Standardization in global environmental antibiotic resistance genes (ARGs) surveillance

References

• Alcock, B. P., Huynh, W., Chalil, R., Smith, K. W., Raphenya, A. R., Wlodarski, M., Edalatmand, A., Petkau, A., Syed, A., Tsang, S. A., Baker, K. K., Dave, S. J. C., McCarthy, M., Mukiri, M. C., Nasir, K. M., Golbon, J. A., Imtiaz, B., Jiang, H., Kaur, X. J., … McArthur, A. G. (2022). CARD 2023: Expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research, 51(D1), D690–D699. https://doi.org/10.1093/nar/gkac920
   Web of Science ®Google Scholar
• Amarasinghe, S. L., Su, S., Dong, X., Zappia, L., Ritchie, M. E., & Gouil, Q. (2020). Opportunities and challenges in long-read sequencing data analysis. Genome Biology, 21(1), 30. https://doi.org/10.1186/s13059-020-1935-5
   PubMed Web of Science ®Google Scholar
• Arango-Argoty, G., Garner, E., Pruden, A., Heath, L. S., Vikesland, P., & Zhang, L. (2018). DeepARG: A deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome, 6(1), 23. https://doi.org/10.1186/s40168-018-0401-z
   PubMedGoogle Scholar
• Bengtsson-Palme, J., Hammarén, R., Pal, C., Östman, M., Björlenius, B., Flach, C.-F., Fick, J., Kristiansson, E., Tysklind, M., & Larsson, D. G. J. (2016). Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics. The Science of the Total Environment, 572, 697–712. https://doi.org/10.1016/j.scitotenv.2016.06.228
   PubMed Web of Science ®Google Scholar
• Bortolaia, V., Kaas, R. S., Ruppe, E., Roberts, M. C., Schwarz, S., Cattoir, V., Philippon, A., Allesoe, R. L., Rebelo, A. R., Florensa, A. F., Fagelhauer, L., Chakraborty, T., Neumann, B., Werner, G., Bender, J. K., Stingl, K., Nguyen, M., Coppens, J., Xavier, B. B., … Aarestrup, F. M. (2020). ResFinder 4.0 for predictions of phenotypes from genotypes. The Journal of Antimicrobial Chemotherapy, 75(12), 3491–3500. https://doi.org/10.1093/jac/dkaa345
   PubMed Web of Science ®Google Scholar
• Cao, Y. P., Raith, M. R., & Griffith, J. F. (2015). Droplet digital PCR for simultaneous quantification of general and human-associated fecal indicators for water quality assessment. Water Research, 70, 337–349. https://doi.org/10.1016/j.watres.2014.12.008
   PubMed Web of Science ®Google Scholar
• Che, Y., Xia, Y., Liu, L., Li, A. D., Yang, Y., & Zhang, T. (2019). Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing. Microbiome, 7(1), 44. https://doi.org/10.1186/s40168-019-0663-0
   PubMedGoogle Scholar
• Che, Y., Xu, X., Yang, Y., Břinda, K., Hanage, W., Yang, C., & Zhang, T. (2022). High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteria. Microbiome, 10(1), 16. https://doi.org/10.1186/s40168-021-01192-w
   PubMed Web of Science ®Google Scholar
• Che, Y., Yang, Y., Xu, X. Q., Brinda, K., Polz, M. F., Hanage, W. P., & Zhang, T. (2021). Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes. Proceedings of the National Academy of Sciences of the United States of America, 118(6), 12.
