O’Neill J. The review on antimicrobial resistance. In: Tackling drug-resistant infections globally: final report and recommendations. London: HM Government and the Wellcome Trust; 2016.
Google Scholar
Braga LPP, Alves RF, Dellias MTF, Navarrete AA, Basso TO, Tsai SM. Vinasse fertirrigation alters soil resistome dynamics: an analysis based on metagenomic profiles. Biodata Min. 2017;10(1):17. https://doi.org/10.1186/s13040-017-0138-4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cytryn E. The soil resistome: The anthropogenic, the native, and the unknown. Soil Biol Biochem. 2013;63:18–23. https://doi.org/10.1016/j.soilbio.2013.03.017.
Article
CAS
Google Scholar
Xiao KQ, Li B, Ma LP, Bao P, Zhou X, Zhang T, et al. Metagenomic profiles of antibiotic resistance genes in paddy soils from South China. FEMS Microbiol Ecol. 2016;92(3):fiw023. https://doi.org/10.1093/femsec/fiw023.
Wang F, Stedtfeld RD, Kim OS, Chai B, Yang L, Stedtfeld TM, et al. Influence of soil characteristics and proximity to Antarctic research stations on abundance of antibiotic resistance genes in soils. Environ Sci Technol. 2016;50(23):12621–9. https://doi.org/10.1021/acs.est.6b02863.
Dantas G, Sommer MOA, Oluwasegun RD, Church GM. Bacteria subsisting on antibiotics. Science. 2008;320(5872):100–3. https://doi.org/10.1126/science.1155157.
Article
CAS
PubMed
Google Scholar
Wellington EMH, Boxall ABA, Cross P, Feil EJ, Gaze WH, Hawkey PM, et al. The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria. Lancet Infect Dis. 2013;13(2):155–65. https://doi.org/10.1016/S1473-3099(12)70317-1.
Wang FH, Qiao M, Su JQ, Chen Z, Zhou X, Zhu YG. High throughput profiling of antibiotic resistance genes in urban park soils with reclaimed water irrigation. Environ Sci Technol. 2014;48(16):9079–85. https://doi.org/10.1021/es502615e.
Article
CAS
PubMed
Google Scholar
Wang F, Xu M, Stedtfeld RD, Sheng H, Fan J, Liu M, et al. Long-term effect of different fertilization and cropping systems on the soil antibiotic resistome. Environ Sci Technol. 2018;52(22):13037–46. https://doi.org/10.1021/acs.est.8b04330.
Wu D, Huang XH, Sun JZ, Graham DW, Xie B. Antibiotic resistance genes and associated microbial community conditions in aging landfill systems. Environ Sci Technol. 2017;51(21):12859–67. https://doi.org/10.1021/acs.est.7b03797.
Article
CAS
PubMed
Google Scholar
Mackelprang R, Grube AM, Lamendella R, Jesus EDC, Copeland A, Liang C, et al. Response of the soil microbiome to cultivation in native tallgrass prairie soils of the Midwestern United States. Front Microbiol. 2018;9:1775. https://doi.org/10.3389/fmicb.2018.01775.
Article
PubMed
PubMed Central
Google Scholar
Soares BS, Nepstad DC, Curran LM, Cerqueira GC, Garcia RA, Ramos CA, et al. Modelling conservation in the Amazon basin. Nature. 2006;440(7083):520–3. https://doi.org/10.1038/nature04389.
Article
CAS
Google Scholar
Rodrigues JLM, Pellizari VH, Mueller R, Baek K, Jesus ED, Paula FS, et al. Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities. Proc Natl Acad Sci U S A. 2013;110(3):988–93. https://doi.org/10.1073/pnas.1220608110.
Article
PubMed
Google Scholar
Sandberg KD, LaPara TM. The fate of antibiotic resistance genes and class 1 integrons following the application of swine and dairy manure to soils. FEMS Microbiol Ecol. 2016;92(2). https://doi.org/10.1093/femsec/fiw001.
Johnson TA, Stedtfeld RD, Wang Q, Cole JR, Hashsham SA, Looft T, et al. Clusters of antibiotic resistance genes enriched together stay together in swine agriculture. Mbio. 2016;7(2):e02214–5. https://doi.org/10.1128/mBio.02214-15.
