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349800.9854Comparative study on the bacterial diversity and antibiotic resistance genes of urban landscape waters replenished by reclaimed water and surface water in Xi'an, China. Pathogenic bacteria and antibiotic resistance genes (ARGs) in urban landscape waters may pose a potential threat to human health. However, the investigation of their occurrence in the urban landscape waters replenished by reclaimed water (RW) and surface water (SW) is still insufficient. The water samples collected from six urban landscape waters replenished by RW or SW were used to analyze bacterial diversity using high-throughput sequencing of 16S rRNA gene and to detect 18 ARGs and 2 integron-integrase genes by means of quantitative PCR array. Results indicated that Proteobacteria was the dominant phylum in all six urban landscape waters. The bacterial species richness was lower in urban landscape waters replenished by RW than that by SW. Sulfonamide resistance genes (sulI and sulIII) were the major ARGs in these urban landscape waters. No significant difference in the relative abundance of sulfonamide resistance genes, tetracycline resistance genes, and most of beta-lactam resistance genes was observed between RW-replenished and SW-replenished urban landscape waters. By contrast, the relative abundance of bla(ampC) gene and qnrA gene in RW-replenished urban landscape waters was significantly higher than that in SW-replenished urban landscape waters (p < 0.05), which suggested that use of RW may increase the amount of specific ARGs to urban landscape waters. Interestingly, among six urban landscape waters, RW-replenished urban landscape waters had a relatively rich variety of ARGs (12-15 of 18 ARGs) but a low relative abundance of ARGs (458.90-1944.67 copies/16S × 10(6)). The RW replenishment was found to have a certain impact on the bacterial diversity and prevalence of ARGs in urban landscape waters, which provide new insight into the effect of RW replenishment on urban landscape waters.202133786766
526110.9849Prevalence of antibiotic resistance genes from effluent of coastal aquaculture, South Korea. The wide use of antibiotics in aquaculture for prophylactic and therapeutic purposes can potentially lead to the prevalence of antibiotic resistance genes (ARGs). This study reports for the first time the profile of ARGs from effluents of coastal aquaculture located in South Jeolla province and Jeju Island, South Korea. Using quantitative PCR (qPCR), twenty-two ARGs encoding tetracycline resistance (tetA, tetB, tetD, tetE, tetG, tetH, tetM, tetQ, tetX, tetZ, tetBP), sulfonamide resistance (sul1, sul2), quinolone resistance (qnrD, qnrS, aac(6')-Ib-cr), β-lactams resistance (bla(TEM), bla(CTX), bla(SHV)), macrolide resistance (ermC), florfenicol resistance (floR) and multidrug resistance (oqxA) and a class 1 integrons-integrase gene (intI1) were quantified. In addition, Illumina Miseq sequencing was applied to investigate microbial community differences across fish farm effluents. Results from qPCR showed that the total number of detected ARGs ranged from 4.24 × 10(-3) to 1.46 × 10(-2) copies/16S rRNA gene. Among them, tetB and tetD were predominant, accounting for 74.8%-98.0% of the total ARGs. Furthermore, intI1 gene showed positive correlation with tetB, tetD, tetE, tetH, tetX, tetZ tetQ and sul1. Microbial community analysis revealed potential host bacteria for ARGs and intI1. Two genera, Vibrio and Marinomonas belonging to Gammaproteobacteria, showed significant correlation with tetB and tetD, the most dominant ARGs in all samples. Also, operational taxonomic units (OTUs)-based network analysis revealed that ten OTUs, classified into the phyla Proteobacteria, Cyanobacteria/Chloroplast, Bacteroidetes, Verrucomicrobia and an unclassified phylum, were potential hosts of tetracycline resistance genes (i.e., tetA, tetG, tetH, tetM, tetQ and tetZ). Further systematic monitoring of ARGs is warranted for risk assessment and management of antibacterial resistance from fish farm effluents.201829031406