   Web of Science ®Google Scholar
• Chen, H. Y., Jing, L. J., Yao, Z. P., Meng, F. S., & Teng, Y. G. (2019). Prevalence, source and risk of antibiotic resistance genes in the sediments of Lake Tai (China) deciphered by metagenomic assembly: A comparison with other global lakes. Environment International, 127, 267–275. https://doi.org/10.1016/j.envint.2019.03.048
   PubMed Web of Science ®Google Scholar
• Christou, A., Papadavid, G., Dalias, P., Fotopoulos, V., Michael, C., Bayona, J. M., Piña, B., & Fatta-Kassinos, D. (2019). Ranking of crop plants according to their potential to uptake and accumulate contaminants of emerging concern. Environmental Research, 170, 422–432. https://doi.org/10.1016/j.envres.2018.12.048
   PubMed Web of Science ®Google Scholar
• Corno, G., Yang, Y., Eckert, E. M., Fontaneto, D., Fiorentino, A., Galafassi, S., Zhang, T., & Di Cesare, A. (2019). Effluents of wastewater treatment plants promote the rapid stabilization of the antibiotic resistome in receiving freshwater bodies. Water Research, 158, 72–81. https://doi.org/10.1016/j.watres.2019.04.031
   PubMed Web of Science ®Google Scholar
• Damashek, J., Westrich, J. R., McDonald, J. M. B., Teachey, M. E., Jackson, C. R., Frye, J. G., Lipp, E. K., Capps, K. A., & Ottesen, E. A. (2022). Non-point source fecal contamination from aging wastewater infrastructure is a primary driver of antibiotic resistance in surface waters. Water Research, 222, 118853. https://doi.org/10.1016/j.watres.2022.118853
   PubMed Web of Science ®Google Scholar
• De Oliveira, D. M. P., Forde, B. M., Kidd, T. J., Harris, P. N. A., Schembri, M. A., Beatson, S. A., Paterson, D. L., & Walker, M. J. (2020). Antimicrobial resistance in ESKAPE pathogens. Clinical Microbiology Reviews, 33(3), e00181–19. https://doi.org/10.1128/CMR.00181-19
   PubMed Web of Science ®Google Scholar
• Delgado-Baquerizo, M., Hu, H. W., Maestre, F. T., Guerra, C. A., Eisenhauer, N., Eldridge, D. J., Zhu, Y. G., Chen, Q. L., Trivedi, P., Du, S., Makhalanyane, T. P., Verma, J. P., Gozalo, B., Ochoa, V., Asensio, S., Wang, L., Zaady, E., Illan, J. G., Siebe, C., … He, J. Z. (2022). The global distribution and environmental drivers of the soil antibiotic resistome. Microbiome, 10(1), 219. https://doi.org/10.1186/s40168-022-01405-w
   PubMed Web of Science ®Google Scholar
• Dias, M. F., Fernandes, G. D., de Paiva, M. C., Salim, A. C. D., Santos, A. B., & Nascimento, A. M. A. (2020). Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings. Water Research, 174, 115630. https://doi.org/10.1016/j.watres.2020.115630
   PubMed Web of Science ®Google Scholar
• Dubey, K. K., Indu., & Sharma, M. (2020). Reprogramming of antibiotics to combat antimicrobial resistance. Archiv der Pharmazie, 353(11), e2000168.
   PubMed Web of Science ®Google Scholar
• Forster, S. C., Liu, J. Y., Kumar, N., Gulliver, E. L., Gould, J. A., Escobar-Zepeda, A., Mkandawire, T., Pike, L. J., Shao, Y., Stares, M. D., Browne, H. P., Neville, B. A., & Lawley, T. D. (2022). Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome. Nature Communications, 13(1), 1445. https://doi.org/10.1038/s41467-022-29096-9
   PubMed Web of Science ®Google Scholar
• Giatsis, C., Sipkema, D., Smidt, H., Heilig, H., Benvenuti, G., Verreth, J., & Verdegem, M. (2015). The impact of rearing environment on the development of gut microbiota in tilapia larvae. Scientific Reports, 5(1), 18206. https://doi.org/10.1038/srep18206
   PubMedGoogle Scholar
• Hardwick, S. A., Deveson, I. W., & Mercer, T. R. (2017). Reference standards for next-generation sequencing. Nature Reviews. Genetics, 18(8), 473–484. https://doi.org/10.1038/nrg.2017.44
   PubMed Web of Science ®Google Scholar
• Hendriksen, R. S., Munk, P., Njage, P., van Bunnik, B., McNally, L., Lukjancenko, O., Röder, T., Nieuwenhuijse, D., Pedersen, S. K., Kjeldgaard, J., Kaas, R. S., Clausen, P. T. L. C., Vogt, J. K., Leekitcharoenphon, P., van de Schans, M. G. M., Zuidema, T., de Roda Husman, A. M., Rasmussen, S., Petersen, B., … Aarestrup, F. M. (2019). Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nature Communications, 10(1), 1124. https://doi.org/10.1038/s41467-019-08853-3
   PubMedGoogle Scholar
