Occurrence of human pathogenic bacteria carrying antibiotic resistance genes revealed by metagenomic approach: A case study from an aquatic environment. - Related Documents




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348401.0000Occurrence of human pathogenic bacteria carrying antibiotic resistance genes revealed by metagenomic approach: A case study from an aquatic environment. Antibiotic resistance genes (ARGs), human pathogenic bacteria (HPB), and HPB carrying ARGs are public issues that pose a high risk to aquatic environments and public health. Their diversity and abundance in water, intestine, and sediments of shrimp culture pond were investigated using metagenomic approach. A total of 19 classes of ARGs, 52 HPB species, and 7 species of HPB carrying ARGs were found. Additionally, 157, 104, and 86 subtypes of ARGs were detected in shrimp intestine, pond water, and sediment samples, respectively. In all the samples, multidrug resistance genes were the highest abundant class of ARGs. The dominant HPB was Enterococcus faecalis in shrimp intestine, Vibrio parahaemolyticus in sediments, and Mycobacterium yongonense in water, respectively. Moreover, E. faecalis (contig Intestine_364647) and Enterococcus faecium (contig Intestine_80272) carrying efrA, efrB and ANT(6)-Ia were found in shrimp intestine, Desulfosaricina cetonica (contig Sediment_825143) and Escherichia coli (contig Sediment_188430) carrying mexB and APH(3')-IIa were found in sediments, and Laribacter hongkongensis (contig Water_478168 and Water_369477), Shigella sonnei (contig Water_880246), and Acinetobacter baumannii (contig Water_525520) carrying sul1, sul2, ereA, qacH, OXA-21, and mphD were found in pond water. Mobile genetic elements (MGEs) analysis indicated that horizontal gene transfer (HGT) of integrons, insertion sequences, and plasmids existed in shrimp intestine, sediment, and water samples, and the abundance of integrons was higher than that of other two MGEs. The results suggested that HPB carrying ARGs potentially existed in aquatic environments, and that these contributed to the environment and public health risk evaluation.201930952342
537010.9993Airborne antibiotic resistance genes in Hong Kong kindergartens. Antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) have become a critical global public health issue in this century. There is increasing evidence for the presence and transmission of ARGs by air transmission. In this research, ARGs and ARB in air conditioner filter dust (AC dust) and urine samples from 55 kindergarten children in 17 kindergartens and nearby 10 soil samples in Hong Kong were analyzed. The results showed the presence of 16 ARG subtypes and the mobile genetic element (MGE) intI1 in AC dust, and 12 ARG subtypes in the soil samples. ARGs presenting resistance to sulfonamide (6.9 × 10(-3)-0.17) (expressed as relative abundance of the 16 S rRNA genes) were most abundant followed by macrolides (1.8 × 10(-3)-3.3 × 10(-2)), sul1, sul2 (sulfonamide), ermF (macrolides) and intI1 genes in AC dust in 17 kindergartens. For soil samples, 12 ARG subtypes and the intI1 were detected, and the genes providing resistance to sulfonamide (1.6 × 10(-3)-2.7 × 10(-1)) were the most abundant ARGs in the 10 soil samples, followed by tetracycline (ND-1.4 × 10(-2)). Multi-resistant bacteria with sul1, sul2, intI1, or tetQ were detected in all AC dust samples and some urine samples. Based on bacterial genera and ARG co-occurrence network analysis and Hong Kong's special geographical location and cultural environment, there might be two origins for the ARGs detected in the kindergartens: β-lactam/macrolide ARGs mainly derived from human medicine use and tetracycline/sulfonamide ARGs mainly from other areas, as well as IntI1 may play a role in the spread of ARGs in Hong Kong. The widely detection of ARGs in AC dust in kindergartens in Hong Kong highlights the need for the improvement of management measures.202032041021
