Transcriptome profiling in imipenem-selected Acinetobacter baumannii

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Chang, Kai Chih ^a   Kuo, Han Yueh ^b,c   Tang, Chuan Y ^d,e   Chang, Cheng Wei ^d   Lu, Chia Wei ^e   Liu, Chih Chin ^d,f   Lin, Huei Ru ^a   Chen, Kuan Hsueh ^d   Liou, Ming Li ^d,g  

^a TZU CHI UNIVERSITY   (Taiwan)

^b NATIONAL TAIWAN UNIVERSITY HOSPITAL   (Taiwan)

^c NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^d PROVIDENCE UNIVERSITY   (Taiwan)

^e NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^f CHUNG HUA UNIVERSITY   (Taiwan)

^g YUANPEI UNIVERSITY   (Taiwan)

Author keywords

Acinetobacter baumannii; Carbapenem resistance; Transcriptome profiling

Indexed keywords

AMIKACIN; BETA LACTAMASE; BETA LACTAMASE OXA 95; CARBAPENEM; CEFEPIME; CEFTAZIDIME; CIPROFLOXACIN; COTRIMOXAZOLE; DNA; GENTAMICIN; IMIPENEM; LEVOFLOXACIN; MEROPENEM; MULTIDRUG RESISTANCE PROTEIN; RECOMBINASE; RNA; RND EFFLUX TRANSPORTER; SULTAMICILLIN; TRANSCRIPTOME; TRANSPOSASE; UNCLASSIFIED DRUG; ANTIINFECTIVE AGENT; BACTERIAL PROTEIN; CARBAPENEMASE;

ACINETOBACTER BAUMANNII; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL STRAIN; BIOFILM; CONTROLLED STUDY; DNA REPAIR; DOWN REGULATION; DRUG HYDROLYSIS; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC RECOMBINATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PROTEIN SECRETION; QUORUM SENSING; RNA SEQUENCE; TRANSCRIPTOMICS; UPREGULATION; BACTERIAL GENE; DRUG EFFECTS; GENETICS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HYDROLYSIS; METABOLISM; MICROBIAL SENSITIVITY TEST; TANDEM MASS SPECTROMETRY;

ACINETOBACTER BAUMANNII;

ACINETOBACTER BAUMANNII; ANTI-BACTERIAL AGENTS; BACTERIAL PROTEINS; BETA-LACTAMASES; BIOFILMS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; GENE EXPRESSION PROFILING; GENES, BACTERIAL; HYDROLYSIS; IMIPENEM; MICROBIAL SENSITIVITY TESTS; TANDEM MASS SPECTROMETRY; TRANSCRIPTOME;

EID: 84907919777     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-815     Document Type: Article

References (36)