• Huijbers, P. M. C., Blaak, H., de Jong, M. C. M., Graat, E. A. M., Vandenbroucke-Grauls, C. M. J. E., & Husman, A. M. D. (2015). Role of the environment in the transmission of antimicrobial resistance to humans: A review. Environmental Science & Technology, 49(20), 11993–12004. https://doi.org/10.1021/acs.est.5b02566
   PubMed Web of Science ®Google Scholar
• Jäger, T., Hembach, N., Elpers, C., Wieland, A., Alexander, J., Hiller, C., Krauter, G., & Schwartz, T. (2018). Reduction of antibiotic resistant bacteria during conventional and advanced wastewater treatment, and the disseminated loads released to the environment. Frontiers in Microbiology, 9, 2599. https://doi.org/10.3389/fmicb.2018.02599
   PubMed Web of Science ®Google Scholar
• Jia, B. F., Raphenya, A. R., Alcock, B., Waglechner, N., Guo, P. Y., Tsang, K. K., Lago, B. A., Dave, B. M., Pereira, S., Sharma, A. N., Doshi, S., Courtot, M., Lo, R., Williams, L. E., Frye, J. G., Elsayegh, T., Sardar, D., Westman, E. L., Pawlowski, A. C., … McArthur, A. G. (2017). CARD 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Research, 45(D1), D566–D573. https://doi.org/10.1093/nar/gkw1004
   PubMed Web of Science ®Google Scholar
• Jia, S. Y., Bian, K. Q., Shi, P., Ye, L., & Liu, C. H. (2020). Metagenomic profiling of antibiotic resistance genes and their associations with bacterial community during multiple disinfection regimes in a full-scale drinking water treatment plant. Water Research, 176, 115721. https://doi.org/10.1016/j.watres.2020.115721
   PubMed Web of Science ®Google Scholar
• Jin, M., Liu, L., Wang, D. N., Yang, D., Liu, W. L., Yin, J., Yang, Z. W., Wang, H. R., Qiu, Z. G., Shen, Z. Q., Shi, D. Y., Li, H. B., Guo, J. H., & Li, J. W. (2020). Chlorine disinfection promotes the exchange of antibiotic resistance genes across bacterial genera by natural transformation. The ISME Journal, 14(7), 1847–1856. https://doi.org/10.1038/s41396-020-0656-9
   PubMed Web of Science ®Google Scholar
• Keenum, I., Liguori, K., Calarco, J., Davis, B. C., Milligan, E., Harwood, V. J., & Pruden, A. (2022). A framework for standardized qPCR-targets and protocols for quantifying antibiotic resistance in surface water, recycled water and wastewater. Critical Reviews in Environmental Science and Technology, 52(24), 4395–4419. https://doi.org/10.1080/10643389.2021.2024739
   Web of Science ®Google Scholar
• Kokkoris, V., Vukicevich, E., Richards, A., Thomsen, C., & Hart, M. (2021). Challenges using droplet digital PCR for environmental samples. Applied Microbiology, 1(1), 74–88. https://doi.org/10.3390/applmicrobiol1010007
   Google Scholar
• Lee, K., Kim, D. W., Lee, D. H., Kim, Y. S., Bu, J. H., Cha, J. H., Thawng, C. N., Hwang, E. M., Seong, H. J., Sul, W. J., Wellington, E. M. H., Quince, C., & Cha, C. J. (2020). Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance. Microbiome, 8(1), 2. https://doi.org/10.1186/s40168-019-0774-7
   PubMed Web of Science ®Google Scholar
• Lekunberri, I., Subirats, J., Borrego, C. M., & Balcázar, J. L. (2017). Exploring the contribution of bacteriophages to antibiotic resistance. Environmental Pollution, 220(Pt B), 981–984. https://doi.org/10.1016/j.envpol.2016.11.059
   PubMedGoogle Scholar
• Li, A. D., Li, L. G., & Zhang, T. (2015). Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants. Frontiers in Microbiology, 6, 1025. https://doi.org/10.3389/fmicb.2015.01025
   PubMed Web of Science ®Google Scholar
• Li, B., Yang, Y., Ma, L., Ju, F., Guo, F., Tiedje, J. M., & Zhang, T. (2015). Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. The ISME Journal, 9(11), 2490–2502. https://doi.org/10.1038/ismej.2015.59
   PubMed Web of Science ®Google Scholar
• Li, J., Cao, J. J., Zhu, Y. G., Chen, Q. L., Shen, F. X., Wu, Y., Xu, S. Y., Fan, H., Da, G., Huang, R. J., Wang, J., de Jesus, A. L., Morawska, L., Chan, C. K., Peccia, J., & Yao, M. S. (2018). Global survey of antibiotic resistance genes in air. Environmental Science & Technology, 52(19), 10975–10984. https://doi.org/10.1021/acs.est.8b02204
   PubMed Web of Science ®Google Scholar
• Li, L. G., Huang, Q., Yin, X. L., & Zhang, T. (2020). Source tracking of antibiotic resistance genes in the environment – Challenges, progress, and prospects. Water Research, 185, 12.