349020.9993Monitoring and evaluation of antibiotic resistance genes in three rivers in northeast China. Antibiotic resistance genes (ARGs) have become an important public health problem. In this study, we used metagenomic sequencing to analyze the composition of ARGs in selected original habitats of northeast China, comprising three different rivers and riverbank soils of the Heilongjiang River, Tumen River, and Yalu River. Twenty types of ARG were detected in the water samples. The major ARGs were multidrug resistance genes, at approximately 0.5 copies/16S rRNA, accounting for 57.5% of the total ARG abundance. The abundance of multidrug, bacitracin, beta-lactam, macrolide-lincosamide-streptogramin, sulfonamide, fosmidomycin, and polymyxin resistance genes covered 96.9% of the total ARG abundance. No significant ecological boundary of ARG diversity was observed. The compositions of the resistance genes in the three rivers were very similar to each other, and 92.1% of ARG subtypes were shared by all water samples. Except for vancomycin resistance genes, almost all ARGs in riverbank soils were detected in the river water. About 31.05% ARGs were carried by Pseudomonas. Opportunistic pathogenic bacteria carrying resistance genes were mainly related to diarrhea and respiratory infections. Multidrug and beta-lactam resistance genes correlated positively with mobile genetic elements (MGEs), indicating a potential risk of diffusion. The composition of ARGs in three different rivers was similar, indicating that climate plays an important role in ARG occurrence. ARG subtypes in river water were almost completely the same as those in riverbank soil. ARGs had no significant geographical distribution characteristics. Many ARGs were carried by human pathogenic bacteria related to diarrhea and respiratory infections, such as Pseudomonas aeruginosa and Aeromonas caviae. In general, our results provide a valuable dataset of river water ARG distribution in northeast China. The related ecological and geographical distribution characteristics should be further explored.202235122641
716230.9992Dissemination of antibiotic resistance genes and human pathogenic bacteria from a pig feedlot to the surrounding stream and agricultural soils. The dissemination of antibiotic resistance genes (ARGs), human pathogenic bacteria (HPB), and antibiotic-resistant HPB (ARHPB) from animal feedlot to nearby environment poses a potentially high risk to environmental ecology and public health. Here, a metagenomic analysis was employed to explore the dissemination of ARGs, HPB, and ARHPB from a pig feedlot to surrounding stream and agricultural soils. In total, not detectable (ND)-1,628.4 μg/kg of antibiotic residues, 18 types of ARGs, 48 HPB species, and 216 ARB isolates were detected in all samples. Antibiotic residues from pig feedlot mainly migrated into stream sediments and greenhouse soil. The dominant ARGs and HPB species from pig feedlot spread into stream sediments (tetracycline resistance genes, Clostridium difficile, and Mycobacterium tuberculosis), stream water (multidrug resistance (MDR) genes, Shigella flexneri, and Bordetella pertussis), and greenhouse soil (MDR genes, Bacillus anthracis, and Brucella melitensis). It is concerning that 54.4% of 216 ARB isolates from all samples were potential ARHPB species, and genome sequencing and functional annotation of 4 MDR HPB isolates showed 9 ARG types. Our findings revealed the potential migration and dissemination of antibiotic residues, ARGs, HPB, and ARHPB from pig feedlot to surrounding stream and agricultural soils via pig sewage discharge and manure fertilization.201829860105
537140.9992Prevalence of antimicrobial resistance in a full-scale drinking water treatment plant. Antibiotic resistance in drinking water has received increasing attention in recent years. In this study, the occurrence and abundance of antibiotic resistance genes (ARGs) in a drinking water treatment plant (DWTP) was comprehensively investigated using metagenomics. Bioinformatics analysis showed that 381 ARG subtypes belonging to 15 ARG types were detected, and bacitracin had the highest abundance (from 0.26 × 10(-2) to 0.86 copies/cell), followed by multidrug (from 0.57 × 10(-1) to 0.47 copies/cell) and sulfonamide (from 0.83 × 10(-2) to 0.35 copies/cell). Additionally, 933 ARG-carrying contigs (ACCs) were obtained from the metagenomic data, among which 153 contigs were annotated as pathogens. The most abundant putative ARG host was Staphylococcus (7.9%), which most frequently carried multidrug ARGs (43.2%). Additionally, 38 high-quality metagenome-assembled genomes (MAGs) were recovered, one of which was identified as Staphylococcus aureus (Bin.624) and harboured the largest number of ARGs (n = 16). Using the cultivation technique, 60 isolates were obtained from DWTP samples, and Staphylococcus spp. (n = 11) were found to be dominant in all isolates, followed by Bacillus spp. (n = 17). Antimicrobial susceptibility testing showed that most Staphylococcus spp. were multidrug resistant (MDR). These results deepen our understanding of the distribution profiles of ARGs and antibiotic resistant bacteria (ARB) in DWTPs for potential health risk evaluation. Our study also highlights the need for new and efficient water purification technologies that can be introduced and applied in DWTPs.202337331316
