Whole-genome sequencing in the prediction of antimicrobial resistance

Expert Review of Anti-Infective Therapy

Volumn 14, Issue 7, 2016, Pages 617-619

  Chan, Kok Gan ^a  

^a UNIVERSITY OF MALAYA   (Malaysia)

Author keywords

bioinformatics; metagenome; multidrug resistant bacteria; Next generation sequencing; single cell transcriptome

Indexed keywords

ANTIBIOTIC AGENT; RNA 16S;

ANTIBIOTIC RESISTANCE; BACTERIAL GENOME; BACTERIAL MUTATION; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BIOINFORMATICS; BIOTECHNOLOGY; EDITORIAL; ESCHERICHIA COLI; GENE MUTATION; GENE SEQUENCE; GENETIC DATABASE; HORIZONTAL GENE TRANSFER; HUMAN; KLEBSIELLA PNEUMONIAE; MYCOBACTERIUM TUBERCULOSIS; NEISSERIA MENINGITIDIS; NEXT GENERATION SEQUENCING; NONHUMAN; PREDICTION; SALMONELLA; WHOLE GENOME SEQUENCING; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; MULTIDRUG RESISTANCE; SINGLE CELL ANALYSIS;

DRUG RESISTANCE, BACTERIAL; DRUG RESISTANCE, MULTIPLE, BACTERIAL; GENE EXPRESSION PROFILING; GENOME, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS, DNA; SINGLE-CELL ANALYSIS;

EID: 84975252135     PISSN: 14787210     EISSN: 17448336     Source Type: Journal    
DOI: 10.1080/14787210.2016.1193005     Document Type: Editorial

References (28)

1. World Health Organization. Antimicrobial resistance: global report on surveillance 2014. 2014. Available from: http://www.who.int/drugresistance/documents/surveillancereport/en/.
2. S.B.Levy, B.Marshall Antibacterial resistance worldwide: causes, challenges and responses. Nat Med. 2004;10:S122–S129.
3. C.Pál, B.Papp, V.Lázár. Collateral sensitivity of antibiotic-resistant microbes. Trends Microbiol. 2015;23:401–407.
4. P.M.Bennett. Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria. Br J Pharmacol. 2008;153(S1):S347–S357.
5. A.C.Fluit, M.R.Visser, F.J.Schmitz. Molecular detection of antimicrobial resistance. Clin Microbiol Rev. 2001;14(4):836–871.
6. S.Suzuki, T.Horinouchi, C.Furusawa. Prediction of antibiotic resistance by gene expression profiles. Nat Commun. 2014;5:5792. doi:10.1038/ncomms6792.
7. C.Tamae, A.Liu, K.Kim, et al. Determination of antibiotic hypersensitivity among 4,000 single-gene-knockout mutants of Escherichia coli. J Bacteriol. 2008;190:5981–5988.
8. E.Zankari, H.Hasman, S.Cosentino, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640–2644.
9. D.F.Warner, V.Mizrahi. Complex genetics of drug resistance in Mycobacterium tuberculosis. Nat Genet. 2013;45(10):1107–1108.
10. K.A.Kleinheinz, K.G.Joensen, M.V.Larsen. Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences. Bacteriophage. 2014;4(2):e27943. doi:10.4161/bact.27943.
11. G.Torres‐Cortés, V.Millán, H.C.Ramírez‐Saad, et al. Characterization of novel antibiotic resistance genes identified by functional metagenomics on soil samples. Environ Microbiol. 2011;13(4):1101–1114.
12. C.B.Ford, R.R.Shah, M.K.Maeda, et al. Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat Genet. 2013;45(7):784–790.
13. N.Stoesser, E.M.Batty, D.W.Eyre, et al. Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemother. 2013;68(10):2234–2244.
14. S.A.Beatson, N.L.B.Zakour, M.Totsika, et al. Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition. Infect Immun. 2015;83(5):1749–1764.
15. T consisting of a chromosome and a circular megaplasmid. J Biotechnol. 2015;204:13–14.
16. A.Carattoli, E.Zankari, A.García-Fernández, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58(7):3895–3903.
17. A.Kwasiborski, S.Mondy, T.-M.Chong, et al. Core genome and plasmidome of the quorum-quenching bacterium Rhodococcus erythropolis. Genetica. 2015;143(2):253–261.
18. T.N.Petersen, S.Rasmussen, H.Hasman, et al. Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance. Sci Rep. 2015;5:11444. doi:10.1038/srep11444.
19. T. J Biotechnol. 2015;204:5–6.
20. Y.Y.Lau, W.-F.Yin, K.-G.Chan. Enterobacter asburiae strain L1: complete genome and whole genome optical mapping analysis of a quorum sensing bacterium. Sensors. 2014;14(8):13913–13924.
21. B.M.Forde, N.L.B.Zakour, M.Stanton-Cook, et al. The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b: H4-ST131 clone. PLoS One. 2014;9(8):e104400. doi:10.1371/journal.pone.0104400.
22. K.W.Hong, D.A.Thinagaran, H.M.Gan, et al. Whole-genome sequence of Cupriavidus sp. strain BIS7, a heavy-metal-resistant bacterium. J Bacteriol. 2012;194(22):6324–6324.
23. Y.-L.Lim, R.Ee, K.-Y.How, et al. Complete genome sequencing of Pandoraea pnomenusa RB38 and molecular characterization of its N-acyl homoserine lactone synthase gene ppnI. PeerJ. 2015;3:e1225. doi:10.7717/peerj.1225.
24. C.U.Köser, L.J.Fraser, A.Ioannou, et al. Rapid single-colony whole-genome sequencing of bacterial pathogens. J Antimicrob Chemother. 2014;69:1275–1281.
25. A.G.McArthur, N.Waglechner, F.Nizam, et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother. 2013;57(7):3348–3357.
26. P.Bradley, N.C.Gordon, T.M.Walker, et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun. 2015;6:10063. doi:10.1038/ncomms1006.
27. K.G.Joensen, F.Scheutz, O.Lund, et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol. 2014;52(5):1501–1510.
28. E.Zankari, H.Hasman, R.S.Kaas, et al. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother. 2012. doi:10.1093/jac/dks496.