   Web of Science ®Google Scholar
• Li, L. G., Yin, X., & Zhang, T. (2018). Tracking antibiotic resistance gene pollution from different sources using machine-learning classification. Microbiome, 6(1), 93. https://doi.org/10.1186/s40168-018-0480-x
   PubMedGoogle Scholar
• Li, X., Rensing, C., Vestergaard, G., Arumugam, M., Nesme, J., Gupta, S., Brejnrod, A. D., & Sørensen, S. J. (2022). Metagenomic evidence for co-occurrence of antibiotic, biocide and metal resistance genes in pigs. Environment International, 158, 106899. https://doi.org/10.1016/j.envint.2021.106899
   PubMed Web of Science ®Google Scholar
• Liang, J., Lin, H., Singh, B., Wang, A., & Yan, Z. (2023). A global perspective on compositions, risks, and ecological genesis of antibiotic resistance genes in biofilters of drinking water treatment plants. Water Research, 233, 119822. https://doi.org/10.1016/j.watres.2023.119822
   PubMed Web of Science ®Google Scholar
• Lin, H. R., Ye, C. S., Chen, S., Zhang, S. H., & Yu, X. (2017). Viable but non-culturable E. coli induced by low level chlorination have higher persistence to antibiotics than their culturable counterparts. Environmental Pollution, 230, 242–249. https://doi.org/10.1016/j.envpol.2017.06.047
   PubMed Web of Science ®Google Scholar
• Liu, J. X., Zhu, Y. T., Jay-Russell, M., Lemay, D. G., & Mills, D. A. (2020). Reservoirs of antimicrobial resistance genes in retail raw milk. Microbiome, 8(1), 99. https://doi.org/10.1186/s40168-020-00861-6
   PubMed Web of Science ®Google Scholar
• Ma, L. P., Li, B., & Zhang, T. (2019). New insights into antibiotic resistome in drinking water and management perspectives: A metagenomic based study of small-sized microbes. Water Research, 152, 191–201. https://doi.org/10.1016/j.watres.2018.12.069
   PubMed Web of Science ®Google Scholar
• Ma, L. P., Li, B., Jiang, X. T., Wang, Y. L., Xia, Y., Li, A. D., & Zhang, T. (2017). Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey. Microbiome, 5(1), 154. https://doi.org/10.1186/s40168-017-0369-0
   PubMedGoogle Scholar
• Ma, L. P., Xia, Y., Li, B., Yang, Y., Li, L. G., Tiedje, J. M., & Zhang, T. (2016). Metagenomic assembly reveals hosts of antibiotic resistance genes and the shared resistome in pig, chicken, and human feces. Environmental Science & Technology, 50(1), 420–427. https://doi.org/10.1021/acs.est.5b03522
   PubMed Web of Science ®Google Scholar
• Maciel-Guerra, A., Baker, M., Hu, Y., Wang, W., Zhang, X. B., Rong, J., Zhang, Y. M., Zhang, J., Kaler, J., Renney, D., Loose, M., Emes, R. D., Liu, L. H., Chen, J. S., Peng, Z. X., Li, F. Q., & Dottorini, T. (2022). Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock. The ISME Journal, 17(1), 21–35. https://doi.org/10.1038/s41396-022-01315-7
   PubMed Web of Science ®Google Scholar
• Marbouty, M., Baudry, L., Cournac, A., & Koszul, R. (2017). Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay. Science Advances, 3(2), e1602105. https://doi.org/10.1126/sciadv.1602105
   PubMed Web of Science ®Google Scholar
• Martínez, J. L., Coque, T. M., & Baquero, F. (2015). What is a resistance gene? Ranking risk in resistomes. Nature Reviews. Microbiology, 13(2), 116–123. https://doi.org/10.1038/nrmicro3399
   PubMed Web of Science ®Google Scholar
• Munk, P., Brinch, C., Moller, F. D., Petersen, T. N., Hendriksen, R. S., Seyfarth, A. M., Kjeldgaard, J. S., Svendsen, C. A., van Bunnik, B., Berglund, F., Global Sewage Surveillance, C., Larsson, D. G. J., Koopmans, M., Woolhouse, M., & Aarestrup, F. M. (2022). Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nature Communications, 13(1), 7251. https://doi.org/10.1038/s41467-022-34312-7
   PubMed Web of Science ®Google Scholar
• Park, S., Rana, A., Sung, W., & Munir, M. J. A. M. (2021). Competitiveness of quantitative polymerase chain reaction (qPCR) and droplet digital polymerase chain reaction (ddPCR) technologies, with a particular focus on detection of antibiotic resistance genes (ARGs). Applied Microbiology, 1(3), 426–444. https://doi.org/10.3390/applmicrobiol1030028