Zhu YG, Johnson TA, Su JQ, Qiao M, Guo GX, Stedtfeld RD, et al. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proc Natl Acad Sci U S A. 2013;110(9):3435–40. https://doi.org/10.1073/pnas.1222743110.
Li B, Yang Y, Ma LP, Ju F, Guo F, Tiedje JM, et al. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. ISME J. 2015;9(11):2490–502. https://doi.org/10.1038/ismej.2015.59.
Ma L, Xia Y, Li B, Yang Y, Li LG, Tiedje JM, et al. Metagenomic assembly reveals hosts of antibiotic resistance genes and the shared resistome in pig, chicken, and human feces. Environ Sci Technol. 2016;50(1):420–7. https://doi.org/10.1021/acs.est.5b03522.
Arango-Argoty G, Garner E, Pruden A, Heath LS, Vikesland P, Zhang L. DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome. 2018;6:1–15.
Article
Google Scholar
Li L, Yin X, Zhang T. Tracking antibiotic resistance gene pollution from different sources using machine-learning classification. Microbiome. 2018;6(1):93. https://doi.org/10.1186/s40168-018-0480-x.
Article
PubMed
PubMed Central
Google Scholar
Martínez JL, Coque TM, Baquero F. What is a resistance gene? Ranking risk in resistomes. Nat Rev Microbiol. 2015;13(2):116–23. https://doi.org/10.1038/nrmicro3399.
Article
CAS
PubMed
Google Scholar
Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ. Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics. 2015;16(1):964. https://doi.org/10.1186/s12864-015-2153-5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, et al. Structure and function of the global topsoil microbiome. Nature. 2018;560(7717):233–7. https://doi.org/10.1038/s41586-018-0386-6.
Van Goethem MW, Pierneef R, Bezuidt OKI, Van De Peer Y, Cowan DA, Makhalanyane TP. A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils. Microbiome. 2018;6(1):40. https://doi.org/10.1186/s40168-018-0424-5.
Article
PubMed
PubMed Central
Google Scholar
Yuan K, Yu K, Yang R, Zhang Q, Yang Y, Chen E, et al. Metagenomic characterization of antibiotic resistance genes in Antarctic soils. Ecotox Environ Safe. 2019;176:300–8. https://doi.org/10.1016/j.ecoenv.2019.03.099.
Yang Y, Jiang XT, Chai BL, Ma LP, Li B, Zhang AN, et al. ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database. Bioinform. 2016;32(15):2346–51. https://doi.org/10.1093/bioinformatics/btw136.
Yin XL, Jiang XT, Chai BL, Li LG, Yang Y, Cole JR, et al. 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. Bioinform. 2018;34:2263–70.
Article
CAS
Google Scholar
Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tiedje JM, Brown CT. Tackling soil diversity with the assembly of large, complex metagenomes. P Natl Acad Sci U S A. 2014;111(13):4904–9. https://doi.org/10.1073/pnas.1402564111.
Article
CAS
Google Scholar
Cheng L, Zhang NF, Yuan MT, Xiao J, Qin YJ, Deng Y, et al. Warming enhances old organic carbon decomposition through altering functional microbial communities. ISME J. 2017;11(8):1825–35. https://doi.org/10.1038/ismej.2017.48.
Johnston ER, Rodriguez-R LM, Luo C, Yuan MM, Wu L, He Z, et al. Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem. Front Microbiol. 2016;7:579.
Article
PubMed
PubMed Central
Google Scholar
Natali SM, Schuur EAG, Trucco C, Pries CEH, Crummer KG, Lopez AFB. Effects of experimental warming of air, soil and permafrost on carbon balance in Alaskan tundra. Glob Chang Biol. 2011;17(3):1394–407. https://doi.org/10.1111/j.1365-2486.2010.02303.x.
Article
Google Scholar
Cox MP, Peterson DA, Biggs PJ. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinform. 2010;11(1):485. https://doi.org/10.1186/1471-2105-11-485.
Article
Google Scholar
Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017;551(7681):457–63. https://doi.org/10.1038/nature24621.
Article
CAS
PubMed
PubMed Central
Google Scholar
von Meijenfeldt FAB, Arkhipova K, Cambuy DD, Coutinho FH, Dutilh BE. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome Biology. 2019;20(1):217. https://doi.org/10.1186/s13059-019-1817-x.
