MEGARes: An antimicrobial resistance database for high throughput sequencing

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D574-D580

  Lakin, Steven M ^a   Dean, Chris ^a   Noyes, Noelle R ^a   Dettenwanger, Adam ^b   Ross, Anne Spencer ^b   Doster, Enrique ^a   Rovira, Pablo ^a   Abdo, Zaid ^a   Jones, Kenneth L ^c   Ruiz, Jaime ^d   Belk, Keith E ^a   Morley, Paul S ^a   Boucher, Christina ^d  

^a Department of Environmental and Radiological Health Sciences   (United States)

^b Department of Computer Science   (United States)

^c UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^d J Crayton Pruitt Family Department of Biomedical Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ANTIBIOTIC RESISTANCE; ARTICLE; BACTEROIDALES; BACTEROIDETES; BIOINFORMATICS; CLASSIFIER; DATA ANALYSIS; DATA BASE; HAPLOTYPE; HIGH THROUGHPUT SEQUENCING; LISTERIA MONOCYTOGENES; METAGENOMICS; PHYLOGENY; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE; STATISTICAL ANALYSIS; BIOLOGY; GENETIC DATABASE; METAGENOME; PROCEDURES; WEB BROWSER;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DRUG RESISTANCE, MICROBIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOME; METAGENOMICS; WEB BROWSER;

EID: 85016164888     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1009     Document Type: Article

References (46)