349920.9848Diverse and abundant antibiotic resistance genes in mangrove area and their relationship with bacterial communities - A study in Hainan Island, China. Antibiotic resistance genes (ARGs) are emerging contaminants in the environment and have been highlighted as a worldwide environmental and health concern. As important participants in the biogeochemical cycles, mangrove ecosystems are subject to various anthropogenic disturbances, and its microbiota may be affected by various contaminants such as ARGs. This study selected 13 transects of mangrove-covered areas in Hainan, China for sediment sample collection. The abundance and diversity of ARGs and mobile genetic elements (MGEs) were investigated using high-throughput quantitative polymerase chain reaction (HT-qPCR), and high-throughput sequencing was used to study microbial structure and diversity. A total of 179 ARGs belonging to 9 ARG types were detected in the study area, and the detection rates of vanXD and vatE-01 were 100%. The abundance of ARGs was 8.30 × 10(7)-6.88 × 10(8) copies per g sediment (1.27 × 10(-2)-3.39 × 10(-2) copies per 16S rRNA gene), which was higher than similar studies, and there were differences in the abundance of ARGs in these sampling transects. The multidrug resistance genes (MRGs) accounted for the highest proportion (69.0%), which indicates that the contamination of ARGs in the study area was very complicated. The ARGs significantly positively correlated with MGEs, which showed that the high level of ARGs was related to its self-enhancement. The dominant bacteria at the genus level were Desulfococcus, Clostridium, Rhodoplanes, Bacillus, Vibrio, Enterococcus, Sedimentibacter, Pseudoalteromonas, Paracoccus, Oscillospira, Mariprofundus, Sulfurimonas, Aminobacterium, and Novosphingobium. There was a significant positive correlation between 133 bacterial genera and some ARGs. Chthoniobacter, Flavisolibacter, Formivibrio, Kaistia, Moryella, MSBL3, Perlucidibaca, and Zhouia were the main potential hosts of ARGs in the sediments of Hainan mangrove area, and many of these bacteria are important participants in biogeochemical cycles. The results contribute to our understanding of the distribution and potential hosts of ARGs and provide a scientific basis for the protection and management of Hainan mangrove ecosystem.202133652188
310530.9847Organic Houttuynia cordata Thunb harbors higher abundance and diversity of antibiotic resistance genes than non-organic origin, suggesting a potential food safe risk. The organic agricultural products has been growing rapidly in recent years. However, a potential food safe risk, resulted by introduction more antibiotic resistant genes (ARGs) accompanied with animal manure using to organic farming, has long been overlooked. In current study, the bacterial community, 22 tetracycline, 3 aminoglycoside and 4 β-lactams ARGs were respectively investigated in the organic, chemical and wild Houttuynia cordata Thunb (HCT). A total of 9 tetracycline, 3 aminoglycoside and 2 β-lactam ARG subtypes were detected, and the organic HCT harbored more ARG subtypes. The absolute and relative abundance of total ARGs in organic HCT was strikingly higher than that in chemical and wild HCT. The Enterobacteriaceae, Aeromonadaceae, Pseudomonadceae, Moraxellaceae and Oxalobacteraceae were the dominant taxa in the chemical and wild HCT, but in the organic HCT, only Enterobacteriaceae posed 83.23% - 87.40% of bacterial community. Fourteen bacterial families might be the possible hosts of ARG subtypes in the HCT. Enterobacteriaceae was a possible host of most ARG subtypes, including tetA, tetB, tetC, tetE and aadA, and it was the main bacteria affecting the behavior of ARGs in the HCT. Additionally, the tetracycline ARG subtypes had more possible hosts. These results help to better understand the ARG potential food safe risk and develop effective measures to prevent the ARG dissemination in organic agricultural product.201931000292
716440.9846Anthropogenic pressures amplify high-risk antibiotic resistome via co-selection among biocide resistance, virulence, and antibiotic resistance genes in the Ganjiang River basin: Drivers diverge in densely versus sparsely populated reaches. As the largest river in the Poyang Lake system, the Ganjiang River faces escalating anthropogenic pressures that amplify resistance gene dissemination. This study integrated antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and virulence factor genes (VFGs) to reveal their co-selection mechanisms and divergent environmental drivers between densely (DES) and sparsely populated (SPAR) regions of the Ganjiang River basin. The microbial and viral communities and structures differed significantly between the DES and SPAR regions (PERMANOVA, p < 0.001). Midstream DES areas were hotspots for ARGs/BRGs/VFGs enrichment, with peak enrichment multiples reaching 10.2, 5.7, and 5.9-fold respectively. Procrustes analysis revealed limited dependence of ARGs transmission on mobile genetic elements (MGEs) (p > 0.05). Separately, 74 % of dominant ARGs (top 1 %) showed strong correlations with BRGs (r(2) = 0.973, p < 0.01) and VFGs (r(2) = 0.966, p < 0.01) via co-selection. Pathogenic Pseudomonas spp. carrying multidrug-resistant ARGs, BRGs, and adhesion-VFGs were identified as high-risk vectors. In SPAR areas, anthropogenic pressure directly dominated ARGs risk (RC = 54.2 %, β = 0.39, p < 0.05), with biological factors as secondary contributors (RC = 45.8 %, β = 0.33, p < 0.05). In contrast, DES regions showed anthropogenic pressure exerting broader, enduring influences across microorganisms, physicochemical parameters, and biological factors, escalating ARGs risks through diverse pathways, with BRGs/VFGs acting as direct drivers. This study proposes establishing a risk prevention system using BRGs and pathogenic microorganisms as early-warning indicators.202540858019
722150.9846Profiles of bacteria/phage-comediated ARGs in pig farm wastewater treatment plants in China: Association with mobile genetic elements, bacterial communities and environmental factors. In this study, the profiles of bacteria/phage-comediated antibiotic resistance genes (b/pARGs) were monitored in water samples collected from 45 pig farm wastewater treatment plants (WWTPs) in seven different regions of China. We found that 8 major types and 112 subtypes of b/pARGs were detected in all the water samples, and the detected number ranged from 53 to 92. The absolute abundances of bARGs and pARGs in the influent were as high as 10(9) copies/mL and 10(6) copies/mL, respectively. Anaerobic anoxic/oxic (AAO) and anaerobic short-cut nitrification/denitrification (ASND) treatment plants can effectively reduce the absolute abundance and amount of b/pARGs. Anaerobic treatment plants cannot reduce the absolute abundance of pARGs, and even increase the amount of pARGs. Mobile genetic elements (MGEs), bacterial communities and environmental factors were important factors impacting the b/pARG profile. Among these factors, the bacterial community was the major driver that impacted the bARG profile, while bacterial community and MGEs were the major codrivers impacting the pARG profile. This study was the first to investigate the profiles of b/pARGs in pig farm WWTPs in China on such a large scale, providing a reference for the prevention and control of ARG pollution in agricultural environments.202133069996
350160.9846Microbial community and antibiotic resistance gene distribution in food waste, anaerobic digestate, and paddy soil. The study assessed the occurrence and distribution of microbial community and antibiotic resistance genes (ARGs) in food waste, anaerobic digestate, and paddy soil samples, and revealed the potential hosts of ARGs and factors influencing their distribution. A total of 24 bacterial phyla were identified, of which 16 were shared by all samples, with Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria accounting for 65.9-92.3 % of the total bacterial community. Firmicutes was the most abundant bacteria in food waste and digestate samples, accounting for 33-83 % of the total microbial community. However, in paddy soil samples with digestate, Proteobacteria had the highest relative abundance of 38-60 %. Further, 22 ARGs were detected in food waste and digestate samples, with multidrug, macrolide-lincosamide-streptogramin (MLS), bacitracin, aminoglycoside, tetracycline, vancomycin, sulfonamide, and rifamycin resistance genes being the most abundant and shared by all samples. The highest total relative abundance of ARGs in food waste, digestate, and soil without and with digestate was detected in samples from January 2020, May 2020, October 2019, and May 2020, respectively. The MLS, vancomycin, tetracycline, aminoglycoside, and sulfonamide resistance genes had higher relative abundance in food waste and anaerobic digestate samples, whereas multidrug, bacteriocin, quinolone, and rifampin resistance genes were more abundant in paddy soil samples. Redundancy analysis demonstrated that aminoglycoside, tetracycline, sulfonamide, and rifamycin resistance genes were positively correlated with total ammonia nitrogen and pH of food waste and digestate samples. Vancomycin, multidrug, bacitracin, and fosmidomycin resistance genes had positive correlations with potassium, moisture, and organic matter in soil samples. The co-occurrence of ARG subtypes with bacterial genera was investigated using network analysis. Actinobacteria, Proteobacteria, Bacteroidetes, and Acidobacteria were identified as potential hosts of multidrug resistance genes.202337196953