   Google Scholar
• Pärnänen, K. M. M., Narciso-da-Rocha, C., Kneis, D., Berendonk, T. U., Cacace, D., Do, T. T., Elpers, C., Fatta-Kassinos, D., Henriques, I., Jaeger, T., Karkman, A., Martinez, J. L., Michael, S. G., Michael-Kordatou, I., O’Sullivan, K., Rodriguez-Mozaz, S., Schwartz, T., Sheng, H., Sørum, H., … Manaia, C. M. (2019). Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence. Science Advances, 5(3), eaau9124. https://doi.org/10.1126/sciadv.aau9124
   PubMed Web of Science ®Google Scholar
• Pazda, M., Kumirska, J., Stepnowski, P., & Mulkiewicz, E. (2019). Antibiotic resistance genes identified in wastewater treatment plant systems – A review. The Science of the Total Environment, 697, 134023. https://doi.org/10.1016/j.scitotenv.2019.134023
   PubMed Web of Science ®Google Scholar
• Peng, Z., Hu, Z., Li, Z., Zhang, X., Jia, C., Li, T., Dai, M., Tan, C., Xu, Z., Wu, B., Chen, H., & Wang, X. (2022). Antimicrobial resistance and population genomics of multidrug-resistant Escherichia coli in pig farms in mainland China. Nature Communications, 13(1), 1116. https://doi.org/10.1038/s41467-022-28750-6
   PubMed Web of Science ®Google Scholar
• Pruden, A., Vikesland, P. J., Davis, B. C., & Husman, A. M. D. (2021). Seizing the moment: Now is the time for integrated global surveillance of antimicrobial resistance in wastewater environments. Current Opinion in Microbiology, 64, 91–99. https://doi.org/10.1016/j.mib.2021.09.013
   PubMed Web of Science ®Google Scholar
• Qamar, F. N., Yousafzai, M. T., Khalid, M., Kazi, A. M., Lohana, H., Karim, S., Khan, A., Hotwani, A., Qureshi, S., Kabir, F., Aziz, F., Memon, N. M., Domki, M. H., & Hasan, R. (2018). Outbreak investigation of ceftriaxone-resistant Salmonella enterica serotype typhi and its risk factors among the general population in Hyderabad, Pakistan: A matched case-control study. The Lancet. Infectious Diseases, 18(12), 1368–1376. https://doi.org/10.1016/S1473-3099(18)30483-3
   PubMed Web of Science ®Google Scholar
• Qian, X., Gunturu, S., Sun, W., Cole, J. R., Norby, B., Gu, J., & Tiedje, J. M. (2021). Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces. Proceedings of the National Academy of Sciences of the United States of America, 118(25), e2024464118. https://doi.org/10.1073/pnas.2024464118
   Web of Science ®Google Scholar
• Qiu, T. L., Huo, L. H., Guo, Y. J., Gao, M., Wang, G. L., Hu, D., Li, C., Wang, Z. W., Liu, G. M., & Wang, X. M. (2022). Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost. Environmental Microbiome, 17(1), 42. https://doi.org/10.1186/s40793-022-00437-x
   PubMedGoogle Scholar
• Qiu, Y., Zhang, J., Li, B., Wen, X. H., Liang, P., & Huang, X. (2018). A novel microfluidic system enables visualization and analysis of antibiotic resistance gene transfer to activated sludge bacteria in biofilm. The Science of the Total Environment, 642, 582–590. https://doi.org/10.1016/j.scitotenv.2018.06.012
   PubMed Web of Science ®Google Scholar
• Raza, S., Choi, S., Lee, M., Shin, J., Son, H., Wang, J. H., & Kim, Y. M. (2022). Spatial and temporal effects of fish feed on antibiotic resistance in coastal aquaculture farms. Environmental Research, 212(Pt A), 113177. https://doi.org/10.1016/j.envres.2022.113177
   PubMedGoogle Scholar
• Rice, E. W., Wang, P., Smith, A. L., & Stadler, L. B. (2020). Determining hosts of antibiotic resistance genes: A review of methodological advances. Environmental Science & Technology Letters, 7(5), 282–291. https://doi.org/10.1021/acs.estlett.0c00202
   Web of Science ®Google Scholar
• Riquelme, M. V. P., Garner, E., Gupta, S., Metch, J., Zhu, N., Blair, M. F., Arango-Argoty, G., Maile-Moskowitz, A., Li, A. D., Flach, C. F., Aga, D. S., Nambi, I. M., Larsson, D. G. J., Burgmann, H., Zhang, T., Pruden, A., & Vikesland, P. J. (2022). Demonstrating a comprehensive wastewater-based surveillance approach that differentiates globally sourced resistomes. Environmental Science Technology, 56(21), 14982–14993.
