Microbiome and Resistome in Poultry Litter-Fertilized and Unfertilized Agricultural Soils. - Related Documents




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536101.0000Microbiome and Resistome in Poultry Litter-Fertilized and Unfertilized Agricultural Soils. Background: Poultry litter is the main waste of poultry farming and is widely used as an agricultural fertilizer. However, owing to the use of antimicrobials in animal production, it can accumulate antimicrobial residues, antimicrobial-resistant bacteria (ARB), and antimicrobial resistance genes (ARGs). This study aimed to evaluate the impact of poultry litter use on the microbiome and resistome of agricultural soils. Methods: Soil samples from fertilized and unfertilized plots were collected from two horticultural farms that intensively use poultry litter. Microbiome composition was assessed using 16S rRNA sequencing. A culture-dependent method was used to isolate resistant strains on CHROMagar plates supplemented with sulfamethoxazole or ciprofloxacin. ARGs and integrase-encoding genes were identified by PCR. Results: Microbiome analysis revealed significant differences in structure and composition between poultry litter-fertilized and unfertilized soils. Fertilized soils exhibited greater alpha diversity and richness. Bacillota, commonly found in the avian gastrointestinal tract, were more abundant in fertilized soils. A total of 62 resistant strains were isolated, and 23 clinically relevant strains harbored ARGs, including fluoroquinolone (qnrA and qnrB) and β-lactam (bla(GES), bla(TEM), and bla(SHV)) resistance genes. Class 1 and 2 integron-associated genes (intI1 and intI2) were also detected. Notably, the rare bla(GES) gene was detected in Bacillus sp. from unfertilized soil. Similarly, qnrA co-occurred with bla(SHV) in a Bosea sp. strain from unfertilized soil. Conclusions: These findings highlight the potential for ARB dissemination in agricultural environments, where ARB and ARGs, once introduced into soils, may spread by weathering and other environmental factors, complicating negative control selection in in situ studies.202540298506
536310.9999Irrigation Ponds as Sources of Antimicrobial-Resistant Bacteria in Agricultural Areas with Intensive Use of Poultry Litter. Poultry litter is widely used worldwide as an organic fertilizer in agriculture. However, poultry litter may contain high concentrations of antibiotics and/or antimicrobial-resistant bacteria (ARB), which can be mobilized through soil erosion to water bodies, contributing to the spread of antimicrobial resistance genes (ARGs) in the environment. To better comprehend this kind of mobilization, the bacterial communities of four ponds used for irrigation in agricultural and poultry production areas were determined in two periods of the year: at the beginning (low volume of rainfall) and at the end of the rainy season (high volume of rainfall). 16S rRNA gene sequencing revealed not only significantly different bacterial community structures and compositions among the four ponds but also between the samplings. When the DNA obtained from the water samples was PCR amplified using primers for ARGs, those encoding integrases (intI1) and resistance to sulfonamides (sul1 and sul2) and β-lactams (bla(GES), bla(TEM) and bla(SHV)) were detected in three ponds. Moreover, bacterial strains were isolated from CHROMagar plates supplemented with sulfamethoxazole, ceftriaxone or ciprofloxacin and identified as belonging to clinically important Enterobacteriaceae. The results presented here indicate a potential risk of spreading ARB through water resources in agricultural areas with extensive fertilization with poultry litter.202236421294
536220.9998Cross-environmental cycling of antimicrobial resistance in agricultural areas fertilized with poultry litter: A one health approach. Poultry litter, commonly used as an organic fertilizer, can contain antimicrobial residues, resistant bacteria, and/or antimicrobial resistance genes. After application to soil, these contaminants can reach crops and be transported to aquatic systems through leaching and runoff. Once in water bodies, they can return to soil and crops through irrigation, establishing a cycle that promotes the selection, spread and persistence of antimicrobial resistance. To investigate the hypothesis of a cyclical event, samples of poultry litter, cultivable soil fertilized with this organic residue, rhizosphere soil from Sechium edule (chayote), water, and sediments from irrigation ponds were collected across two agricultural and poultry-producing areas during the dry and rainy seasons. Clinically significant bacteria, especially bacteria belonging to the Enterobacteriaceae family, were isolated. Fifty-three strains exhibited one or more antimicrobial resistance