350670.9845Occurrence and distribution of antibiotic resistance genes in sediments in a semi-enclosed continental shelf sea. Extensive and improper overuse of antibiotics resulted in the prevalence of antibiotic resistance genes (ARGs). As the typical semi-enclosed continental shelf sea, the Bohai Sea has been considered as one of the most polluted marine areas in China. However, no comprehensive investigation on the spatial distribution of ARGs in sediments from the Bohai Sea has been reported. A large-scale sampling was performed in the Bohai Sea areas. The abundances of ARGs (6 classes, 29 ARG subtypes), class 1 integron-integrase gene (intI1), hmt-DNA and 16S rRNA gene were evaluated. IntI1 was detected with higher abundances in coastal areas ranging from 2.8 × 10(5) to 2.5 × 10(8) copies/g. The total ARGs abundances varied over 3 orders of magnitude in different sampling sites with the maximum at 4.9 × 10(8) copies/g. Sulfonamides resistance genes were ubiquitous and abundant with the abundances ranging from 5.7 × 10(4) to 1.8 × 10(7) copies/g, and quinolones resistance genes varied greatly in different samples. The contour map demonstrated that ARGs were more abundant in the Laizhou Bay, the south of Bohai Bay and the eastern of central sea basin. Most of the target ARG subtypes were detected with 100% detection frequencies. The genes of sul1, sul2 and tetX were detected with both higher absolute and relative abundance, while the abundance of β-lactams ARG subtypes was lower. Principal component analysis (PCA) and redundancy analysis (RDA) indicated that no significant differences in the ARGs abundance existed in different samples, and the sediment qualities played important roles in the distribution of ARGs. Bacterial communities were investigated and 768 strong and significant connections between ARGs and bacteria were identified. The possible hosts of ARGs were revealed by network analysis with higher relative abundance in coastal areas than the sea.202032325606
700980.9845Antibiotic resistance genes and bacterial communities in cornfield and pasture soils receiving swine and dairy manures. Land application of animal manure could change the profiles of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and bacterial communities in receiving soils. Using high-throughput real-time quantitative PCR and 16S rRNA amplicon sequencing techniques, this study investigated the ARGs and bacterial communities in field soils under various crop (corn and pasture) and manure (swine and dairy) managements, which were compared with those of two non-manured reference soils from adjacent golf course and grassland. In total 89 unique ARG subtypes were found in the soil samples and they conferred resistance via efflux pump, cellular protection and antibiotic deactivation. Compared to the ARGs in the golf course and grassland soils (28 and 34 subtypes respectively), manured soils generally had greater ARG diversity (36-55 subtypes). Cornfield soil frequently receiving raw swine manure had the greatest ARG abundance. The short-term (one week) application of composted and liquid swine manures increased the diversity and total abundance of ARGs in cornfield soils. Intriguingly the composted swine manure only marginally increased the total abundance of ARGs, but substantially increased the number of ARG subtypes in the cornfield soils. The network analysis revealed three major network modules in the co-occurrence patterns of ARG subtypes, and the hubs of these major modules (intl1-1, vanC, and pncA) may be candidates for selecting indicator genes for surveillance of ARGs in manured soils. The network analyses between ARGs and bacteria taxa revealed the potential host bacteria for the detected ARGs (e.g., aminoglycoside resistance gene aacC4 may be mainly carried by Acidobacteriaceae). Overall, this study highlighted the potentially varying impact of various manure management on antibiotic resistome and microbiome in cornfield and pasture soils.201930861417
