Bioinformatics of antimicrobial resistance in the age of molecular epidemiology

Current Opinion in Microbiology

Volumn 27, Issue , 2015, Pages 45-50

  McArthur, Andrew G ^a   Wright, Gerard D ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ANTIMICROBIAL ACTIVITY; BIOINFORMATICS; DNA SEQUENCE; GENETIC ASSOCIATION; GENOTYPE; HUMAN; MOLECULAR EPIDEMIOLOGY; NONHUMAN; PHENOTYPE; PUBLIC HEALTH; REVIEW; BACTERIAL INFECTIONS; BACTERIUM; BIOLOGY; DRUG DEVELOPMENT; DRUG EFFECTS; GENETIC DATABASE; GENETICS; INFORMATION DISSEMINATION; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; PROCEDURES;

BACTERIA; BACTERIAL INFECTIONS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DRUG DISCOVERY; DRUG RESISTANCE, BACTERIAL; GENOTYPE; HUMANS; INFORMATION DISSEMINATION; MICROBIAL SENSITIVITY TESTS; MOLECULAR EPIDEMIOLOGY; PHENOTYPE; SEQUENCE ANALYSIS, DNA;

EID: 84938339240     PISSN: 13695274     EISSN: 18790364     Source Type: Journal    
DOI: 10.1016/j.mib.2015.07.004     Document Type: Review

References (32)

1. Smith R.A., M'ikanatha N.M., Read A.F. Antibiotic resistance: a primer and call to action. Health Commun 2015, 30:309-314.
2. Wright G.D. Solving the antibiotic crisis. ACS Infect Dis 2015, 10.1021/id500052s.
3. McArthur A.G., Waglechner N., Nizam F., Yan A., Azad M.A., Baylay A.J., Bhullar K., Canova M.J., de Pascale G., Ejim L., et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 2013, 57:3348-3357.
4. Bush K., Jacoby G.A. Updated functional classification of beta-lactamases. Antimicrob Agents Chemother 2010, 54:969-976.
5. Liu B., Pop M. ARDB - Antibiotic Resistance Genes Database. Nucleic Acids Res 2009, 37:D443-D447.
6. Pal C., Bengtsson-Palme J., Rensing C., Kristiansson E., Larsson D.G.J. BacMet: antibacterial biocide and metal resistance genes database. Nucleic Acids Res 2014, 42:D737-D743.
7. Antezana E., Kuiper M., Mironov V. Biological knowledge management: the emerging role of the Semantic Web technologies. Brief Bioinformatics 2009, 10:392-407.
8. Dauga D. Biocuration: a new challenge for the tunicate community. Genesis 2015, 53:132-142.
9. Tibiche C, Wang E: GeneNetMiner: accurately mining gene regulatory networks from literature. arXiv 2014, [no volume].
10. Rutherford K.M., Harris M.A., Lock A., Oliver S.G., Wood V. Canto: an online tool for community literature curation. Bioinformatics 2014, 30:1791-1792.
11. Davis A.P., Murphy C.G., Johnson R., Lay J.M., Lennon-Hopkins K., Saraceni-Richards C., Sciaky D., King B.L., Rosenstein M.C., Wiegers T.C., et al. The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Res 2013, 41:D1104-D1114.
12. Jamieson D.G., Roberts P.M., Robertson D.L., Sidders B., Nenadic G. Cataloging the biomedical world of pain through semi-automated curation of molecular interactions. Database 2013, 2013:bat033.
13. Névéol A, Wilbur WJ, Lu Z: Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. Database 2012, 2012:bas026.
14. Didelot X., Bowden R., Wilson D.J., Peto T.E.A., Crook D.W. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 2012, 13:601-612.
15. Bertelli C., Greub G. Rapid bacterial genome sequencing: methods and applications in clinical microbiology. Clin Microbiol Infect 2013, 19:803-813.
16. Gibson M.K., Forsberg K.J., Dantas G. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J 2015, 9:207-216.
17. Gupta S.K., Padmanabhan B.R., Diene S.M., Lopez-Rojas R., Kempf M., Landraud L., Rolain J.-M. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 2014, 58:212-220.
18. Courvalin P. Vancomycin resistance in gram-positive cocci. Clin Infect Dis 2006, 42(Suppl 1):S25-S34.
19. Morar M., Wright G.D. The genomic enzymology of antibiotic resistance. Annu Rev Genet 2010, 44:25-51.
20. Sakhanenko N.A., Galas D.J. Probabilistic logic methods and some applications to biology and medicine. J Comput Biol 2012, 19:316-336.
21. Mourad R., Sinoquet C., Leray P. Probabilistic graphical models for genetic association studies. Brief Bioinformatics 2012, 13:20-33.
22. Wang J., Cheung L.W-K., Delabie J. New probabilistic graphical models for genetic regulatory networks studies. J Biomed Inform 2005, 38:443-455.
23. Friedman N. Inferring cellular networks using probabilistic graphical models. Science 2004, 303:799-805.
24. Perry J.A., Westman E.L., Wright G.D. The antibiotic resistome: what's new?. Curr Opin Microbiol 2014, 21:45-50.
25. Wright G.D. Mechanisms of resistance to antibiotics. Curr Opin Chem Biol 2003, 7:563-569.
26. Davies J., Wright G.D. Bacterial resistance to aminoglycoside antibiotics. Trends Microbiol 1997, 5:234-240.
27. Poole K. Aminoglycoside resistance in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2005, 49:479-487.
28. Drawz S.M., Bonomo R.A. Three decades of beta-lactamase inhibitors. Clin Microbiol Rev 2010, 23:160-201.
29. Laxminarayan R., Duse A., Wattal C., Zaidi A.K.M., Wertheim H.F.L., Sumpradit N., Vlieghe E., Hara G.L., Gould I.M., Goossens H., et al. Antibiotic resistance - the need for global solutions. Lancet Infect Dis 2013, 13:1057-1098.
30. Rex J.H., Eisenstein B.I., Alder J., Goldberger M., Meyer R., Dane A., Friedland I., Knirsch C., Sanhai W.R., Tomayko J., et al. A comprehensive regulatory framework to address the unmet need for new antibacterial treatments. Lancet Infect Dis 2013, 13:269-275.
31. Wright G.D. Antibiotics: a new hope. Chem Biol 2012, 19:3-10.
32. Alam M.T., Petit R.A., Crispell E.K., Thornton T.A., Conneely K.N., Jiang Y., Satola S.W., Read T.D. Dissecting vancomycin-intermediate resistance in Staphylococcus aureus using genome-wide association. Genome Biol Evol 2014, 6:1174-1185.