348550.9992Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach. In this study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community, and antibiotic resistance genes (ARGs). Utilizing data from Illumina platform, 4,174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, ∼86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium and (128) phages show the highest abundance and account for ∼90% of the total identified phages. In addition, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (∼69.3%) dominates the microbial population structure. Primarily, orders such as Caulobacterales (∼28%), Burkholderiales (∼13.9%), Actinomycetales (∼13.7%), and Pseudomonadales (∼7.5%) signify the core section. Furthermore, 21,869 (∼0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes), among which 4 ARG types, namely multidrug resistance (12,041 reads, ∼55%), bacitracin (3,202 reads, ∼15%), macrolide-lincosamide-streptogramin (1,744 reads, ∼7.98%), and fosmidomycin (990 reads, ∼4.53%), have the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15,919 reads). The results unveil the distribution of (pro)-phages; microbial community; and various ARGs in the Ganges river sediments.202133913739
348760.9992A comparison of antibiotic resistance genes and mobile genetic elements in wild and captive Himalayan vultures. As the most widely distributed scavenger birds on the Qinghai-Tibetan Plateau, Himalayan vultures (Gyps himalayensis) feed on the carcasses of various wild and domestic animals, facing the dual selection pressure of pathogens and antibiotics and are suitable biological sentinel species for monitoring antibiotic resistance genes (ARGs). This study used metagenomic sequencing to comparatively investigate the ARGs and mobile genetic elements (MGEs) of wild and captive Himalayan vultures. Overall, the resistome of Himalayan vultures contained 414 ARG subtypes resistant to 20 ARG types, with abundances ranging from 0.01 to 1,493.60 ppm. The most abundant resistance type was beta-lactam (175 subtypes), followed by multidrug resistance genes with 68 subtypes. Decreases in the abundance of macrolide-lincosamide-streptogramin (MLS) resistance genes were observed in the wild group compared with the zoo group. A total of 75 genera (five phyla) of bacteria were predicted to be the hosts of ARGs in Himalayan vultures, and the clinical (102 ARGs) and high-risk ARGs (35 Rank I and 56 Rank II ARGs) were also analyzed. Among these ARGs, twenty-two clinical ARGs, nine Rank I ARG subtypes, sixteen Rank II ARG subtypes were found to differ significantly between the two groups. Five types of MGEs (128 subtypes) were found in Himalayan vultures. Plasmids (62 subtypes) and transposases (44 subtypes) were found to be the main MGE types. Efflux pump and antibiotic deactivation were the main resistance mechanisms of ARGs in Himalayan vultures. Decreases in the abundance of cellular protection were identified in wild Himalayan vultures compared with the captive Himalayan vultures. Procrustes analysis and the co-occurrence networks analysis revealed different patterns of correlations among gut microbes, ARGs, and MGEs in wild and captive Himalayan vultures. This study is the first step in describing the characterization of the ARGs in the gut of Himalayan vultures and highlights the need to pay more attention to scavenging birds.202439006014
320970.9992The Antibiotic Resistome and Its Association with Bacterial Communities in Raw Camel Milk from Altay Xinjiang. Raw camel milk is generally contaminated with varied microbiota, including antibiotic-resistant bacteria (ARB), that can act as a potential pathway for the spread of antibiotic resistance genes (ARGs). In this study, high-throughput quantitative PCR and 16S rRNA gene-based Illumine sequencing data were used to establish a comprehensive understanding of the antibiotic resistome and its relationship with the bacterial community in Bactrian camel milk from Xinjiang. A total of 136 ARGs and up to 1.33 × 10(8) total ARG copies per gram were identified, which predominantly encode resistance to β-lactamas and multidrugs. The ARGs' profiles were mainly explained by interactions between the bacteria community and physicochemical indicators (77.9%). Network analysis suggested that most ARGs exhibited co-occurrence with Corynebacterium, Leuconostoc and MGEs. Overall, raw camel milk serves as a reservoir for ARGs, which may aggravate the spread of ARGs through vertical and horizontal gene transfer in the food chain.202337959048