genes, as detected by PCR amplification, including those conferring resistance to sulfonamides (sul1 and sul2), fluoroquinolones (qnrB, qnrA, and qnrS), and β-lactams (bla(GES), bla(TEM), bla(SHV), bla(CTX-M-1/2,)bla(CTX-M-8), and bla(CTX-M-14)). Genes encoding integrases related to class-1 and 2 integrons (intI1 and intI2) were also observed. A rare occurrence of the bla(GES) gene was observed in Stenotrophomonas sp. and Brevundimonas sp. Strains of Escherichia sp. were multidrug resistant. Sequencing of the 16S rRNA encoding gene indicated unique operational taxonomic units (OTUs) originating from poultry litter and found in the soil, rhizosphere, water, and sediment, highlighting the dissemination of this material across agricultural substrates. These findings strongly suggest the spread of antimicrobial-resistant bacteria in agricultural environments, posing potential risks to both human and animal health.202439447633
534830.9998Characterization of microbial community and antibiotic resistome in intra urban water, Wenzhou China. The present study investigated the water quality index, microbial composition and antimicrobial resistance genes in urban water habitats. Combined chemicals testing, metagenomic analyses and qualitative PCR (qPCR) were conducted on 20 locations, including rivers from hospital surrounds (n = 7), community surrounds (n = 7), and natural wetlands (n = 6). Results showed that the indexes of total nitrogen, phosphorus, and ammonia nitrogen of hospital waters were 2-3 folds high than that of water from wetlands. Bioinformatics analysis revealed a total of 1,594 bacterial species from 479 genera from the three groups of water samples. The hospital-related samples had the greatest number of unique genera, followed by those from wetlands and communities. The hospital-related samples contained a large number of bacteria associated with the gut microbiome, including Alistipes, Prevotella, Klebsiella, Escherichia, Bacteroides, and Faecalibacterium, which were all significantly enriched compared to samples from the wetlands. Nevertheless, the wetland waters enriched bacteria from Nanopelagicus, Mycolicibacterium and Gemmatimonas, which are typically associated with aquatic environments. The presence of antimicrobial resistance genes (ARGs) that were associated with different species origins in each water sample was observed. The majority of ARGs from hospital-related samples were carried by bacteria from Acinetobacter, Aeromonas and various genera from Enterobacteriaceae, which each was associated with multiple ARGs. In contrast, the ARGs that were exclusively in samples from communities and wetlands were carried by species that encoded only 1 to 2 ARGs each and were not normally associated with human infections. The qPCR showed that water samples of hospital surrounds had higher concentrations of intI1 and antimicrobial resistance genes such as tetA, ermA, ermB, qnrB, sul1, sul2 and other beta-lactam genes. Further genes of functional metabolism reported that the enrichment of genes associated with the degradation/utilization of nitrate and organic phosphodiester were detected in water samples around hospitals and communities compared to those from wetlands. Finally, correlations between the water quality indicators and the number of ARGs were evaluated. The presence of total nitrogen, phosphorus, and ammonia nitrogen were significantly correlated with the presence of ermA and sul1. Furthermore, intI1 exhibited a significant correlation with ermB, sul1, and bla(SHV), indicating a prevalence of ARGs in urban water environments might be due to the integron intI1's diffusion-promoting effect. However, the high abundance of ARGs was limited to the waters around the hospital, and we did not observe the geographical transfer of ARGs along with the river flow. This may be related to water purifying capacity of natural riverine wetlands. Taken together, continued surveillance is required to assess the risk of bacterial horizontal transmission and its potential impact on public health in the current region.202337396356
530340.9998Wastewater irrigation increases the abundance of potentially harmful gammaproteobacteria in soils in Mezquital Valley, Mexico. Wastewater contains large amounts of pharmaceuticals, pathogens, and antimicrobial resistance determinants. Only a little is known about the dissemination of resistance determinants and changes in soil microbial communities affected by wastewater irrigation. Community DNAs from Mezquital Valley soils under irrigation with untreated wastewater for 0 to 100 years were analyzed by quantitative real-time PCR for the presence of sul genes, encoding resistance to sulfonamides. Amplicon sequencing of bacterial 16S rRNA genes from community DNAs from soils irrigated for 0, 8, 10, 85, and 100 years was performed and revealed a 14% increase of the relative abundance of Proteobacteria in rainy season soils and a 26.7% increase in dry season soils for soils irrigated for 100 years with wastewater. In particular, Gammaproteobacteria, including potential pathogens, such as Pseudomonas, Stenotrophomonas, and Acinetobacter spp., were found in wastewater-irrigated fields. 