1. The White House (2015) National Action Plan for Combating Antibiotic Resistant Bacteria. https://www.whitehouse.gov/sites/default/files/docs/national-action-plan-for-combating-antibotic-resistant-bacteria.pdf (25 October 2016, date last accessed).
2. United Nations News Centre (2016) At Resistance UN, global leaders commit to act on antimicrobial resistance: New York UN, global leaders commit to act on antimicrobial resistance: New York. http://www.un.org/apps/news/story.asp?NewsID=55011#.WBDSdeErLTo (25 October 2016, date last accessed).
3. Food and Agricultural Organization of the United Nations (2016) The FAO action plan on antimicrobial resistance 2016-2020: Rome, Italy. http://www.fao.org/3/a-i5996e.pdf (25 October 2016, date last accessed).
4. United States Department of Agriculture, Office of Inspector General (2016) Resistance USDA's Response to Antibiotic Resistance: Audit Report 50601-0004-31 : Washington, D.C. https://www.usda.gov/oig/webdocs/50601-0004-31.pdf (25 October 2016, date last accessed).
5. European Commission (2016) Evaluation of the Action Plan against the rising threats from antimicrobial resistance. http://ec.europa.eu/dgs/health-food-safety/amr/docs/amr-evaluation-2011-16-evaluation-action-plan.pdf (25 October 2016, date last accessed).
6. United States Food and Drug Administration (2013) Report National Antimicrobial Resistance Monitoring System-Enteric Bacteria. NARMS Integrated Report: 2012-2013: Silver Spring, MD. http://www.fda.gov/downloads/AnimalVeterinary/SafetyHealth/AntimicrobialResistance/NationalAntimicrobialResistanceMonitoringSystem/UCM453398.pdf (25 October 2016, date last accessed).
7. Public Health Agency of Canada (2016) Canadian Antimicrobial Resistance Surveillance System - Report 2016: Guelph, Canada. http://healthycanadians.gc.ca/publications/drugs-products-medicamentsproduits/antibiotic-resistance-antibiotique/alt/pub-eng.pdf. (25 October 2016, date last accessed).
8. World Health Organization (2015) Implementation Global Antimicrobial Surveillance System: Manual for Early Implementation: Geneva, Switzerland. http://apps.who.int/iris/bitstream/10665/188783/1/9789241549400-eng.pdf (25 October 2016, date last accessed).
9. Baquero, F., Tedim, A.-S.P. and Coque, T.M. (2013) Antibiotic resistance shaping multi-level population biology of bacteria. Front. Microbiol., 4, 15.
10. MacLean, R.C., Hall, A.R., Perron, G.G. and Buckling, A. (2010) The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts. Nat. Rev. Genet., 11, 405-414.
11. Zhu, Y.-G., Johnson, T.A., Su, J.-Q., Qiao, M., Guo, G.-X., Stedtfeld, R.D., Hashsham, S.A. and Tiedje, J.M. (2013) Diverse and abundant antibiotic resistance genes in Chinese swine farms. PNAS, 110, 3435-3440.
12. Li, B., Yang, Y., Ma, L., Ju, F., Guo, F., Tiedje, J.M. and Zhang, T. (2015) Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. ISME J., doi:10.1038/ismej.2015.59.
13. Noyes, N.R., Yang, X., Linke, L.M., Magnuson, R.J., Dettenwanger, A., Cook, S., Geornaras, I., Woerner, D.E., Gow, S.P., McAllister, T.A. et al. (2016) Resistome diversity in cattle and the environment decreases during beef production. eLife, 5, e13195.
14. EMBL-EBI Metagenomics (2016) Local surveillance of infectious diseases and antimicrobial resistance from sewage: Project (ERP015410). https://www.ebi.ac.uk/metagenomics/projects/ERP015410 (25 October 2016, date last accessed).
15. Miller, R.R., Montoya, V., Gardy, J.L., Patrick, D.M. and Tang, P. (2013) Metagenomics for pathogen detection in public health. Genome Med., 5, 81.
16. Centers for Disease Control and Prevention (2016) AMD Projects: Combatting Healthcare-associated Infections: Washington, D.C. http://www.cdc.gov/amd/pdf/factsheets/amd-projects-hai-2016.pdf (25 October 2016, date last accessed).
17. Interagency Task Force on Antimicrobial Resistance (2012) Update a public health action plan to combat antimicrobial resistance - 2012 Update: Washington, D.C. http://www.cdc.gov/drugresistance/pdf/action-plan-2012.pdf (25 October 2016, date last accessed).
18. NIH HMP Working Group, Peterson, J, Garges, S., Giovanni, M., McInnes, P., Wang, L., Schloss, J.A., Bonazzi, V., McEwen, J.E., Wetterstrand, K.A. et al. (2009) The NIH Human Microbiome Project. Genome Res., 19, 2317-2323.
19. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Peña, A.G., Goodrich, J.K., Gordon, J.I. et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat. Methods, 7, 335-336.
20. Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D.H., Robinson, C.J. et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol., 75, 7537-7541.
21. Oulas, A., Pavloudi, C., Polymenakou, P., Pavlopoulos, G.A., Papanikolaou, N., Kotoulas, G., Arvanitidis, C. and Iliopoulos, I. (2015) Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol. Insights, 9, 75-88.
22. Ju, F. and Zhang, T. (2015) Experimental design and bioinformatics analysis for the application of metagenomics in environmental sciences and biotechnology. Environ. Sci. Technol., 49, 12628-12640.
23. Cole, J.R., Wang, Q., Fish, J.A., Chai, B., McGarrell, D.M., Sun, Y., Brown, C.T., Porras-Alfaro, A., Kuske, C.R. and Tiedje, J.M. (2014) Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res., 42, D633-D642.
24. Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J. and Glöckner, F.O. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res., 41, D590-D596.
25. DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., Huber, T., Dalevi, D., Hu, P. and Andersen, G.L. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol., 72, 5069-5072.
26. Gupta, S.K., Padmanabhan, B.R., Diene, S.M., Lopez-Rojas, R., Kempf, M., Landraud, L. and Rolain, J.-M. (2014) ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob. Agents Chemother., 58, 212-220.
27. Zankari, E., Hasman, H., Cosentino, S., Vestergaard, M., Rasmussen, S., Lund, O., Aarestrup, F.M. and Larsen, M.V. (2012) Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother., 67, 2640-2644.
28. McArthur, A.G., Waglechner, N., Nizam, F., Yan, A., Azad, M.A., Baylay, A.J., Bhullar, K., Canova, M.J., Pascale, G.D., Ejim, L. et al. (2013) The comprehensive antibiotic resistance database. Antimicrob. Agents Chemother., 57, 3348-3357.
29. Merkel, D. (2014) Docker: lightweight Linux containers for consistent development and deployment. Linux J. 239, 2.
30. Connell, S.R., Tracz, D.M., Nierhaus, K.H. and Taylor, D.E. (2003) Ribosomal Protection Proteins and Their Mechanism of Tetracycline Resistance. Antimicrob. Agents Chemother., 47, 3675-3681.
31. Kong, K.-F., Schneper, L. and Mathee, K. (2010) Beta-lactam antibiotics: from antibiosis to resistance and bacteriology. APMIS, 118, 1-36.
32. Bush, K. and Jacoby, G.A. (2010) Updated functional classification of beta-lactamases. Antimicrob. Agents Chemother., 54, 969-976.
33. Kent, W.J. (2002) BLAT-the BLAST-Like Alignment Tool. Genome Res., 12, 656-664.
34. Cock, P.J.A., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B. et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423.
35. Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
36. NCBI Resource Coordinators (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 41, D8-D20.
37. Teller, S. (2013) Data Visualization with d3.Js. Packt Publishing Ltd., Birmingham, pp. 1-180.
38. Morrison-Smith, S., Boucher, C., Bunt, A. and Ruiz, J. (2015) Elucidating the role and use of bioinformatics software in life science research. Proceedings of the 2015 British HCI Conference, doi:10.1145/2783446.2783581.
39. Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455.
40. Bolger, A.M., Lohse, M. and Usadel, B. (2014) Trimmomatic: a flexible trimmer for Illumina Sequence Data. Bioinformatics, doi:10.1093/bioinformatics/btu170.
41. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
42. Li, H. (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics., 27, 2987-2993.
43. Gibson, M.K., Forsberg, K.J. and Dantas, G. (2015) Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J., 9, 207-216.
44. Mielczarek, M. and Szyda, J. (2016) Review of alignment and SNP calling algorithms for next-generation sequencing data. J. Appl. Genet., 57, 71-79.
45. Martínez, J.L., Coque, T.M. and Baquero, F. (2015) What is a resistance gene? Ranking risk in resistomes. Nat. Rev. Micro, 13, 116-123.
46. Baquero, F. (2012) Metagenomic epidemiology: a public health need for the control of antimicrobial resistance. Clin. Microbiol. Infect., 18(Suppl. 4), 67-73.