687290.9845Insight into co-hosts of nitrate reduction genes and antibiotic resistance genes in an urban river of the qinghai-tibet plateau. Microbial co-hosts of nitrate reduction genes (NRGs) and antibiotic resistance genes (ARGs) have been recently reported, but their ecology and biochemical role in urban waterways remain largely unknown. Here, we collected 29 surface water and 29 sediment samples in the Huangshui River on the Qinghai-Tibet Plateau during the wet and dry season, and 11 water samples from wastewater treatment plants and wetlands along the river. Using metagenomic sequencing, we retrieved 278 medium-to-high-quality metagenome-assembled genomes (MAGs) of NRG-ARG co-hosts, mainly belonging to the phyla Proteobacteria, Actinobacteriota, and Bacteroidota. Of microorganisms carrying ARGs, a high proportion (75.3%‒94.9%) also encoded NRGs, supporting nitrate reducing bacteria as dominant hosts of ARGs. Seasonal changes in antibiotic levels corresponded to significant variation in the relative abundance of NRG-ARG co-host in both water and sediments, resulting in a concomitant change in antibiotic resistance pathways. In contrast, the contribution of NRG-ARG co-hosts to nitrate reduction was stable between seasons. We identify specific antibiotics (e.g., sulphonamides) and microbial taxa (e.g., Acinetobacter and Hafnia) that may disproportionately impact these relationships to serve as a basis for laboratory investigations into bioremediation strategies. Our study suggests that highly abundant nitrate reducing microorganisms in contaminated environments may also directly impact human health as carriers of antibiotic resistance.202236215840
7237100.9845Dominant denitrifying bacteria are important hosts of antibiotic resistance genes in pig farm anoxic-oxic wastewater treatment processes. The anoxic-oxic (A/O) wastewater treatment process that is widely used in pig farms in China is an important repository for antibiotic resistance genes (ARGs). However, the distribution of ARGs and their hosts in the A/O process has not been well characterized. In this study, the wastewaters in the anoxic and oxic tanks for A/O processes were collected from 38 pig farms. The concentrations of 20 subtypes of ARGs, 5 denitrification-related genes, 2 integrons, and bacterial community composition were investigated. Bacterial genome binning was performed using metagenome sequencing. In this study, 20 subtypes of ARGs and integrons were detected in all sampling sites. A total of 16 of the 20 subtypes of ARGs were detected with the highest abundance in anoxic tanks, and sul1 was detected with a maximum average abundance of 19.21 ± 0.24 log(10) (copies/mL). Cooccurrence patterns were observed for some genes in the pig farm A/O process, such as sul1 and intl1, sul1 and tetG, and tetO and tetW. There was a significant cooccurrence pattern between the dominant denitrifying bacteria and some ARGs (bla(TEM), ermB, tetC, tetH and tetQ), so the dominant denitrifying bacteria were considered to be potential ARG hosts. In addition, 170 highly abundant bacterial genome bins were assembled and further confirmed that the denitrifying bacteria Brachymonas, Candidatus Competibacter, Thiobacillus and Steroidobacter were the important ARG hosts in the pig farm A/O process, providing a useful reference for the surveillance and risk management of ARGs in pig farm wastewater.202032615347
7167110.9844Occurrence and distribution of antibiotic pollution and antibiotic resistance genes in seagrass meadow sediments based on metagenomics. Seagrass meadows are one of the most important coastal ecosystems that provide essential ecological and economic services. The contamination levels of antibiotic and antibiotic resistance genes (ARGs) in coastal ecosystems are severely elevated owing to anthropogenic disturbances, such as terrestrial input, aquaculture effluent, and sewage discharge. However, few studies have focused on the occurrence and distribution of antibiotics and their corresponding ARGs in this habitat. Thus, we investigated the antibiotic and ARGs profiles, microbial communities, and ARG-carrying host bacteria in typical seagrass meadow sediments collected from Swan Lake, Caofeidian shoal harbor, Qingdao Bay, and Sishili Bay in the Bohai Sea and northern Yellow Sea. The total concentrations of 30 detected antibiotics ranged from 99.35 to 478.02 μg/kg, tetracyclines were more prevalent than other antibiotics. Metagenomic analyses showed that 342 ARG subtypes associated with 22 ARG types were identified in the seagrass meadow sediments. Multidrug resistance genes and RanA were the most dominant ARG types and subtypes, respectively. Co-occurrence network analysis revealed that Halioglobus, Zeaxanthinibacter, and Aureitalea may be potential hosts at the genus level, and the relative abundances of these bacteria were higher in Sishili Bay than those in other areas. This study provided important insights into the pollution status of antibiotics and ARGs in typical seagrass meadow sediments. Effective management should be performed to control the potential ecological health risks in seagrass meadow ecosystems.202438782270