351580.9991Impact of reclaimed water irrigation on antibiotic resistance in public parks, Beijing, China. The abundance and distribution of antibiotics and antibiotic resistance genes (ARGs) in soils from six parks using reclaimed water in Beijing, China, were characterized. Three classes of commonly used antibiotics (tetracycles, quinolones, and sulfonamides) were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The highest concentrations of tetracyclines and quinolones were 145.2 μg kg(-1) and 79.2 μg kg(-1), respectively. Detected tetG, tetW, sulI, and sulII genes were quantified by quantitative PCR. ARGs exhibited various abundances for different park soils. The integrase gene (intI1) as an indicator of horizontal gene transfer potential was also detected in high abundance, and had significant positive correlation with tetG, sulI, and sulII genes, suggesting that intI1 may be involved in ARGs dissemination. Both sulII and intI1 clones had high homology with some classes of pathogenic bacteria, such as Klebsiella oxytoca, Acinetobacter baumannii, Shigella flexneri, which could trigger potential public health concern.201424071635
350690.9991Occurrence 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
5374100.9991Molecular characterization of antibiotic resistance in cultivable multidrug-resistant bacteria from livestock manure. Diverse antibiotic-resistance genes (ARGs) are frequently reported to have high prevalence in veterinary manure samples due to extensive use of antibiotics in farm animals. However, the characteristics of the distribution and transmission of ARGs among bacteria, especially among different species of multiple antibiotic-resistant bacteria (MARB), have not been well explored. By applying high-throughput sequencing methods, our study uncovered a vast MARB reservoir in livestock manure. The genera Escherichia, Myroides, Acinetobacter, Proteus, Ignatzschineria, Alcaligenes, Providencia and Enterococcus were the predominant cultivable MARB, with compositions of 40.6%-85.7%. From chicken manure isolates, 33 MARB were selected for investigation of the molecular characteristics of antibiotic resistance. A total of 61 ARGs and 18 mobile genetic elements (MGEs) were investigated. We found that 47 ARGs were widely distributed among the 33 MARB isolates. Each isolate carried 27-36 genes responsible for resistance to eight classes of antibiotics frequently used in clinic or veterinary settings. ARGs to the six classes of antibiotics other than streptogramins and vancomycin were present in all 33 MARB isolates with a prevalence of 80%-100%. A total of 12 MGEs were widely distributed among the 33 MARB, with intI1, IS26, ISaba1, and ISEcp1 simultaneously present in 100% of isolates. In addition, 9 gene cassettes within integrons and ISCR1 were detected among MARB isolates encoding resistance to different antibiotic classes. This is the first report revealing the general co-presence of multiple ARGs, various MGEs and ARG cassettes in different species of individual MARB isolates in chicken manure. The results highlight a much higher risk of ARGs spreading through livestock manure to humans than we expected.201728599203
3088110.9991Occurrence of sulfonamide and tetracycline-resistant bacteria and resistance genes in aquaculture environment. The occurrence of sulfonamide and tetracycline resistance and their pollution profile in the aquaculture environment of Tianjin, northern China, were investigated. The presence of antibiotic-resistant bacteria was identified and the corresponding antibiotic resistance genes (ARGs) were quantified at 6 aquaculture farms in Tianjin. Sulfonamide-resistance genes were prevalent and their concentrations were the highest detected (3.0 × 10(-5) to 3.3 × 10(-4) for sul1/16S rDNA, 2.0 × 10(-4) to 1.8 × 10(-3) for sul2/16S rDNA) among the various ARGs, most likely because the use of sulfonamides is more prevalent than tetracyclines in this area. Bacillus was the most dominant bacterial genus in both sulfamethoxazole resistant bacteria (63.27% of the total resistant bacteria) and tetracycline-resistant bacteria (57.14% of the total resistant bacteria). At least two of those genes (tetM, tetO, tetT, tetW, sul1 and sul2) were detected in the isolates of Bacillus cereus, Bacillus subtilis, Bacillus megaterium and Acinetobacter lwofii, and all of the above genes were detected in B. cereus, suggesting the occurrence of multi-resistance in the studied area. The genetic transfer of sul1 between intestinal bacteria (e.g., Enterococcus spp.) and indigenous bacteria (e.g., Bacillus spp.) was implied by phylogenetic analysis. Several strains of resistant opportunistic pathogens (e.g., Acinetobacter spp.) were found in indigenous bacteria, which increase the risk of ARGs to public health. Overall, this is the first study to comprehensively investigate the antibiotic resistance profile by analyzing the species of antibiotic-resistant bacteria and adopting qualitative and quantitative methods to investigate ARGs at a typical aquaculture area in northern China.201222377146
