Metagenomic Analysis Reveals the Fate of Antibiotic Resistance Genes in a Full-Scale Wastewater Treatment Plant in Egypt
Abstract
:1. Introduction
2. Materials & Methods
2.1. Sample Collection and Processing
2.2. DNA Extraction
2.3. Metagenomic Sequencing and Bioinformatic Analysis
3. Results
3.1. Metagenomic Sequencing
3.2. Profiling of ARGs
3.3. ARGs Persistence in Influent
4. Removal Efficiency of ARG Types and Subtypes from Influent to Effluent
5. Microbial Composition of Metagenomic Datasets
6. Discussion
7. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
References
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Sample Name | Count of Raw Reads (PE-150 bp) | Count of Reads after QC Filter (PE-150 bp) | Total Read Size (bp) | Q20% | GC% | MG-RAST_ID |
---|---|---|---|---|---|---|
INF_W | 137,739,660 | 121,944,908 | 18,291,736,200 | 96.13% | 51.11% | mgm4754064.3 |
INF_S | 154,503,234 | 119,535,370 | 17,930,305,500 | 97.22% | 57.24% | mgm4757477.3 |
EFF_W | 112,815,582 | 100,211,020 | 15,031,653,000 | 96.04% | 52.68% | mgm4760706.3 |
EFF_S | 161,601,122 | 125,803,650 | 18,870,547,500 | 97.15% | 57.27% | mgm4798629.3 |
SL_W | 167,104,122 | 148,048,024 | 22,207,203,600 | 95.53% | 57.68% | mgm4798679.3 |
SL_S | 167,341,294 | 126,323,822 | 18,948,573,300 | 97.27% | 60.55% | mgm4798702.3 |
Totals | 901,105,014 | 741,866,794 | 111,280,019,100 |
ARG_Type | Average ARG Type Abundance/16s rRNA Gene Copies | Average ARG Type Abundance Percentage | ||||
---|---|---|---|---|---|---|
INF | EFF | SL | INF | EFF | SL | |
aminoglycoside | 0.49249 | 0.27827 | 0.27436 | 14.51% | 17.93% | 23.54% |
bacitracin | 0.20776 | 0.04949 | 0.12194 | 6.12% | 3.19% | 10.46% |
beta-lactam | 0.56731 | 0.23430 | 0.15422 | 16.72% | 15.09% | 13.23% |
bleomycin | 0.00007 | 0.00000 | 0.00000 | 0.00% | 0.00% | 0.00% |
chloramphenicol | 0.17374 | 0.09708 | 0.04270 | 5.12% | 6.25% | 3.66% |
fosfomycin | 0.00345 | 0.00133 | 0.00029 | 0.10% | 0.09% | 0.03% |
fosmidomycin | 0.03518 | 0.00625 | 0.00219 | 1.04% | 0.40% | 0.19% |
kasugamycin | 0.03480 | 0.00659 | 0.00177 | 1.03% | 0.42% | 0.15% |
MLS* | 0.17033 | 0.07764 | 0.10525 | 5.02% | 5.00% | 9.03% |
multidrug | 0.72730 | 0.22423 | 0.12269 | 21.44% | 14.44% | 10.53% |
polymyxin | 0.02261 | 0.00573 | 0.00336 | 0.67% | 0.37% | 0.29% |
quinolone | 0.05330 | 0.02437 | 0.01018 | 1.57% | 1.57% | 0.87% |
rifamycin | 0.01824 | 0.00736 | 0.00370 | 0.54% | 0.47% | 0.32% |
sulfonamide | 0.18931 | 0.20277 | 0.19647 | 5.58% | 13.06% | 16.86% |
tetracycline | 0.39135 | 0.22796 | 0.08977 | 11.53% | 14.68% | 7.70% |
trimethoprim | 0.09795 | 0.05218 | 0.01830 | 2.89% | 3.36% | 1.57% |
unclassified | 0.20608 | 0.05600 | 0.01498 | 6.07% | 3.61% | 1.29% |
vancomycin | 0.00174 | 0.00079 | 0.00320 | 0.05% | 0.05% | 0.27% |
Totals | 3.39303 | 1.55233 | 1.16537 |
ARG Type | Average Abundance/16s-rRNA Gene Copies | Removal Efficiency | |
---|---|---|---|
Influent | Effluent | ||
aminoglycoside | 0.49249 | 0.27827 | 97.25% |
bacitracin | 0.20776 | 0.04949 | 98.70% |