Article
CAS
Google Scholar
Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res. 2017;45:535–42.
Article
Google Scholar
Wang Q, Fish JA, Gilman M, Sun Y, Brown CT, Tiedje JM, et al. Xander: employing a novel method for efficient gene-targeted metagenomic assembly. Microbiome. 2015;3(1):32. https://doi.org/10.1186/s40168-015-0093-6.
Guo J, Quensen J, Sun Y, Wang Q, Brown CT, Cole JR, et al. Review, evaluation and directions for gene-targeted assembly for ecologic analyses of metagenomes. Front. Genet. 2019;10:957. https://doi.org/10.3389/fgene.2019.00957.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo JR, Cole JR, Zhang QP, Brown CT, Tiedje JM. Microbial community analysis with ribosomal gene fragments from shotgun metagenomes. Appl Environ Microbiol. 2016;82(1):157–66. https://doi.org/10.1128/AEM.02772-15.
Article
CAS
PubMed
Google Scholar
Davies J, Davies D. Origins and evolution of antibiotic resistance. Microbiol Mol Biol R. 2010;74(3):417–33. https://doi.org/10.1128/MMBR.00016-10.
Article
CAS
Google Scholar
Allen HK, Moe LA, Rodbumrer J, Gaarder A, Handelsman J. Functional metagenomics reveals diverse beta-lactamases in a remote Alaskan soil. ISME J. 2009;3(2):243–51. https://doi.org/10.1038/ismej.2008.86.
Article
CAS
PubMed
Google Scholar
Lang KS, Anderson JM, Schwarz S, Williamson L, Handelsman J, Singer RS. Novel florfenicol and chloramphenicol resistance gene discovered in Alaskan soil by using functional metagenomics. Appl Environ Microbiol. 2010;76(15):5321–6. https://doi.org/10.1128/AEM.00323-10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wright GD. The antibiotic resistome: The nexus of chemical and genetic diversity. Nat Rev Microbiol. 2007;5(3):175–86. https://doi.org/10.1038/nrmicro1614.
Article
CAS
PubMed
Google Scholar
D'Costa VM, King CE, Kalan L, Morar M, Sung WWL, Schwarz C, et al. Antibiotic resistance is ancient. Nature. 2011;477(7365):457–61. https://doi.org/10.1038/nature10388.
Article
CAS
PubMed
Google Scholar
Yushchuk O, Binda E, Marinelli F. Glycopeptide antibiotic resistance genes: distribution and function in the producer actinomycetes. Front Microbiol. 2020;11. https://doi.org/10.3389/fmicb.2020.01173.
Fang H, Wang H, Cai L, Yu Y. Prevalence of antibiotic resistance genes and bacterial pathogens in long-term manured greenhouse soils as revealed by metagenomic survey. Environ Sci Technol. 2015;49(2):1095–104. https://doi.org/10.1021/es504157v
Li Y, Mima T, Komori Y, Morita Y, Kuroda T, Mizushima T, et al. A new member of the tripartite multidrug efflux pumps, MexVW-OprM, in Pseudomonas aeruginosa. J Antimicrob Chemoth. 2003;52(4):572–5. https://doi.org/10.1093/jac/dkg390.
Article
CAS
Google Scholar
Aendekerk S, Diggle SP, Song Z, Høiby N, Cornelis P, Williams P, et al. The MexGHI-OpmD multidrug efflux pump controls growth, antibiotic susceptibility and virulence in Pseudomonas aeruginosa via 4-quinolone-dependent cell-to-cell communication. Microbiology. 2005;151(4):1113–25. https://doi.org/10.1099/mic.0.27631-0.
Okusu H, Ma D, Nikaido H. AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants. J Bacteriol. 1996;178(1):306–8. https://doi.org/10.1128/JB.178.1.306-308.1996.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu EW, McDermott G, Zgurskaya HI, Nikaido H, Koshland DEJ. Structural basis of multiple drugbinding capacity of the AcrB multidrug efflux pump. Science. 2003;300(5621):976–80. https://doi.org/10.1126/science.1083137.
Article
CAS
PubMed
Google Scholar
Roberts MC. Update on macrolide-lincosamide-streptogramin, ketolide, and oxazolidinone resistance genes. FEMS Microbiol Lett. 2008;282(2):147–59. https://doi.org/10.1111/j.1574-6968.2008.01145.x.