   PubMed Web of Science ®Google Scholar
• Schreiber, C., Zacharias, N., Essert, S. M., Wasser, F., Müller, H., Sib, E., Precht, T., Parcina, M., Bierbaum, G., Schmithausen, R. M., Kistemann, T., & Exner, M. (2021). Clinically relevant antibiotic-resistant bacteria in aquatic environments – An optimized culture-based approach. The Science of the Total Environment, 750, 142265. https://doi.org/10.1016/j.scitotenv.2020.142265
   PubMed Web of Science ®Google Scholar
• Schwermer, C. U., & Uhl, W. (2021). Calculating expected effects of treatment effectivity and river flow rates on the contribution of WWTP effluent to the ARG load of a receiving river. Journal of Environmental Management, 288, 112445. https://doi.org/10.1016/j.jenvman.2021.112445
   PubMed Web of Science ®Google Scholar
• Sharma, M., Rajput, D., Kumar, V., Jatain, I., Aminabhavi, T. M., Mohanakrishna, G., Kumar, R., & Dubey, K. K. (2023). Photocatalytic degradation of four emerging antibiotic contaminants and toxicity assessment in wastewater: A comprehensive study. Environmental Research, 231(Pt 2), 116132. https://doi.org/10.1016/j.envres.2023.116132
   PubMedGoogle Scholar
• Smillie, C. S., Smith, M. B., Friedman, J., Cordero, O. X., David, L. A., & Alm, E. J. (2011). Ecology drives a global network of gene exchange connecting the human microbiome. Nature, 480(7376), 241–244. https://doi.org/10.1038/nature10571
   PubMed Web of Science ®Google Scholar
• Stalder, T., Press, M. O., Sullivan, S., Liachko, I., & Top, E. M. (2019). Linking the resistome and plasmidome to the microbiome. The ISME Journal, 13(10), 2437–2446. https://doi.org/10.1038/s41396-019-0446-4
   PubMed Web of Science ®Google Scholar
• Su, Z., Wen, D., Gu, A. Z., Zheng, Y., Tang, Y., & Chen, L. (2022). Industrial effluents boosted antibiotic resistome risk in coastal environments. Environment International, 171, 107714. https://doi.org/10.1016/j.envint.2022.107714
   PubMed Web of Science ®Google Scholar
• Vaz-Moreira, I., Nunes, O. C., & Manaia, C. M. (2014). Bacterial diversity and antibiotic resistance in water habitats: Searching the links with the human microbiome. FEMS Microbiology Reviews, 38(4), 761–778. https://doi.org/10.1111/1574-6976.12062
   PubMed Web of Science ®Google Scholar
• Wang, B., Xu, J., Wang, Y., Stirling, E., Zhao, K., Lu, C., Tan, X., Kong, D., Yan, Q., He, Z., Ruan, Y., & Ma, B. (2023). Tackling soil ARG-carrying pathogens with global-scale metagenomics. Advanced Science, 10(26), e2301980.