3483120.9844Abundance and diversity of antibiotic resistance genes and bacterial communities in the western Pacific and Southern Oceans. This study investigated the abundance and diversity of antibiotic resistance genes (ARGs) and the composition of bacterial communities along a transect covering the western Pacific Ocean (36°N) to the Southern Ocean (74°S) using the Korean icebreaker R/V Araon (total cruise distance: 14,942 km). The relative abundances of ARGs and bacteria were assessed with quantitative PCR and next generation sequencing, respectively. The absolute abundance of ARGs was 3.0 × 10(6) ± 1.6 × 10(6) copies/mL in the western Pacific Ocean, with the highest value (7.8 × 10(6) copies/mL) recorded at a station in the Tasman Sea (37°S). The absolute abundance of ARGs in the Southern Ocean was 1.8-fold lower than that in the western Pacific Ocean, and slightly increased (0.7-fold) toward Terra Nova Bay in Antarctica, possibly resulting from natural terrestrial sources or human activity. β-Lactam and tetracycline resistance genes were dominant in all samples (88-99%), indicating that they are likely the key ARGs in the ocean. Correlation and network analysis showed that Bdellovibrionota, Bacteroidetes, Cyanobacteria, Margulisbacteria, and Proteobacteria were positively correlated with ARGs, suggesting that these bacteria are the most likely ARG carriers. This study highlights the latitudinal profile of ARG distribution in the open ocean system and provides insights that will help in monitoring emerging pollutants on a global scale.202235085628
3072130.9844Faecal microbiota and antibiotic resistance genes in migratory waterbirds with contrasting habitat use. Migratory birds may have a vital role in the spread of antimicrobial resistance across habitats and regions, but empirical data remain scarce. We investigated differences in the gut microbiome composition and the abundance of antibiotic resistance genes (ARGs) in faeces from four migratory waterbirds wintering in South-West Spain that differ in their habitat use. The white stork Ciconia ciconia and lesser black-backed gull Larus fuscus are omnivorous and opportunistic birds that use highly anthropogenic habitats such as landfills and urban areas. The greylag goose Anser anser and common crane Grus grus are herbivores and use more natural habitats. Fresh faeces from 15 individuals of each species were analysed to assess the composition of bacterial communities using 16S rRNA amplicon-targeted sequencing, and to quantify the abundance of the Class I integron integrase gene (intI1) as well as genes encoding resistance to sulfonamides (sul1), beta-lactams (bla(TEM), bla(KPC) and bla(NDM)), tetracyclines (tetW), fluoroquinolones (qnrS), and colistin (mcr-1) using qPCR. Bacterial communities in gull faeces were the richest and most diverse. Beta diversity analysis showed segregation in faecal communities between bird species, but those from storks and gulls were the most similar, these being the species that regularly feed in landfills. Potential bacterial pathogens identified in faeces differed significantly between bird species, with higher relative abundance in gulls. Faeces from birds that feed in landfills (stork and gull) contained a significantly higher abundance of ARGs (sul1, bla(TEM), and tetW). Genes conferring resistance to last resort antibiotics such as carbapenems (bla(KPC)) and colistin (mcr-1) were only observed in faeces from gulls. These results show that these bird species are reservoirs of antimicrobial resistant bacteria and suggest that waterbirds may disseminate antibiotic resistance across environments (e.g., from landfills to ricefields or water supplies), and thus constitute a risk for their further spread to wildlife and humans.202133872913
3502140.9843Microbial dynamics in a swine wastewater treatment plant and prediction of potential hosts of antibiotic resistance genes. Using a culture-independent approach, this study aimed to evaluate microbial community changes in a swine wastewater treatment plant (SWWTP) and investigate the presence of bacteria for public health concerns, particularly those harboring antibiotic resistance genes (ARG) with pathogenic potential. Through sequencing of fifteen samples collected across five sampling campaigns - at the influent, biodigester outlet, and final effluent - higher microbial diversity was observed in the untreated waste, reflected by a greater relative abundance of operational taxonomic units (OTUs) linked to the families Streptococcaceae (up to 27 %), unidentified members of the order Clostridiales (up to 33 %), and Moraxellaceae (up to 19 %). A