16S rRNA gene sequencing of 96 isolates from soils irrigated with wastewater for 100 years (48 from dry and 48 from rainy season soils) revealed that 46% were affiliated with the Gammaproteobacteria (mainly potentially pathogenic Stenotrophomonas strains) and 50% with the Bacilli, whereas all 96 isolates from rain-fed soils (48 from dry and 48 from rainy season soils) were affiliated with the Bacilli. Up to six types of antibiotic resistance were found in isolates from wastewater-irrigated soils; sulfamethoxazole resistance was the most abundant (33.3% of the isolates), followed by oxacillin resistance (21.9% of the isolates). In summary, we detected an increase of potentially harmful bacteria and a larger incidence of resistance determinants in wastewater-irrigated soils, which might result in health risks for farm workers and consumers of wastewater-irrigated crops.201424951788
530050.9998From Pig Breeding Environment to Subsequently Produced Pork: Comparative Analysis of Antibiotic Resistance Genes and Bacterial Community Composition. It is well verified that pig farms are an important reservoir and supplier of antibiotic resistance genes (ARGs). However, little is known about the transmission of ARGs between the breeding environment and subsequently produced pork. This study was conducted to investigate if ARGs and associated host bacteria spread from the breeding environment onto the meat through the food production chain. We thus analyzed the occurrence and abundance of ARGs, as well as comparing both ARG and bacterial community compositions in farm soil, pig feces and pork samples from a large-scale pig farm located in Xiamen, People's Republic of China. Among the 26 target ARGs, genes conferring resistance to sulfonamide, trimethoprim, aminoglycoside, chloramphenicol, macrolide, florfenicol, and tetracycline were observed at high frequency in both the pig breeding environment and pork. The prevalence of ARGs in pork was surprisingly consistent with breeding environments, especially between the pork and feces. The relative abundance of 10 representative ARGs conferring resistance to six classes of antibiotics ranged from 3.01 × 10(-1) to 1.55 × 10(-6) copies/16S rRNA copies. The ARGs conferring resistance to sulfanilamide (sulI and sulII), aminoglycoside (aadA), and tetracycline [tet(A) and tet(M)] were most highly abundant across most samples. Samples from feces and meat possessed a higher similarity in ARG compositions than samples from the farms soil. Enterobacteriaceae found on the meat samples were further identical with previously isolated multidrug-resistant bacteria from the same pig farm. Our results strongly indicate that ARGs can be potentially spreading from pig breeding environment to meat via the pork industry chain, such as feed supply, pig feeding and pork production.201930761096
530160.9998High levels of antibiotic resistance genes and opportunistic pathogenic bacteria indicators in urban wild bird feces. This study analyzed fresh feces from three common bird species that live in urban environments and interact with human communities. Antibiotic resistance genes (ARGs) encoding resistance to three major classes of antibiotics (i.e., tetracyclines, β-lactams, and sulfonamides) and the mobile genetic element integrase gene (intI1) were abundant (up to 10(9), 10(8), 10(9), and 10(10) copies/g dry feces for tetW, bla(TEM), sul1, and intI1, respectively), with relative concentrations surprisingly comparable to that in poultry and livestock that are occasionally fed antibiotics. Biomarkers for opportunistic pathogens were also abundant (up to 10(7) copies/g dry feces) and the dominant isolates (i.e., Enterococcus spp. and Pseudomonas aeruginosa) harbored both ARGs and virulence genes. ARGs in bird feces followed first-order attenuation with half-lives ranging from 1.3 to 11.1 days in impacted soil. Although residual antibiotics were detected in the feces, no significant correlation was observed between fecal antibiotic concentrations and ARG relative abundance. Thus, other unaccounted factors likely contributed selective pressure for ARG maintenance. These findings highlight the contribution of wild urban bird feces to the maintenance and dissemination of ARGs, and the associated health risks.202032663725
