Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments

Environmental Health Perspectives

Volumn 122, Issue 3, 2014, Pages 222-228

  Port, Jesse A ^a   Cullen, Alison C ^a   Wallace, James C ^a   Smith, Marissa N ^a   Faustman, Elaine M ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; GENOMIC DNA;

ANTIBIOTIC RESISTANCE; AQUATIC ENVIRONMENT; ARTICLE; BIOINFORMATICS; DECISION MAKING; DNA SEQUENCE; ECOSYSTEM MONITORING; GENE TRANSFER; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL GENE; NONHUMAN; PATHOGENICITY; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PUBLIC HEALTH; PYROSEQUENCING;

ANTI-BACTERIAL AGENTS; BACTERIA; DRUG RESISTANCE, MICROBIAL; ECOSYSTEM; ENVIRONMENTAL MONITORING; FRESH WATER; INDIA; METAGENOME; PRINCIPAL COMPONENT ANALYSIS; PUBLIC HEALTH SURVEILLANCE; SEAWATER; UNITED STATES;

EID: 84895138159     PISSN: 00916765     EISSN: 15529924     Source Type: Journal    
DOI: 10.1289/ehp.1307009     Document Type: Article

References (41)

1. Allen HK, Donato J, Wang HH, Cloud-Hansen KA, Davies J, Handelsman J. 2010. Call of the wild: antibiotic resistance genes in natural environments. Nat Rev Microbiol 8:251-259.
2. Allen LZ, Allen EE, Badger JH, McCrow JP, Paulsen IT, Elbourne LD, et al. 2012. Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME J 6:1403-1414.
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403-410.
4. Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation. Microbiol Rev 59:143-169.
5. Baquero F. 2012. Metagenomic epidemiology: a public health need for the control of antimicrobial resistance. Clin Microbiol Infect 18(suppl 4):67-73.
6. Bibby K, Peccia J. 2013. Identification of viral pathogen diversity in sewage sludge by metagenome analysis. Environ Sci Technol 47:1945-1951.
7. Breitbart M. 2012. Marine viruses: Truth or dare. Ann Rev Mar Sci 4:425-448.
8. Bush K, Courvalin P, Dantas G, Davies J, Eisenstein B, Huovinen P, et al. 2011. Tackling antibiotic resistance. Nat Rev Microbiol 9:894-896.
9. Centers for Disease Control and Prevention. 2014. National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS) Homepage. Available: http://www.cdc.gov/narms/ [accessed 8 January 2014].
10. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, et al. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141-D145.
11. Davies J, Davies D. 2010. Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74:417-433.
12. Ecker DJ, Sampath R, Willett P, Wyatt JR, Samant V, Massire C, et al. 2005. The Microbial Rosetta Stone Database: a compilation of global and emerging infectious microorganisms and bioterrorist threat agents. BMC Microbiol 5:19; doi:10.1186/1471-2180-5-19.
13. European Centre for Disease Prevention and Control. 2014. European Antimicrobial Resistance Surveillance Network (EARS-Net) Homepage. Available: http://www.ecdc.europa.eu/en/activities/surveillance/EARS-Net [accessed 8 January 2014].
14. Glenn TC. 2011. Field guide to next-generation DNA sequencers. Mol Ecol Resour 11:759-769.
15. Grundmann H, Klugman KP, Walsh T, Ramon-Pardo P, Sigauque B, Khan W, et al. 2011. A framework for global surveillance of antibiotic resistance. Drug Resist Update 14:79-87.
16. Handelsman J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669-685.
17. Hugenholtz P, Tyson GW. 2008. Microbiology: metagenomics. Nature 455:481-483.
18. Kristiansson E, Fick J, Janzon A, Grabic R, Rutgersson C, Weijdegard B, et al. 2011. Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PLoS One 6:e17038; doi:10.1371/journal.pone.0017038.
19. Liu B, Pop M. 2009. ARDB-Antibiotic Resistance Genes Database. Nucleic Acids Res 37:D443-447.
20. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380.
21. Martinez JL. 2009. The role of natural environments in the evolution of resistance traits in pathogenic bacteria. Proc Biol Sci 276:2521-2530.
22. McLellan SL, Huse SM, Mueller-Spitz SR, Andreishcheva EN, Sogin ML. 2010. Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ Microbiol 12:378-392.
23. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, et al. 2008. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386; doi:10.1186/1471-2105-9-386.
24. Oh S, Caro-Quintero A, Tsementzi D, DeLeon-Rodriguez N, Luo C, Poretsky R, et al. 2011. Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. Appl Environ Microbiol 77:6000-6011.
25. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, et al. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691-5702.
26. Port JA, Wallace JC, Griffith WC, Faustman EM. 2012. Metagenomic profiling of microbial composition and antibiotic resistance determinants in Puget Sound. PLoS One 7:e48000; doi:10.1371/journal.pone.0048000.
27. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, et al. 2012. The Pfam protein families database. Nucleic Acids Res 40:D290-D301.
28. Sanapareddy N, Hamp TJ, Gonzalez LC, Hilger HA, Fodor AA, Clinton SM. 2009. Molecular diversity of a North Carolina wastewater treatment plant as revealed by pyrosequencing. Appl Environ Microbiol 75:1688-1696.
29. Schmieder R, Edwards R. 2012. Insights into antibiotic resistance through metagenomic approaches. Future Microbiol 7:73-89.
30. Scholz MB, Lo CC, Chain PS. 2012. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr Opin Biotech 23:9-15.
31. Segura PA, Francçois M, Gagnon C, Sauve S. 2009. Review of the occurrence of anti-infectives in contaminated wastewaters and natural and drinking waters. Environ Health Perspect 117:675-684; doi:10.1289/ehp.11776.
32. Staley C, Gordon KV, Schoen ME, Harwood VJ. 2012. Performance of two quantitative PCR methods for microbial source tracking of human sewage and implications for microbial risk assessment in recreational waters. Appl Environ Microbiol 78:7317-7326.
33. State of Washington. 2014. WAC 173-201A-210. Marine Water Designated Uses and Criteria. Available: http://apps.leg.wa.gov/wac/default.aspx?cite=173-201A-210 [accessed 8 Janurary 2014].
34. Wellington EM, Boxall AB, Cross P, Feil EJ, Gaze WH, Hawkey PM, et al. 2013. The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria. Lancet Infect Dis 13:155-165.
35. Wright GD. 2007. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol 5:175-186.
36. Wright GD. 2010. Antibiotic resistance in the environment: a link to the clinic? Curr Opin Microbiol 13:589-594.
37. Wu CH, Sercu B, Van de Werfhorst LC, Wong J, DeSantis TZ, Brodie EL, et al. 2010. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators. PLoS One 5:e11285; doi:10.1371/journal.pone.0011285.
38. Ye L, Zhang T. 2011. Pathogenic bacteria in sewage treatment plants as revealed by 454 pyrosequencing. Environ Sci Technol 45:7173-7179.
39. Zhang T, Zhang XX, Ye L. 2011. Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge. PLoS One 6:e26041; doi:10.1371/journal.pone.0026041.
40. Zhang XX, Zhang T, Fang HH. 2009. Antibiotic resistance genes in water environment. Appl Microbiol Biotechnol 82:397-414.
41. Zhu W, Lomsadze A, Borodovsky M. 2010. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res 38:e132; doi:10.1093/nar/gkq275.