microbial succession was observed across subsequent treatment stages, characterized by an increased relative abundance of OTUs associated with Clostridiaceae (0-68 %) and Peptostreptococcaceae (8-25 %), likely driven by environmental conditions. Sequences related to the order Clostridiales and the family Moraxellaceae showed correlations with the resistance genes blaTEM, ermB, qnrB, sul1, and tetA, suggesting that members of these groups could serve as potential gene hosts. The detection of residual ARGs and OTUs related to potentially pathogenic genera such as Clostridium butyricum and Terrisporobacter glycolicus species in the treated effluent raises concerns about the final disposal of this waste, given the possibility of horizontal gene transfer in the environment.202541145054
7214150.9843Long-term application of fresh and composted manure increase tetracycline resistance in the arable soil of eastern China. The aim of this study was to compare the occurrence, abundance, and diversity of tetracycline resistance genes (tet) in agricultural soils after 6 years' application of fresh or composted swine manure. Soil samples were collected from fresh or composted manure-treated farmland at three depths (0-5 cm, 5-10 cm, and 10-20 cm). Nine classes of tet genes [tetW, tetB(P), tetO, tetS, tetC, tetG, tetZ, tetL, and tetX] were detected; tetG, tetZ, tetL, and tetB(P) were predominant in the manure-treated soil. The abundances of tetB(P), tetW, tetC, and tetO were reduced, while tetG and tetL were increased by fertilizing with composted versus fresh manure; thus, the total abundance of tet genes was not significantly reduced by compost manuring. tetG was the most abundant gene in manure-treated soil; the predominant tetG genotypes shared high homology with pathogenic bacteria. The tetG isolates were more diverse in soils treated with fresh versus composted manure, although the residual tet genes in composted manure remain a pollutant and produce a different influence on the tet gene resistome in field soil.201525460961
7213160.9842Distribution characteristics of antibiotic resistant bacteria and genes in fresh and composted manures of livestock farms. Livestock manure is a major reservoir of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). This study investigated the distribution characteristics of ARB, ARGs in fresh and composted manures of traditional breading industry in rural areas in China. Samples collected were naturally piled without professional composting, and will be applied to farmland. The real-time quantitative polymerase chain reaction (qPCR) results showed the presence of ten target ARGs and two mobile genetic elements (MGEs) in the tested manure samples. The relative abundance of tetracycline and sulfonamide resistance genes (TRGs and SRGs) was generally higher than that of macrolide resistance genes (MRGs), followed by quinolone resistance genes (QRGs). There were significant positive correlations between the abundance of sul1, sul2, tetW and MGEs (intl1, intl2). In addition, the distribution of target ARGs was associated with the residual concentrations of doxycycline (DOX), sulfamethazine (SM2), enrofloxacin (ENR) and tylosin (TYL). Overall, a total of 24 bacterial genera were identified. The resistance rates of ARB were 17.79%-83.70% for SM2, followed 0.40%-63.77% for TYL, 0.36%-43.90% for DOX and 0.00%-13.36% for ENR, which showed a significant dose-effect. This study also demonstrated that the abundance of clinically relevant ARB and ARGs in chicken, swine and cow fresh manures significantly greater than that in composted manures, and chicken and swine manures had higher proportion of ARB and higher abundance of ARGs than that in cow manures.201931756854
7160170.9842High-throughput profiling of antibiotic resistance genes in the Yellow River of Henan Province, China. Profiling antibiotic resistance genes (ARGs) in the Yellow River of China's Henan Province is essential for understanding the health risks of antibiotic resistance. The profiling of ARGs was investigated using high-throughput qPCR from water samples in seven representative regions of the Yellow River. The absolute and relative abundances of ARGs and moble genetic elements (MGEs) were higher in summer than in winter (ANOVA, p < 0.001). The diversity and abundance of ARGs were higher in the Yellow River samples from PY and KF than the other sites. Temperature (r = 0.470 ~ 0.805, p < 0.05) and precipitation (r = 0.492 ~ 0.815, p < 0.05) positively influenced the ARGs, while pH had a negative effect (r = - 0.462 ~ - 0.849, p < 0.05). Network analysis indicated that the pathogenic bacteria Rahnella, Bacillus, and Shewanella were the possible hub hosts of ARGs, and tnpA1 was the potential MGE hub. These findings provide insights into the factors influencing ARG dynamics and the complex interaction among the MGEs, pathogenic bacteria and environmental parameters in enriching ARGs in the Yellow River of Henan Province.202439080455