536070.9998Diversity, distribution and quantification of antibiotic resistance genes in goat and lamb slaughterhouse surfaces and meat products. The distribution and quantification of tetracycline, sulfonamide and beta-lactam resistance genes were assessed in slaughterhouse zones throughout meat chain production and the meat products; this study represents the first to report quantitatively monitor antibiotic resistance genes (ARG) in goat and lamb slaughterhouse using a culture independent approach, since most studies focused on individual bacterial species and their specific resistance types. Quantitative PCR (qPCR) revealed a high prevalence of tetracycline resistance genes tetA and tetB in almost all slaughterhouse zones. Sulfonamide resistance genes were largely distributed, while beta-lactam resistance genes were less predominant. Statistical analysis revealed that resistant bacteria, in most cases, were spread by the same route in almost all slaughterhouse zones, except for tetB, blaCTX and blaTEM genes, which occurred in few zones as isolated 'hot spots.' The sum of all analyzed ARG indicated that slaughterhouse surfaces and end products act as reservoirs of ARG, mainly tet genes, which were more prevalent in slaughtering room (SR), cutting room (CR) and commercial meat products (MP). Resistance gene patterns suggest they were disseminated throughout slaughterhouse zones being also detected in commercial meat products, with significant correlations between different sampling zones/end products and total resistance in SR, CR and white room (WR) zones, and also refrigerator 4 (F4) and MP were observed. Strategically controlling key zones in slaughterhouse (SR, CR and WR) by adequate disinfection methods could strategically reduce the risks of ARG transmission and minimize the issues of food safety and environment contamination.201425479100
313980.9998Sulfonamide-resistant bacteria and their resistance genes in soils fertilized with manures from Jiangsu Province, Southeastern China. Antibiotic-resistant bacteria and genes are recognized as new environmental pollutants that warrant special concern. There were few reports on veterinary antibiotic-resistant bacteria and genes in China. This work systematically analyzed the prevalence and distribution of sulfonamide resistance genes in soils from the environments around poultry and livestock farms in Jiangsu Province, Southeastern China. The results showed that the animal manure application made the spread and abundance of antibiotic resistance genes (ARGs) increasingly in the soil. The frequency of sulfonamide resistance genes was sul1 > sul2 > sul3 in pig-manured soil DNA and sul2 > sul1 > sul3 in chicken-manured soil DNA. Further analysis suggested that the frequency distribution of the sul genes in the genomic DNA and plasmids of the SR isolates from manured soil was sul2 > sul1 > sul3 overall (p<0.05). The combination of sul1 and sul2 was the most frequent, and the co-existence of sul1 and sul3 was not found either in the genomic DNA or plasmids. The sample type, animal type and sampling time can influence the prevalence and distribution pattern of sulfonamide resistance genes. The present study also indicated that Bacillus, Pseudomonas and Shigella were the most prevalent sul-positive genera in the soil, suggesting a potential human health risk. The above results could be important in the evaluation of antibiotic-resistant bacteria and genes from manure as sources of agricultural soil pollution; the results also demonstrate the necessity and urgency of the regulation and supervision of veterinary antibiotics in China.201425405870
712090.9998Impact of liquid hog manure applications on antibiotic resistance genes concentration in soil and drainage water in field crops. Agricultural practices such as manure applications could contribute to the spread of antibiotic resistance genes (ARGs) within the environment. Our objective was to assess the impact of certain fertilization methods (mineral or manure) and tillage practices (reduced or conventional) on the presence of ARGs and bacteria in soil and drainage water under wheat and grain corn crops. Targeted ARGs tet(T), sul1, and bla(CTX-M-1) in liquid hog manure, soil, and water samples were quantified by qPCR. Conventional PCR was used to detect mcr-1 and mcr-2. ARGs in control plots were detected despite the absence of manure, representing an environmental reservoir of resistant microorganisms. The manure application rate higher than 39 m(3)/ha increased tet(T) and sul1 gene concentrations in soil for more than 180 days. Tillage practices had no impact on ARG concentrations in soil and water samples. The bla(CTX-M-1) gene was only detected in seven water samples in 2016, but no link was established with the treatments. The mcr-1 and mcr-2 genes were not detected in all tested samples. This study demonstrated that tet(T) and sul1 gene concentrations increased in soil after liquid hog manure application as well as in drainage water in the next weeks.202032330390