3514120.9991Potential risks of microplastics combined with superbugs: Enrichment of antibiotic resistant bacteria on the surface of microplastics in mariculture system. Microplastics have become emerging pollutants and served as potential vectors for harmful bacteria, while rare information on the emergency and propagation of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) on the surface of microplastics is available. This study investigated the enrichment of ARB, especially multi-antibiotic resistant bacteria (MARB), on the surface of microplastics in mariculture system. Polyethylene terephthalate accounted for the highest proportion (75%) in the collected microplastics. The counts of cultivable ARB in microplastic samples were 6.40 × 10(6)-2.48 × 10(8) cfu/g, which were 100-5000 times higher than those in water samples. The ratios of cultivable ARB to total cultivable bacteria from microplastic samples were higher than those from water samples. High-throughput sequencing showed that the diversity and abundance of cultivable ARB in the microplastic samples was high with the predominant bacterial genera of Vibrio, Muricauda and Ruegeria. Total 160 MARB isolates were obtained and most of isolates were obtained from the microplastic samples. MARB isolates resisting or intermediating to four and three antibiotics accounted for much higher proportions in the microplastic samples, and the higher percentage of antibiotic resistance was to penicillin, sulfafurazole, erythromycin and tetracycline. The dominant multiple antibiotic resistance profile was TET-SFX-ERY-PEN, which accounted for 25.4% in microplastic samples and 23.9% in water samples. In typical MARB isolates, the positive detection rate of ARGs was up to 80.0% in microplastic samples while that was 65.3% in water samples. Five types of class 1 integrons (intI1) associated gene cassette arrays and seven types of gene cassettes were detected in microplastic samples, which were more than those in water samples. These results revealed that microplastics were hazardous pollutants for the enrichment of ARB, especially superbugs, and the spread of antibiotic resistance.202031670243
3489130.9991Metagenomics-based antibiotic resistance genes diversity and prevalence risk revealed by pathogenic bacterial host in Taihu Lake, China. In recent decades, antibiotics and antibiotic resistance genes (ARGs) have been regarded as emerging pollutants. In Taihu Lake, as a typical representative of freshwater system in China, the ARGs occurrence and abundance was of great importance for ecological risk control and public health protection. In this research, high-throughput sequencing and metagenomics technique were used to investigate the seasonal ARGs profile in overlying water and sediment at typical area of Taihu Lake. Besides, taxonomy pattern of ARGs host bacteria and potential pathogens were identified. The results showed that 33 ARG subtypes and 11 ARG types were detected in research area, among which bacitracin, multidrug and sulfonamides resistance gene were with the highest abundance. The relative abundance of ARGs in overlying water and sediment ranged from 1.68 to 661.05 ppm and from 1.93 to 49.47 ppm, respectively. ARG host (18 bacteria genus) were identified and annotated, among which Clostridium botulinum, Pseudomonas aeruginosa and Klebsiella pneumonia were pathogenic bacteria. The pathogens were mostly detected at Xukou Bay in spring and fall, which might be caused by the inlet water from aquaculture area of Yangcheng Lake. Pseudomonas was the most abundant ARGs host (ant2ib, baca, bl2d_oxa2,mexb, mexf, mexw and oprn), which may facilitate the propagation of ARGs in freshwater system.202234292452