Article
CAS
PubMed
Google Scholar
Chen QL, An XL, Li H, Su JQ, Ma YB, Zhu YG. Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil. Environ Int. 2016;92-93:1–10.
Article
CAS
PubMed
Google Scholar
Gibson MK, Forsberg KJ, Dantas G. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J. 2015;9(1):207–16. https://doi.org/10.1038/ismej.2014.106.
Article
CAS
PubMed
Google Scholar
Guo N, Wang YK, Tong TZ, Wang SG. The fate of antibiotic resistance genes and their potential hosts during bio-electrochemical treatment of high-salinity. Water Res. 2018;133:79–86. https://doi.org/10.1016/j.watres.2018.01.020.
Article
CAS
PubMed
Google Scholar
Qian X, Sun W, Gu J, Wang XJ, Sun JJ, Yin YN, et al. Variable effects of oxytetracycline on antibiotic resistance gene abundance and the bacterial community during aerobic composting of cow manure. J Hazard Mater. 2016;315:61–9. https://doi.org/10.1016/j.jhazmat.2016.05.002.
Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. P Natl Acad Sci U S A. 2006;103(3):626–31. https://doi.org/10.1073/pnas.0507535103.
Article
CAS
Google Scholar
Nottingham AT, Fierer N, Turner BL, Whitaker J, Ostle NJ, McNamara NP, et al. Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes. Ecology. 2018;99(11):2455–66. https://doi.org/10.1002/ecy.2482.
Article
PubMed
Google Scholar
Prober SM, Leff JW, Bates ST, Borer ET, Firn J, Harpole WS, et al. Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide. Ecol Lett. 2015;18(1):85–95. https://doi.org/10.1111/ele.12381.
Peng S, Feng YZ, Wang YM, Guo XS, Chu HY, Lin XG. Prevalence of antibiotic resistance genes in soils after continually applied with different manure for 30 years. J Hazard Mater. 2017;340:16–25. https://doi.org/10.1016/j.jhazmat.2017.06.059.
Article
CAS
PubMed
Google Scholar
Poirel L, Kampfer P, Nordmann P. Chromosome-encoded Ambler class A beta-lactamase of Kluyvera georgiana, a probable progenitor of a subgroup of CTX-M extendedspectrum beta-lactamases. Antimicrob Agents Chemother. 2002;46(12):4038–40. https://doi.org/10.1128/AAC.46.12.4038-4040.2002.
Article
CAS
PubMed
PubMed Central
Google Scholar
Patel R, Piper K, Cockerill FR, Steckelberg JM, Yousten AA. The biopesticide Paenibacillus popilliae has a vancomycin resistance gene cluster homologous to the Enterococcal VanA vancomycin resistance gene cluster. Antimicrob Agents Chemother. 2000;44(3):705–9. https://doi.org/10.1128/AAC.44.3.705-709.2000.
Article
CAS
PubMed
PubMed Central
Google Scholar
van Hoek AH, Mevius D, Guerra B, Mullany P, Roberts AP, Aarts HJ. Acquired antibiotic resistance genes: an overview. Front Microbiol. 2011;2:203.
PubMed
PubMed Central
Google Scholar
Rodriguez-R LM, Gunturu S, Tiedje JM, Cole JR, Konstantinidis KT. Nonpareil 3: Fast estimation of metagenomic coverage and sequence diversity. mSystems. 2018;3:e00039–18.
Article
PubMed
PubMed Central
Google Scholar
Hulko M, Berndt F, Gruber M, Linder JU, Truffault V, Schultz A, et al. The HAMP domain structure implies helix rotation in transmembrane signaling. Cell. 2006;126(5):929–40. https://doi.org/10.1016/j.cell.2006.06.058.
Jia BF, Raphenya AR, Alcock B, Waglechner N, Guo PY, Tsang KK, et al. Card 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 2017;45:566–73.
Article
Google Scholar
Arthur M, Molinas C, Courvalin P. The VanS-VanR two-component regulatory system controls synthesis of depsipeptide peptidoglycan precursors in Enterococcus faecium BM4147. J Bacteriolo. 1992;174(8):2582–91. https://doi.org/10.1128/JB.174.8.2582-2591.1992.
Article
CAS
Google Scholar