5346100.9998Metagenomic Analysis of Urban Wastewater Treatment Plant Effluents in Tokyo. PURPOSE: Urban wastewater treatment plant (WWTP) effluents, even with proper treatment, may cause antimicrobial resistance (AMR) burden, with a high frequency of acquired antimicrobial resistance genes (ARGs). The dissemination of ARGs into the environment increases the risk of infectious diseases; however, there is little direct evidence regarding their epidemiological effects. This study aimed to assess effluents from urban WWTPs around the Tama River and Tokyo Bay using metagenomic analysis of (AMR) genes (ARGs) and heavy-metal resistance genes. METHODS: Metagenomic DNA-seq analysis of water samples and resistome analysis were performed. RESULTS: The most prevalent ARG was the sulfonamide resistance gene, sul1, followed by the quaternary ammonium compound resistance gene, qacE, suggesting that basic gene sets (sul1 and ∆qacE) in the class 1 integrons are the predominant ARGs. The aminoglycoside resistance genes, aadA and aph, and macrolide resistance genes, msr(E) and mph(E), were the predominant ARGs against each antimicrobial. bla (OXA) and bla (GES) were frequently detected, whereas the bla (CTX-M) cluster was faintly detected. Non-metric multidimensional scaling plot analysis and canonical correspondence analysis results suggested that marked differences in ARGs could be involved in the seasonal differences; qnrS2, aac(6')-Ib, and mef(C) increased markedly in summer, whereas msr(E) was more frequently detected in winter. Heavy-metal (Hg and Cu) resistance genes (HMRGs) were significantly detected in effluents from all WWTPs. CONCLUSION: We characterized a baseline level of the environmental ARG/HMRG profile in the overall community, suggesting that environmental AMR surveillance, particularly in urban WWTPs, is a valuable first step in monitoring the AMR dissemination of bacteria from predominantly healthy individuals carrying notable ARG/Bs.202236039320
3217110.9998Distribution and environmental dissemination of antibiotic resistance genes in poultry farms and surrounding ecosystems. Antibiotic resistance poses a significant threat to human and animal health worldwide, with farms serving as crucial reservoirs of Antibiotic Resistance Genes (ARGs) and Antibiotic-resistant bacteria. However, the distribution of ARGs in poultry farms and their transmission patterns in the environment remain poorly understood. This study collected samples of aerosol microorganisms, cloacal matter, soil, and vegetables from poultry farms and surrounding environments at three different distances. We used 16S rRNA gene sequencing and HT-qPCR to analyze the characteristics of aerosol microbial communities and the abundance of ARGs. At the phylum level, Proteobacteria, Firmicutes, and Bacteroidetes were dominant in cloacal samples, aerosol samples, and vegetable samples, while Proteobacteria Actinobacteriota and Acidobacteria dominated soil. Pseudomonas was dominant in cloacal samples at the genus level, whereas Fusobacterium was prevalent in soil. The diversity and richness of bacterial communities were more similar between cloacal samples than those observed between either sample type compared with soil. Our results showed that tetracycline and aminoglycoside ARG relative abundance was high across all sample types but significantly increased within feces/air compared to soils/vegetables. Association analysis revealed five potential host genera for ARG/MGE presence among various microbiota populations studied here. Our findings confirm that farms are important sources for the environmental dissemination of pathogens and ARGs.202539689477
5373120.9998Impact of soil supplemented with pig manure on the abundance of antibiotic resistant bacteria and their associated genes. This study was conducted to evaluate the abundance of antibiotic resistant bacteria and their resistance genes from agriculture soil supplemented with pig manure. Uncultivable soil sample was supplemented with pig manure samples under microcosm experimental conditions and plated on Luria-Bertani (LB) agar incorporated with commercial antibiotics. The supplementation of soil with 15% pig manure resulted in the highest increase in the population of antibiotic resistant bacteria (ARB)/multiple antibiotic resistant bacteria (MARB). Seven genera that included Pseudomonas, Escherichia, Providencia, Salmonella, Bacillus, Alcaligenes and Paenalcaligenes were the cultivable ARB identified. A total of ten antibiotic resistant bacteria genes (ARGs) frequently used in clinical or veterinary settings and two mobile genetic elements (MGEs) (Class 1 and Class 2 integrons) were detected. Eight heavy metal, copper, cadmium, chromium, manganese, lead, zinc, iron, and