1. Perez F, Hujer AM, Hujer KM, Decker BK, Rather PN, Bonomo RA. Global challenge of multidrug-resistant Acinetobacter baumannii. Antimicrob Agents Chemother 2007, 51(10):3471-3484. 10.1128/AAC.01464-06, 2043292, 17646423.
2. Hsueh PR. Study for Monitoring Antimicrobial Resistance Trends (SMART) in the Asia-pacific region, 2002-2010. Int J Antimicrob Agents 2012, 40(Suppl):S1-S3.
3. Peleg AY, Seifert H, Paterson DL. Acinetobacter baumannii: emergence of a successful pathogen. Clin Microbiol Rev 2008, 21(3):538-582. 10.1128/CMR.00058-07, 2493088, 18625687.
4. Yun SH, Choi CW, Kwon SO, Park GW, Cho K, Kwon KH, Kim JY, Yoo JS, Lee JC, Choi JS, Kim S, Kim SI. Quantitative proteomic analysis of cell wall and plasma membrane fractions from multidrug-resistant Acinetobacter baumannii. J Proteome Res 2011, 10(2):459-469. 10.1021/pr101012s, 21053951.
5. Chopra S, Ramkissoon K, Anderson DC. A systematic quantitative proteomic examination of multidrug resistance in Acinetobacter baumannii. J Proteomics 2013, 84:17-39.
6. Siroy A, Cosette P, Seyer D, Lemaitre-Guillier C, Vallenet D, Van Dorsselaer A, Boyer-Mariotte S, Jouenne T, De E. Global comparison of the membrane subproteomes between a multidrug-resistant Acinetobacter baumannii strain and a reference strain. J Proteome Res 2006, 5(12):3385-3398. 10.1021/pr060372s, 17137340.
7. Coyne S, Guigon G, Courvalin P, Perichon B. Screening and quantification of the expression of antibiotic resistance genes in Acinetobacter baumannii with a microarray. Antimicrob Agents Chemother 2010, 54(1):333-340. 10.1128/AAC.01037-09, 2798560, 19884373.
8. Camarena L, Bruno V, Euskirchen G, Poggio S, Snyder M. Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing. PLoS Pathog 2010, 6(4):e1000834. 10.1371/journal.ppat.1000834, 2848557, 20368969.
9. Dotsch A, Eckweiler D, Schniederjans M, Zimmermann A, Jensen V, Scharfe M, Geffers R, Haussler S. The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing. PLoS One 2012, 7(2):e31092. 10.1371/journal.pone.0031092, 3272035, 22319605.
10. Eijkelkamp BA, Stroeher UH, Hassan KA, Elbourne LD, Paulsen IT, Brown MH. H-NS plays a role in expression of Acinetobacter baumannii virulence features. Infect Immun 2013, 81(7):2574-2583. 10.1128/IAI.00065-13, 3697591, 23649094.
11. Rumbo-Feal S, Gomez MJ, Gayoso C, Alvarez-Fraga L, Cabral MP, Aransay AM, Rodriguez-Ezpeleta N, Fullaondo A, Valle J, Tomas M, Bou G, Poza M. Whole transcriptome analysis of Acinetobacter baumannii assessed by RNA-sequencing reveals different mRNA expression profiles in biofilm compared to planktonic cells. PLoS One 2013, 8(8):e72968. 10.1371/journal.pone.0072968, 3758355, 24023660.
12. Cerqueira GM, Kostoulias X, Khoo C, Aibinu I, Qu Y, Traven A, Peleg AY. A global virulence regulator in Acinetobacter baumannii and its control of the phenylacetic acid catabolic pathway. J Infect Dis 2014, doi:10.1093/infdis/jiu024.
13. Costerton JW, Stewart PS, Greenberg EP. Bacterial biofilms: a common cause of persistent infections. Science 1999, 284(5418):1318-1322. 10.1126/science.284.5418.1318, 10334980.
14. Kuo HY, Chang KC, Liu CC, Tang CY, Peng JH, Lu CW, Tu CC, Liou ML. Insertion sequence transposition determines imipenem resistance in Acinetobacter baumannii. Microb Drug Resist 2014, doi:10.1089/mdr.2014.0004.
15. Smith MG, Gianoulis TA, Pukatzki S, Mekalanos JJ, Ornston LN, Gerstein M, Snyder M. New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev 2007, 21(5):601-614. 10.1101/gad.1510307, 1820901, 17344419.
16. Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically: approved standard. [http://www.clsi.org/source/orders/free/m07-a8.pdf].