   Web of Science ®Google Scholar
• Wang, C., Yin, X., Xu, X., Wang, D., Liu, L., Zhang, X., Yang, C., Zhang, X., & Zhang, T. (2024). Metagenomic absolute quantification of antibiotic resistance genes and virulence factor genes-carrying bacterial genomes in anaerobic digesters. Water Research, 253, 121258. https://doi.org/10.1016/j.watres.2024.121258
   PubMed Web of Science ®Google Scholar
• Wang, M., Liu, P., Zhou, Q., Tao, W., Sun, Y., & Zeng, Z. (2018). Estimating the contribution of bacteriophage to the dissemination of antibiotic resistance genes in pig feces. Environmental Pollution, 238, 291–298. https://doi.org/10.1016/j.envpol.2018.03.024
   PubMed Web of Science ®Google Scholar
• Wang, Y., Lyu, N., Liu, F., Liu, W. J., Bi, Y., Zhang, Z., Ma, S., Cao, J., Song, X., Wang, A., Zhang, G., Hu, Y., Zhu, B., & Gao, G. F. (2021). More diversified antibiotic resistance genes in chickens and workers of the live poultry markets. Environment International, 153, 106534. https://doi.org/10.1016/j.envint.2021.106534
   PubMed Web of Science ®Google Scholar
• WHO (2020). GLASS report: Early implementation 2020. Global Antimicrobial Resistance and Use Surveillance System (GLASS). https://www.who.int/publications/i/item/9789240005587
   Google Scholar
• Xie, J., Jin, L., Wu, D., Pruden, A., & Li, X. (2022). Inhalable antibiotic resistome from wastewater treatment plants to urban areas: Bacterial hosts, dissemination risks, and source contributions. Environmental Science & Technology, 56(11), 7040–7051. https://doi.org/10.1021/acs.est.1c07023
   PubMed Web of Science ®Google Scholar
• Xu, N. H., Qiu, D. Y., Zhang, Z. Y., Wang, Y., Chen, B. F., Zhang, Q., Wang, T. Z., Hong, W. J., Zhou, N. Y., Penuelas, J., Gillings, M., Zhu, Y. G., & Qian, H. F. (2023). A global atlas of marine antibiotic resistance genes and their expression. Water Research, 244, 120488. https://doi.org/10.1016/j.watres.2023.120488
   PubMed Web of Science ®Google Scholar
• Yang, Y., Che, Y., Liu, L., Wang, C. X., Yin, X. L., Deng, Y., Yang, C., & Zhang, T. (2022). Rapid absolute quantification of pathogens and ARGs by nanopore sequencing. The Science of the Total Environment, 809, 152190. https://doi.org/10.1016/j.scitotenv.2021.152190
   PubMed Web of Science ®Google Scholar
• Yang, Y., Deng, Y., Liu, L., Yin, X., Xu, X., Wang, D., & Zhang, T. (2023). Establishing reference material for the quest towards standardization in environmental microbial metagenomic studies. Water Research, 245, 120641. https://doi.org/10.1016/j.watres.2023.120641
   PubMed Web of Science ®Google Scholar
• Yang, Y., Deng, Y., Shi, X., Liu, L., Yin, X., Zhao, W., Li, S., Yang, C., & Zhang, T. (2023). QMRA of beach water by nanopore sequencing-based viability-metagenomics absolute quantification. Water Research, 235, 119858. https://doi.org/10.1016/j.watres.2023.119858
   PubMed Web of Science ®Google Scholar
• Yang, Y., Jiang, X. T., Chai, B. L., Ma, L. P., Li, B., Zhang, A. N., Cole, J. R., Tiedje, J. M., & Zhang, T. (2016). ARGs-OAP: Online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database. Bioinformatics, 32(15), 2346–2351. https://doi.org/10.1093/bioinformatics/btw136
   PubMed Web of Science ®Google Scholar
• Yin, X. L., Deng, Y., Ma, L. P., Wang, Y. L., Chan, L., & Zhang, T. (2019). Exploration of the antibiotic resistome in a wastewater treatment plant by a nine-year longitudinal metagenomic study. Environment International, 133(Pt B), 105270. https://doi.org/10.1016/j.envint.2019.105270
   PubMedGoogle Scholar
• Yin, X. L., Jiang, X. T., Chai, B. L., Li, L. G., Yang, Y., Cole, J. R., Tiedje, J. M., & Zhang, T. (2018). ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes. Bioinformatics, 34(13), 2263–2270. https://doi.org/10.1093/bioinformatics/bty053
   PubMed Web of Science ®Google Scholar
• Yin, X. L., Yang, Y., Deng, Y., Huang, Y., Li, L. G., Chan, L. Y. L., & Zhang, T. (2022). An assessment of resistome and mobilome in wastewater treatment plants through temporal and spatial metagenomic analysis. Water Research, 209, 117885. https://doi.org/10.1016/j.watres.2021.117885
   PubMed Web of Science ®Google Scholar
• Yin, X., Li, L., Chen, X., Liu, Y. Y., Lam, T. T., Topp, E., & Zhang, T. (2023). Global environmental resistome: Distinction and connectivity across diverse habitats benchmarked by metagenomic analyses. Water Research, 235, 119875. https://doi.org/10.1016/j.watres.2023.119875
   PubMed Web of Science ®Google Scholar
• Yin, X., Zheng, X., Li, L., Zhang, A.-N., Jiang, X.-T., & Zhang, T. J. E. (2022). ARGs-OAP v3.0: Antibiotic-resistance gene database curation and analysis pipeline optimization.