cobalt were found in all of the manure samples at different concentrations. Tetracycline resistance genes were widely distributed with prevalence of 50%, while aminoglycoside and quinolone-resistance gene had 16% and 13%, respectively. Eighteen ARB isolates carried more than two ARGs in their genome. Class 1 integron was detected among all the 18 ARB with prevalence of 90-100%, while Class 2 integron was detected among 11 ARB. The two classes of integron were found among 10 ARB. Undoubtedly, pig manure collected from farms in Akure metropolis are rich in ARB and their abundance might play a vital role in the dissemination of resistance genes among clinically-relevant pathogens.202337308603
5341130.9998Occurrence of Bacterial Markers and Antibiotic Resistance Genes in Sub-Saharan Rivers Receiving Animal Farm Wastewaters. Antibiotic resistant bacteria and genes which confer resistance to antibiotics from human/animal sources are currently considered a serious environmental and a public health concern. This problem is still little investigated in aquatic environment of developing countries according to the different climatic conditions. In this research, the total bacterial load, the abundance of relevant bacteria (Escherichia coli (E. coli), Enterococcus (Ent), and Pseudomonas), and antibiotic resistance genes (ARGs: bla(OXA-48), bla(CTX-M), sul1, sul2, sul3, and tet(B)) were quantified using Quantitative Polymerase Chain Reaction (qPCR) in sediments from two rivers receiving animal farming wastewaters under tropical conditions in Kinshasa, capital city of the Democratic Republic of the Congo. Human and pig host-specific markers were exploited to examine the sources of contamination. The total bacterial load correlated with relevant bacteria and genes bla(OXA-48), sul3, and tet(B) (P value < 0.01). E. coli strongly correlated with 16s rDNA, Enterococcus, Pseudomonas spp., bla(OXA-48), sul3, and tet(B) (P value < 0.01) and with bla(CTX-M), sul1, and sul2 at a lower magnitude (P value < 0.05). The most abundant and most commonly detected ARGs were sul1, and sul2. Our findings confirmed at least two sources of contamination originating from pigs and anthropogenic activities and that animal farm wastewaters didn't exclusively contribute to antibiotic resistance profile. Moreover, our analysis sheds the light on developing countries where less than adequate infrastructure or lack of it adds to the complexity of antibiotic resistance proliferation with potential risks to the human exposure and aquatic living organisms. This research presents useful tools for the evaluation of emerging microbial contaminants in aquatic ecosystems which can be applied in the similar environment.201931619758
5295140.9998Occurrence of (fluoro)quinolones and (fluoro)quinolone resistance in soil receiving swine manure for 11 years. Because of the widespread use of antibiotics in animal breeding, the agricultural application of animal manure can lead to the introduction of antibiotics, antibiotic-resistant bacteria and antibiotic resistance genes to the soil and surrounding environment, which may pose a threat to public health. In this study, we investigated the status of (fluoro)quinolone (FQ) residues and FQ resistance levels in soil with and without receiving long-term swine manure. Six FQs (pipemidic acid, lomefloxacin, enrofloxacin, norfloxacin, ciprofloxacin, and ofloxacin) were only detected in manured soil, with individual concentrations ranging from below the detection limit to 27.2 μg kg(-1) and increasing with the increase in swine manure application rates. Higher load rates of swine manure yielded a higher number of ciprofloxacin-resistant (CIPr) bacteria after spreading. A total of 24 CIPr bacterial isolates were obtained from the tested soil, which belonged to four phyla (Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes) or were related to nine different genera. Only 18 isolates from manured soil were positive for five plasmid-mediated quinolone resistance (PMQR) genes (aac(6')-Ib-cr, qnrD, qepA, oqxA, and oqxB). To our knowledge, this study is the first to examine the occurrence of PMQR genes in FQ-resistant bacteria from the soil environment. A similar result was observed for the total DNA from soil, with the exception of aac(6')-Ib being detected in the control sample. The absolute and relative abundances of total PMQR genes also increased with fertilization quantity. Significant correlations were observed between FQ resistance levels and FQ concentrations. These results indicated that the agricultural application of swine manure led to FQ residues and enhanced FQ resistance. This investigation provides baseline data on FQ resistance profiles in soils receiving long-term swine manure.201526042895