5357140.9991Occurrence and diversity of antibiotic resistance in untreated hospital wastewater. Antibiotics, antibiotic-resistant bacteria (ARB), antibiotic-resistance genes (ARGs), and mobile genetic elements (MGEs) have been reported in many environments. However, the investigation of their occurrence and diversity in untreated hospital wastewater is still insufficient. High concentrations of antibiotic residues were found in hospital wastewater using solid-phase extraction and UPLC-MS/MS analysis. The concentrations of six of 14 antibiotics reached μg/L levels in the hospital wastewater, which is higher than reported in other aquatic environments. Results of high-throughput sequencing analysis indicated that sequences affiliated to genera Escherichia and Acinetobacter were the predominant in the cultivable multiple-antibiotic-resistant bacteria (CMARB) recovered from the wastewater of three hospitals in China, with compositions of 34%-74%. Notably, several genera containing clinically pathogenic or opportunistic CMARB (e.g., Escherichia, Acinetobacter, Aeromonas, Myroides, Enterococcus, Proteus, Pseudomonas, and Streptococcus) were detected at high relative abundances in the wastewaters of the three hospitals. High-capacity quantitative PCR showed that 131-139 unique ARGs of the 178 targeted genes were detected in the hospital wastewaters. The high prevalence of five MGEs and 12 ARGs was confirmed with qPCR, and some positive correlations between ARGs and MGEs were identified, such as between intI1 and qnrD, intI2 and sul3, intI3 and tetX, Tn916/Tn1545 and sul2, and ISCR1 and sul3. These results suggest that highly abundant antibiotic-resistant pathogens and highly mobile ARGs already exist in the human body, and that their release from hospitals without effective treatment poses high risks to environments and human health.201829054666
7772150.9991Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant. BACKGROUND: Wastewater treatment plants are an essential part of maintaining the health and safety of the general public. However, they are also an anthropogenic source of antibiotic resistance genes. In this study, we characterized the resistome, the distribution of classes 1-3 integron-integrase genes (intI1, intI2, and intI3) as mobile genetic element biomarkers, and the bacterial and phage community compositions in the North End Sewage Treatment Plant in Winnipeg, Manitoba. Samples were collected from raw sewage, returned activated sludge, final effluent, and dewatered sludge. A total of 28 bacterial and viral metagenomes were sequenced over two seasons, fall and winter. Integron-integrase genes, the 16S rRNA gene, and the coliform beta-glucuronidase gene were also quantified during this time period. RESULTS: Bacterial classes observed above 1% relative abundance in all treatments were Actinobacteria (39.24% ± 0.25%), Beta-proteobacteria (23.99% ± 0.16%), Gamma-proteobacteria (11.06% ± 0.09%), and Alpha-proteobacteria (9.18 ± 0.04%). Families within the Caudovirales order: Siphoviridae (48.69% ± 0.10%), Podoviridae (23.99% ± 0.07%), and Myoviridae (19.94% ± 0.09%) were the dominant phage observed throughout the NESTP. The most abundant bacterial genera (in terms of average percent relative abundance) in influent, returned activated sludge, final effluent, and sludge, respectively, includes Mycobacterium (37.4%, 18.3%, 46.1%, and 7.7%), Acidovorax (8.9%, 10.8%, 5.4%, and 1.3%), and Polaromonas (2.5%, 3.3%, 1.4%, and 0.4%). The most abundant class of antibiotic resistance in bacterial samples was tetracycline resistance (17.86% ± 0.03%) followed by peptide antibiotics (14.24% ± 0.03%), and macrolides (10.63% ± 0.02%). Similarly, the phage samples contained a higher prevalence of macrolide (30.12% ± 0.30%), peptide antibiotic (10.78% ± 0.13%), and tetracycline (8.69% ± 0.11%) resistance. In addition, intI1 was the most abundant integron-integrase gene throughout treatment (1.14 × 10(4) gene copies/mL) followed by intI3 (4.97 × 10(3) gene copies/mL) while intI2 abundance remained low (6.4 × 10(1) gene copies/mL). CONCLUSIONS: Wastewater treatment successfully reduced the abundance of bacteria, DNA phage and antibiotic resistance genes although many antibiotic resistance genes remained in effluent and biosolids. The presence of integron-integrase genes throughout treatment and in effluent suggests that antibiotic resistance genes could be actively disseminating resistance between both environmental and pathogenic bacteria.202235033203
5301160.9991High 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