3497180.9842Biomarkers of antibiotic resistance genes during seasonal changes in wastewater treatment systems. To evaluate the seasonal distribution of antibiotic resistance genes (ARGs) and explore the reason for their patterns in different seasons and different systems, two wastewater treatment systems were selected and analyzed using high-throughput qPCR. Linear discriminant analysis (LDA) effect size (LEfSe) was used to discover the differential ARGs (biomarkers) and estimate the biomarkers' effect size. We found that the total absolute abundances of ARGs in inflows and excess sludge samples had no obvious seasonal fluctuations, while those in winter outflow samples decreased in comparison with the inflow samples. Eleven differentially abundant ARGs (biomarker genes, BmGs) (aadA5-02, aac-6-II, cmlA1-01, cmlA1-02, blaOXA10-02, aadA-02, tetX, aadA1, ereA, qacEΔ1-01, and blaTEM) in summer samples and 10 BmGs (tet-32, tetA-02, aacC2, vanC-03, aac-6-I1, tetE, ermB, mefA, tnpA - 07, and sul2) in winter samples were validated. According to 16S rRNA gene sequencing, the relative abundance of bacteria at the phylum level exhibited significant seasonal changes in outflow water (OW), and biomarker bacteria (BmB) were discovered at the family (or genus) level. Synechococcus and vadinCA02 are BmB in summer, and Trichococcus, Lactococcus, Pelosinus, Janthinobacterium, Nitrosomonadaceae and Sterolibacterium are BmB in winter. In addition, BmB have good correlations with BmGs in the same season, which indicates that bacterial community changes drive different distributions of ARGs during seasonal changes and that LEfSe is an acute and effective method for finding significantly different ARGs and bacteria between two or more classes. In conclusion, this study demonstrated the seasonal changes of BmGs and BmB at two wastewater treatment systems.201829169020
3075190.9842Comparison of environmental microbiomes in an antibiotic resistance-polluted urban river highlights periphyton and fish gut communities as reservoirs of concern. Natural waterways near urban areas are heavily impacted by anthropogenic activities, including their microbial communities. A contaminant of growing public health concern in rivers is antibiotic resistant genes (ARGs), which can spread between neighboring bacteria and increase the potential for transmission of AR bacteria to animals and humans. To identify the matrices of most concern for AR, we compared ARG burdens and microbial community structures between sample types from the Scioto River Watershed, Ohio, the United States, from 2017 to 2018. Five environmental matrices (water, sediment, periphyton, detritus, and fish gut) were collected from 26 river sites. Due to our focus on clinically relevant ARGs, three carbapenem resistance genes (bla(KPC), bla(NDM), and bla(OXA-48)) were quantified via DropletDigital™ PCR. At a subset of nine urbanized sites, we conducted16S rRNA gene sequencing and functional gene predictions. Carbapenem resistance genes were quantified from all matrices, with bla(KPC) being the most detected (88 % of samples), followed by bla(NDM) (64 %) and bla(OXA-48) (23 %). Fish gut samples showed higher concentrations of bla(KPC) and bla(NDM) than any other matrix, indicating potential ARG bioaccumulation, and risk of broader dissemination through aquatic and nearshore food webs. Periphyton had higher concentrations of bla(NDM) than water, sediment, or detritus. Microbial community analysis identified differences by sample type in community diversity and structure. Sediment samples had the most diverse microbial communities, and detritus, the least. Spearman correlations did not reveal significant relationships between the concentrations of the monitored ARGs and microbial community diversity. However, several differentially abundant taxa and microbial functions were identified by sample type that is definitive of these matrices' roles in the river ecosystem and habitat type. In summary, the fish gut and periphyton are a concern as AR reservoirs due to their relatively high concentration of carbapenem resistance genes, diverse microbial communities, and natural functions that promote AR.202235973543