3213150.9998Investigating antibiotics, antibiotic resistance genes, and microbial contaminants in groundwater in relation to the proximity of urban areas. Groundwater is an essential public and drinking water supply and its protection is a goal for global policies. Here, we investigated the presence and prevalence of antibiotic residues, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial contamination in groundwater environments at various distances from urban areas. Antibiotic concentrations ranged from below detection limit to 917 ng/L, being trimethoprim, macrolide, and sulfonamide the most abundant antibiotic classes. A total of eleven ARGs (aminoglycoside, β-lactam, chloramphenicol, Macrolide-Lincosamide-Streptogramin B - MLSB, sulfonamide, and tetracycline), one antiseptic resistance gene, and two MGEs were detected by qPCR with relative abundances ranging from 6.61 × 10(-7) to 2.30 × 10(-1) copies/16S rRNA gene copies. ARGs and MGEs were widespread in the investigated groundwater environments, with increased abundances not only in urban, but also in remote areas. Distinct bacterial community profiles were observed, with a higher prevalence of Betaproteobacteria and Bacteroidetes in the less-impacted areas, and that of Firmicutes in the contaminated groundwater. The combined characteristics of increased species diversity, distinct phylogenetic composition, and the possible presence of fecal and/or pathogenic bacteria could indicate different types of contamination. Significant correlations between ARGs, MGEs and specific taxa within the groundwater bacterial community were identified, revealing the potential hosts of resistance types. Although no universal marker gene could be determined, a co-selection of int1, qacEΔ1 and sulI genes, a proxy group for anthropogenic pollution, with the tetC, tetO, tetW resistance genes was identified. As the tet group was observed to follow the pattern of environmental contamination for the groundwater samples investigated in this study, our results strongly support the proposal of this group of genes as an environmental tracer of human impact. Overall, the present study investigated several emerging contaminants in groundwater habitats that may be included in monitoring programs to enable further regulatory and protection measures.201829454283
5364160.9998Raw wastewater irrigation for urban agriculture in three African cities increases the abundance of transferable antibiotic resistance genes in soil, including those encoding extended spectrum β-lactamases (ESBLs). A study was conducted to investigate the impact of raw wastewater use for irrigation on dissemination of bacterial resistance in urban agriculture in African cities. The pollution of agricultural fields by selected antibiotic residues was assessed. The structure and functions of the soil microbial communities, presence of antibiotic resistance genes of human clinical importance and Enterobacteriaceae plasmid replicons were analysed using high throughput metagenomic sequencing. In irrigated fields, the richness of Bacteroidetes and Firmicutes phyla increased by 65% and 15.7%, respectively; functions allocated to microbial communities' adaptation and development increased by 3%. Abundance of antibiotic resistance genes of medical interest was 27% greater in irrigated fields. Extended spectrum β-lactamase genes identified in irrigated fields included bla(CARB-3), bla(OXA-347), bla(OXA-5) and bla(Rm3). The presence of ARGs encoding resistance to amphenicols, β-lactams, and tetracyclines were associated with the higher concentrations of ciprofloxacin, enrofloxacin and sulfamethoxazole in irrigated fields. Ten Enterobacteriaceae plasmid amplicon groups involved in the wide distribution of ARGs were identified in the fields. IncQ2, ColE, IncFIC, IncQ1, and IncFII were found in both farming systems; IncW and IncP1 in irrigated fields; and IncY, IncFIB and IncFIA in non-irrigated fields. In conclusion, raw wastewater irrigated soils in African cities could represent a vector for the spread of antibiotic resistance, thus threatening human and animal health. Consumers of products from these farms and farmers could be at risk of acquiring infections due to drug-resistant bacteria.202031505362