beta-lactam | 0.56731 | 0.23430 | 97.93% |
bleomycin | 0.00007 | 0.00000 | 99.75% |
chloramphenicol | 0.17374 | 0.09708 | 97.28% |
fosfomycin | 0.00345 | 0.00133 | 98.05% |
fosmidomycin | 0.03518 | 0.00625 | 98.97% |
kasugamycin | 0.03480 | 0.00659 | 98.91% |
MLS* | 0.17033 | 0.07764 | 97.74% |
multidrug | 0.72730 | 0.22423 | 98.39% |
polymyxin | 0.02261 | 0.00573 | 98.63% |
quinolone | 0.05330 | 0.02437 | 97.73% |
rifamycin | 0.01824 | 0.00736 | 97.97% |
sulfonamide | 0.18931 | 0.20277 | 95.02% |
tetracycline | 0.39135 | 0.22796 | 97.18% |
trimethoprim | 0.09795 | 0.05218 | 97.40% |
unclassified | 0.20608 | 0.05600 | 98.55% |
vancomycin | 0.00174 | 0.00079 | 97.73% |
Totals | 3.39303 | 1.55233 | 97.73% |
Phylum | Influent | Effluent | Activated Sludge | ||||||
---|---|---|---|---|---|---|---|---|---|
INF_W | INF_S | INF Avg | EFF_W | EFF_S | EFF Avg | SL_W | SL_S | SL Avg | |
Acidobacteria | 0.01 | 0.10 | 0.05 | 0.00 | 0.12 | 0.06 | 0.06 | 0.96 | 0.51 |
Actinobacteria | 1.60 | 1.02 | 1.31 | 4.27 | 7.41 | 5.84 | 2.65 | 8.36 | 5.50 |
Bacteroidetes | 30.98 | 13.66 | 22.32 | 40.81 | 27.55 | 34.18 | 34.10 | 20.63 | 27.37 |
Chlamydiae | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.29 | 0.00 | 0.14 |
Chlorobi | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.55 | 0.00 | 0.28 |
Cyanobacteria | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 |
Deinococcus_Thermus | 0.00 | 0.00 | 0.00 | 0.02 | 0.13 | 0.07 | 0.00 | 0.00 | 0.00 |
Euryarchaeota | 0.04 | 0.08 | 0.06 | 0.10 | 0.02 | 0.06 | 0.05 | 0.16 | 0.11 |
Firmicutes | 19.55 | 8.66 | 14.11 | 11.00 | 11.41 | 11.20 | 2.32 | 5.21 | 3.76 |
Fusobacteria | 0.09 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
Lentisphaerae | 0.03 | 0.07 | 0.05 | 0.02 | 0.07 | 0.05 | 0.00 | 0.00 | 0.00 |
Proteobacteria | 47.47 | 75.40 | 61.43 | 43.45 | 52.28 | 47.86 | 59.98 | 64.61 | 62.29 |
Spirochaetes | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
Synergistetes | 0.04 | 0.64 | 0.34 | 0.00 | 0.19 | 0.09 | 0.00 | 0.08 | 0.04 |
Verrucomicrobia | 0.16 | 0.36 | 0.26 | 0.33 | 0.81 | 0.57 | 0.00 | 0.00 | 0.00 |
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Ali, O.S.; Hozayen, W.G.; Almutairi, A.S.; Edris, S.A.; Abulfaraj, A.A.; Ouf, A.A.; Mahmoud, H.M. Metagenomic Analysis Reveals the Fate of Antibiotic Resistance Genes in a Full-Scale Wastewater Treatment Plant in Egypt. Sustainability 2021, 13, 11131. https://doi.org/10.3390/su132011131
Ali OS, Hozayen WG, Almutairi AS, Edris SA, Abulfaraj AA, Ouf AA, Mahmoud HM. Metagenomic Analysis Reveals the Fate of Antibiotic Resistance Genes in a Full-Scale Wastewater Treatment Plant in Egypt. Sustainability. 2021; 13(20):11131. https://doi.org/10.3390/su132011131
Chicago/Turabian StyleAli, Osama S., Walaa G. Hozayen, Abdulwahab S. Almutairi, Sherif A. Edris, Aala A. Abulfaraj, Amged A. Ouf, and Hamada M. Mahmoud. 2021. "Metagenomic Analysis Reveals the Fate of Antibiotic Resistance Genes in a Full-Scale Wastewater Treatment Plant in Egypt" Sustainability 13, no. 20: 11131. https://doi.org/10.3390/su132011131