3086170.9991Seasonal variation, virulence gene and antibiotic resistance of Vibrio in a semi-enclosed bay with mariculture (Dongshan Bay, Southern China). In this study, the virulence genes, antibiotic resistance of culturable Vibrio and the environmental factors affecting Vibrio abundance were analyzed in four seasons in DongShan Bay with different intensity of aquaculture practice. A total of 253 bacteria isolates were obtained, of which 177 Vibrio strains belonged to 26 species. Annual Vibrio abundance in this region ranged from 20 to 11,600 CFU mL(-1) and the most significant positive correlation occurred with temperature. Detection of 9 different Vibrio virulence genes revealed that most isolates contained atypical virulence genes in addition to the typical ones. In particular, virulence genes of hemolysin such as tdh, trh, and hlyA (6.32 %, 15.52 %, and 11.30 %) showed different degrees of horizontal gene transfer (HGT). In our antibiotic resistance test, the multiple antibiotic resistance (MAR) index of the isolates ranged from 0.01 to 0.03 in different seasons, and three MAR Vibrio strains were detected. Overall, our study sheds new light on the spatial distribution patterns and the occurrence of virulence genes and antibiotics resistance Vibrio isolated from a subtropical bay with intensive aquaculture. Our study provides a suitable microbial quality surveillance in a mariculture impacted coastal environment. It will help to establish effective disease prevention measures in this area and provide useful guidance and support for formulating local antibiotics use policies.202236113173
3486180.9990Insights into antibiotic and heavy metal resistance interactions in Escherichia coli isolated from livestock manure and fertilized soil. Heavy metal and antibiotic-resistant bacteria from livestock feces are ecological and public health problems. However, the distribution and relationships of antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs), and virulence factors (VFs) and their transmission mechanisms remain unclear. Therefore, we investigated the resistance of Escherichia coli, the prevalence of its ARGs, HMRGs, and VFs, and their transmission mechanisms in livestock fresh feces (FF), composted feces (CF), and fertilized soil (FS). In total, 99.54% (n = 221) and 91.44% (n = 203) of E. coli were resistant to at least one antibiotic and one heavy metal, respectively. Additionally, 72.52% (n = 161) were multi-drug resistant (MDR), of which Cu-resistant E. coli accounted for 72.67% (117/161). More than 99.34% (88/89) of E. coli carried multidrug ARGs, VFs, and the Cu resistance genes cueO and cusABCRFS. The Cu resistance genes cueO and cusABCRFS were mainly located on chromosomes, and cueO and cusF were positively associated with HMRGs, ARGs, and VFs. The Cu resistance genes pcoABCDRS were located on the plasmid pLKYL-P02 flanked by ARGs in PF18C from FF group and on chromosomes flanked by HMRGs in SAXZ1-1 from FS group. These results improved our understanding of bacterial multidrug and heavy metal resistance in the environment.202438154221
7159190.9990Profiles and natural drivers of antibiotic resistome in multiple environmental media in penguin-colonized area in Antarctica. Profiles and driving mechanisms of antibiotic resistome in the polar region are important for exploring the natural evolution of antibiotic resistance genes (ARGs). Here, we evaluated the profiles of antibiotic resistome in multiple media on Inexpressible Island, Terra Nova Bay, Antarctica. Average concentrations of ARGs in intracellular DNA (iARGs) among water (3.98 × 10(6) copies/L), soil (3.41 × 10(7) copies/kg), and penguin guano (7.04 × 10(7) copies/kg) were higher than those of ARGs in extracellular DNA (eARGs) among water (1.99 × 10(4) copies/L), soil (1.75 × 10(6) copies/kg), and penguin guano (8.02 × 10(6) copies/kg). It was indicated that the transmission of ARGs across different media occurs with around 77.8% of iARGs from soil and 86.7% of iARGs from penguins observed in water, and 80.7% of iARGs and 56.7% of eARGs from penguins found in soil. Annual inputs of ARGs from Adélie penguins on Inexpressible Island have increased since 1983. Bacitracin, multidrug, and aminoglycoside resistance genes were the main ARGs among water, soil, and penguin guano. Primary medium-risk ARGs associated with human pathogenic bacteria were multidrug resistance genes, and main low-risk ARGs associated with mobile genetic elements (MGEs) were aminoglycoside resistance genes. Antibiotic-resistant bacteria (ARB) from soil and penguins were more phylogenetically related to aquatic antibiotic-resistant mesophiles than aquatic antibiotic-resistant psychrophiles. MGEs, ARB, bacterial diversities, antibiotics, and metals could explain total ARGs between water and soil. Intracellular MGEs were the most significant in-situ driver of iARGs in water, reflecting that horizontal gene transfer could facilitate the spread of ARGs in water. Penguins were important ex-situ drivers of environmental antibiotic resistome, which was linked with risky ARGs between water and soil. These findings highlight the major roles of natural drivers (e.g., MGEs and penguins) in shaping environmental antibiotic resistome in polar areas, improving our understanding of the evolution of environmental microbiome.202540166126