5365170.9998Drinking Water and Biofilm as Sources of Antimicrobial Resistance in Free-Range Organic Broiler Farms. Drinking water distribution systems (DWDSs) represent an ideal environment for biofilm formation, which can harbor pathogenic and antimicrobial-resistant bacteria. This study aimed to assess longitudinally the microbial community composition and antimicrobial resistance (AMR), as determined by 16S rRNA NGS and qPCR, respectively, in drinking water (DW) and biofilm from DWDSs, as well as faeces, of free-range organic broiler farms. The role of DWDSs in AMR gene (ARG) dissemination within the farm environment and transmission to animals, was also assessed. DW and biofilm microbial communities differed from those of faecal samples. Moreover, potentially pathogenic and opportunistic bacteria (e.g., Staphylococcaceae) were identified in water and biofilms. High prevalence and abundance of ARGs conferring resistance to carbapenems (i.e., bla(NDM)), 3rd and 4th generation cephalosporins (i.e., bla(CMY-2)), (fluoro)quinolones (i.e., qnrS), and polymyxins (i.e., mcr-3 and mcr-5) were detected in DW, biofilm, and faecal samples, which is of concern for both animal and human health. Although other factors (e.g., feed, pests, and wildlife) may contribute to the dissemination of AMR in free-range organic poultry farms, this study indicates that DWDSs can also play a role.202439334983
5349180.9998Spread and persistence of antimicrobial resistance genes in wastewater from human and animal sources in São Paulo, Brazil. The spread of antimicrobial resistance (AMR) through multiple reservoirs is a global concern. Wastewater is a critical AMR dissemination source, so this study aimed to assess the persistence of resistance genetic markers in wastewater using a culture-independent approach. Raw and treated wastewater samples (n = 121) from a wastewater treatment plant (WWTP), a human hospital, a veterinary hospital, and a pig farm were monthly collected and concentrated by filtration. DNA was extracted directly from filter membranes, and PCR was used in the qualitative search of 32 antimicrobial resistance genes (ARGs). Selected genes (bla(CTX-M), bla(KPC), qnrB, and mcr-1) were enumerated by quantitative real-time PCR (qPCR). Twenty-six ARGs were detected in the qualitative ARGs search, while quantitative data showed a low variation of the ARG's relative abundance (RA) throughout the months, especially at the human hospital and the WWTP. At the WWTP, despite significantly reducing the absolute number of gene copies/L after each treatment stage (p < 0.05), slight increases (p > 0.05) in the RAs of genes bla(CTX-M), qnrB, and mcr-1 were observed in reused water (tertiary treatment) when compared with secondary effluent. Although the increase is not statistically significant, it is worth noting that there was some level of ARGs concentration after the disinfection process. No significant absolute or relative after-treatment quantification reductions were observed for any ARGs at the veterinary hospital or the pig farm. The spread of ARGs through sewage needs to be continuously addressed, because their release into natural environments may pose potential risks of exposure to resistant bacteria and impact local ecosystems.202438545908
3212190.9998Distribution and driving factors of antibiotic resistance genes in treated wastewater from different types of livestock farms. Treated wastewater from livestock farms is an important reservoir for antibiotic resistance genes (ARGs), and is a main source of ARGs in the environment. However, the distribution and driving factors of ARGs in treated wastewater from different types of livestock farms are rarely reported. In this study, treated wastewater from 69 large-scale livestock farms of different types, including broiler, layer, and pig farms, was collected, and 11 subtypes of ARGs, 2 mobile genetic elements (MGEs) and bacterial community structure were analyzed. The results revealed detection rates of NDM-1 and mcr-1 of 90 % and 43 %, respectively, and the detection rates of other ARGs were 100 %. The relative abundance of ARGs, such as tetA, tetX and strB, in broiler farms was significantly higher than that in layer farms, but the bacterial α diversity was significantly lower than that in other farm types. Furthermore, although the treatment process had a greater impact on the physicochemical properties of the treated wastewater than the livestock type, livestock type was the main factor affecting the bacterial community in the treated wastewater. The analysis of potential host bacteria of ARGs revealed significant differences in the host bacteria of ARGs in treated wastewater from different types of livestock farms. The host bacteria of ARGs in broiler farms mainly belonged to Actinobacteria, layer farms mainly belonged to Proteobacteria, and pig farms mainly belonged to Firmicutes. Additionally, redundancy analysis showed that the distribution of ARGs may have resulted from the combination of multiple driving factors in different types of livestock farms, among which tnpA and NH(4)(+)-N were the main influencing factors. This study revealed multiple driving factors for the distribution of typical ARGs in treated wastewater from different types of livestock farms, providing basic data for the prevention and control of ARG pollution in agricultural environments.202235934031