17. Mugnier PD, Poirel L, Nordmann P. Functional analysis of insertion sequence ISAba1, responsible for genomic plasticity of Acinetobacter baumannii. J Bacteriol 2009, 191(7):2414-2418. 10.1128/JB.01258-08, 2655512, 19136598.
18. Snitkin ES, Zelazny AM, Montero CI, Stock F, Mijares L, Murray PR, Segre JA. Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii. Proc Natl Acad Sci U S A 2011, 108(33):13758-13763. 10.1073/pnas.1104404108, 3158218, 21825119.
19. Vila J, Marti S, Sanchez-Cespedes J. Porins, efflux pumps and multidrug resistance in Acinetobacter baumannii. J Antimicrob Chemother 2007, 59(6):1210-1215. 10.1093/jac/dkl509, 17324960.
20. Hu WS, Yao SM, Fung CP, Hsieh YP, Liu CP, Lin JF. An OXA-66/OXA-51-like carbapenemase and possibly an efflux pump are associated with resistance to imipenem in Acinetobacter baumannii. Antimicrob Agents Chemother 2007, 51(11):3844-3852. 10.1128/AAC.01512-06, 2151406, 17724156.
21. Perez LR. Acinetobacter baumannii displays inverse relationship between meropenem resistance and biofilm production. J Chemother 2014, doi:http://dx.doi.org/10.1179/1973947813Y.0000000159.
22. Dijkshoorn L, Nemec A, Seifert H. An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii. Nat Rev Microbiol 2007, 5(12):939-951. 10.1038/nrmicro1789, 18007677.
23. Eijkelkamp BA, Hassan KA, Paulsen IT, Brown MH. Investigation of the human pathogen Acinetobacter baumannii under iron limiting conditions. BMC Genomics 2011, 12:126. 10.1186/1471-2164-12-126, 3055841, 21342532.
24. Jacobs AC, Sayood K, Olmsted SB, Blanchard CE, Hinrichs S, Russell D, Dunman PM. Characterization of the Acinetobacter baumannii growth phase-dependent and serum responsive transcriptomes. FEMS Immunol Med Microbiol 2012, 64(3):403-412. 10.1111/j.1574-695X.2011.00926.x, 22211672.
25. Coyne S, Courvalin P, Perichon B. Efflux-mediated antibiotic resistance in Acinetobacter spp. Antimicrob Agents Chemother 2011, 55(3):947-953. 10.1128/AAC.01388-10, 3067115, 21173183.
26. Kuo HY, Chang KC, Kuo JW, Yueh HW, Liou ML. Imipenem: a potent inducer of multidrug resistance in Acinetobacter baumannii. Int J Antimicrob Agents 2012, 39(1):33-38. 10.1016/j.ijantimicag.2011.08.016, 21996406.
27. Kuo HY, Yang CM, Lin MF, Cheng WL, Tien N, Liou ML. Distribution of blaOXA-carrying imipenem-resistant Acinetobacter spp. in 3 hospitals in Taiwan. Diagn Microbiol Infect Dis 2010, 66(2):195-199. 10.1016/j.diagmicrobio.2009.09.013, 19836186.
28. Liu W, Yu YH, Cao SY, Niu XN, Jiang W, Liu GF, Jiang BL, Tang DJ, Lu GT, He YQ, Tang JL. Transcriptome profiling of Xanthomonas campestris pv. campestris grown in minimal medium MMX and rich medium NYG. Res Microbiol 2013, 164(5):466-479. 10.1016/j.resmic.2013.02.005, 23470514.
29. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
30. Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 2011, 12(3):R22. 10.1186/gb-2011-12-3-r22, 3129672, 21410973.
31. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 2013, 31(1):46-53. 3869392, 23222703.
32. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28(1):33-36. 10.1093/nar/28.1.33, 102395, 10592175.
33. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30. 10.1093/nar/28.1.27, 102409, 10592173.
34. Tomaras AP, Dorsey CW, Edelmann RE, Actis LA. Attachment to and biofilm formation on abiotic surfaces by Acinetobacter baumannii: involvement of a novel chaperone-usher pili assembly system. Microbiology 2003, 149(Pt 12):3473-3484.
35. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25(4):402-408. 10.1006/meth.2001.1262, 11846609.
36. Carricajo A, Verhoeven PO, Guezzou S, Fonsale N, Aubert G. Detection of carbapenemase-producing bacteria by using an ultra-performance liquid chromatography-tandem mass spectrometry method. Antimicrob Agents Chemother 2014, 58(2):1231-1234. 10.1128/AAC.01540-13, 3910862, 24295978.