   Google Scholar
• Zainab, S. M., Junaid, M., Xu, N., & Malik, R. N. (2020). Antibiotics and antibiotic resistant genes (ARGs) in groundwater: A global review on dissemination, sources, interactions, environmental and human health risks. Water Research, 187, 116455. https://doi.org/10.1016/j.watres.2020.116455
   PubMed Web of Science ®Google Scholar
• Zhang, A.-N., Gaston, J. M., Dai, C. L., Zhao, S., Poyet, M., Groussin, M., Yin, X., Li, L.-G., van Loosdrecht, M. C. M., Topp, E., Gillings, M. R., Hanage, W. P., Tiedje, J. M., Moniz, K., Alm, E. J., & Zhang, T. (2021). An omics-based framework for assessing the health risk of antimicrobial resistance genes. Nature Communications, 12(1), 4765. https://doi.org/10.1038/s41467-021-25096-3
   PubMed Web of Science ®Google Scholar
• Zhang, L., Ji, L., Liu, X., Zhu, X., Ning, K., & Wang, Z. (2022). Linkage and driving mechanisms of antibiotic resistome in surface and ground water: Their responses to land use and seasonal variation. Water Research, 215, 118279. https://doi.org/10.1016/j.watres.2022.118279
   PubMed Web of Science ®Google Scholar
• Zhang, Y., Pei, M., Zhang, B., He, Y., & Zhong, Y. (2021). Changes of antibiotic resistance genes and bacterial communities in the advanced biological wastewater treatment system under low selective pressure of tetracycline. Water Research, 207, 117834. https://doi.org/10.1016/j.watres.2021.117834
   PubMed Web of Science ®Google Scholar
• Zhang, Z. Y., Zhang, Q., Wang, T. Z., Xu, N. H., Lu, T., Hong, W. J., Penuelas, J., Gillings, M., Wang, M. X., Gao, W. W., & Qian, H. F. (2022). Assessment of global health risk of antibiotic resistance genes. Nature Communications, 13(1), 1553. https://doi.org/10.1038/s41467-022-29283-8
   PubMed Web of Science ®Google Scholar
• Zhao, J., Jin, L., Wu, D., Xie, J. W., Li, J., Fu, X. W., Cong, Z. Y., Fu, P. Q., Zhang, Y., Luo, X. S., Feng, X. B., Zhang, G., Tiedje, J. M., & Li, X. D. (2022). Global airborne bacterial community-interactions with Earth’s microbiomes and anthropogenic activities. Proceedings of the National Academy of Sciences of the United States of America, 119(42), e2204465119.
   PubMed Web of Science ®Google Scholar
• Zheng, D., Yin, G., Liu, M., Hou, L., Yang, Y., Van Boeckel, T. P., Zheng, Y., & Li, Y. (2022). Global biogeography and projection of soil antibiotic resistance genes. Science Advances, 8(46), eabq8015. https://doi.org/10.1126/sciadv.abq8015
   PubMed Web of Science ®Google Scholar
• Zignol, M., Dean, A. S., Falzon, D., van Gemert, W., Wright, A., van Deun, A., Portaels, F., Laszlo, A., Espinal, M. A., Pablos-Méndez, A., Bloom, A., Aziz, M. A., Weyer, K., Jaramillo, E., Nunn, P., Floyd, K., & Raviglione, M. C. (2016). Twenty years of global surveillance of antituberculosis-drug resistance. The New England Journal of Medicine, 375(11), 1081–1089. https://doi.org/10.1056/NEJMsr1512438
   PubMed Web of Science ®Google Scholar