulfadiazine (SDZ), sulfadimethoxine (SDM) and SMX as most detected. Hospital wastewater effluent was detected with the highest SA residues concentration followed by the slaughterhouse and zoo wastewater effluents. The wastewater effluents also harbored the highest abundance of SMX^r-bacteria (10⁷ CFU mL^-1) and SRGs (10^-1/16S copies mL^-1). Pearson correlation showed only positive correlation between the PO₄ and SMX^r-bacteria. In conclusion, wastewater effluents from the zoo, hospital and slaughterhouse could serve as important sources of SA residues that could lead to the consequent emergence of SMX^r-bacteria and SRGs in the river.

Swine waste: A reservoir of high-risk blaNDM and mcr-1

Multidrug resistance associated with pigs not only affects pig production but also threatens human health by influencing the farm surrounding and contaminating the food chain. This paper focused on the occurrence and prevalence of high-risk resistance genes (using bla_NDM and mcr-1 as marker genes) in two Chinese swine farms, and investigated their fate and seasonal changes in piggery wastewater treatment systems (PWWTSs). Results revealed that bla_NDM and mcr-1 were prevalent in both confined swine farms, and even prevailed through various processing stages of PWWTSs. Moreover, the abundance of bla_NDM and mcr-1 in winter was higher than that in summer, with 0.01-1.01 logs variation in piggery wastewater. Of concern is that considerable amounts of bla_NDM and mcr-1 were present in final effluent that is applied to farmland (up to 10²-10⁴copies/mL), raising the risk of propagation to indigenous bacteria. Worse still, those pig-derived isolates harboring the bla_NDM/mcr-1 gene were confirmed to spread multidrug resistance to other bacteria, which further increased their dissemination potential in agricultural environment. This study highlights the prevalence of bla_NDM and mcr-1 in swine farms, meanwhile, also emphasizes the necessary to mitigate the release and propagation of these high-risk genes from swine farms following land fertilization and wastewater usage.

Diverse Mobile Genetic Elements and Conjugal Transferability of Sulfonamide Resistance Genes (sul1, sul2, and sul3) in Escherichia coli Isolates From Penaeus vannamei and Pork From Large Markets in Zhejiang, China

High prevalence rates of sulfonamide resistance genes sul1, sul2, and sul3 have been observed in Gram-negative bacteria isolated from humans, domestic animals, and aquaculture species worldwide. We investigated the distribution characteristics, location, conjugative transferability, and genetic environments of sul genes from Escherichia coli isolates collected from Penaeus vannamei and pork samples from three large markets in Zhejiang, China. The prevalence rates of sul genes in sulfonamide-resistant E. coli isolates from P. vannamei and pork samples were 90.0 and 88.6%, respectively, and the prevalence of sul1 and sul2 was significantly higher than that of sul3 (p < 0.05). Twenty-four representative sul-positive E. coli isolates were analyzed in detail. Southern blot hybridization confirmed that sul genes of E. coli isolates were located on plasmids and/or chromosomes. Transfer of resistance through conjugation was observed in all 18 E. coli isolates harboring sul genes on plasmids. Replicon typing identified seven different incompatibility groups and IncF was the dominant replicon type among sul gene-containing plasmids from both sources. PCR walking analysis indicated that 87.5% (35/40) of sul gene-related fragments carried insertion sequences (ISs) belonging to a variety of families in diverse sites, with IS26 occurring most frequently. In addition, the sul1 gene was detected mainly in fragments carrying class 1 integrons. Co-location on the same fragment with resistance genes that may contribute to the persistence and dissemination of sul1 and/or sul2 genes. The diversity of mobile genetic elements and resistance genes adjacent to sul3 was much lower than those adjacent to sul1 and sul2, especially those located in chromosomes, which reduced the transmission potential of the sul3 gene. In conclusion, combined with the results of clonal relatedness analysis by PFGE and MLST of 24 representative E. coli isolates from P. vannamei and pork samples, it showed that a small number of sul genes were vertically transmitted among E. coli from P. vannamei and that horizontal gene transfer was likely the main transmission mechanism of sul genes from both sources. Our results provide important information to better understand the risk of transmission of sul genes from seafood and meat to humans.

Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

CRISPR-Cas systems are widespread in bacterial and archaeal genomes, and in their canonical role in phage defence they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. Newly discovered features within these evolutionary dynamics are anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In Pseudomonas aeruginosa, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance is likely to be very different in particular pathogenic species and clinical environments. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.

Evaluating the net effect of sulfadimidine on nitrogen removal in an aquatic microcosm environment

Antibiotics enter into aquatic pond sediments by wastewater and could make detrimental effects on microbial communities. In this study, we examined the effects of sulfadimidine on nitrogen removal when added to experimental pond sediments. We found that sulfadimidine increased the number of sulfadimidine resistant bacteria and significantly increased the abundance of sul2 at the end of the incubation time (ANOVA test at Tukey HSD, P < 0.05). In addition, sulfadimidine decreased the N₂O reduction rate as well as the amount of nitrate reduction. Pearson correlation analysis revealed that the N₂O reduction rate was significantly and negatively correlated with narG (r = -0.679, P < 0.05). In contrast, we found a significant positive correlation between the amount of nitrate reduction and the abundance of narG (r = 0.609, P < 0.05) and nirK (r = 0.611, P < 0.05). High-throughput sequencing demonstrated that Actinobacteria, Euryarchaeota, Gemmatimonadetes, Nitrospirae, Burkholderiaceae (a family of Proteobacteria), and Thermoanaerobaculaceae (a family of Firmicutes) decreased with sulfadimidine exposure. In sediments, Actinobacteria, Bacteroidetes, Cyanobacteria, Epsilonbacteraeota, Euryarchaeota, Firmicutes, Gemmatimonadetes, and Spirochaetesat may play key roles in nitrogen transformation. Overall, the study exhibited a net effect of antibiotic exposure regarding nitrogen removal in an aquatic microcosm environment through a combination of biochemical pathways and molecular pathways, and draws attention to controlling antibiotic pollution in aquatic ecosystems.

Response of antibiotic resistance to the co-existence of chloramphenicol and copper during bio-electrochemical treatment of antibiotic-containing wastewater

Concerns have been raised regarding co-selection for antibiotic resistance among microorganisms exposed to antibiotics and metals. As a promising approach for treating antibiotics and heavy metal-containing wastewater, a bio-electrochemical system (BES) can be used for antibiotic and heavy metal removal. This study determined the fate of antibiotic resistance genes (ARGs) in a BES when exposed to chloramphenicol (CAP) and Cu²⁺. The ARGs encoding the efflux pump (cmlA, floR, and tetC), the class 1 integron integrase-encoding gene, and the sul1 gene were analyzed. The results indicated that the co-existence of CAP and different concentrations of Cu²⁺ had significant influence on the relative abundances of the ARGs. The changes in the bacterial community structure and the results of a quantitative correlation analysis between the bacterial community and the ARGs confirmed that the shift in the potential hosts was the key reason for the changes of the ARGs. This study sheds new light on the mechanisms of ARGs variations in BES under the co-selection pressure of antibiotics and heavy metals.