Investigation of antibiotic resistance in the genomic era of multidrug-resistant Gram-negative bacilli, especially Enterobacteriaceae, Pseudomonas and Acinetobacter

Expert Review of Anti-Infective Therapy

Volumn 11, Issue 3, 2013, Pages 277-296

  Diene, Seydina M ^a   Rolain, Jean Marc ^a  

^a AIX MARSEILLE UNIVERSITÉ   (France)

Author keywords

antibiotic resistance; Enterobacteriaceae Pseudomonas and Acinetobacter species; genome sequence analysis; high throughput sequencing technologies; multidrug resistant bacteria; Pseudomonas

Indexed keywords

ACINETOBACTER; ANTIBIOTIC RESISTANCE; BACTERIAL GENOME; BACTERIAL STRAIN; ENTEROBACTERIACEAE; ESCHERICHIA; GENE SEQUENCE; GENE TECHNOLOGY; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; INTERMETHOD COMPARISON; KLEBSIELLA; MULTIDRUG RESISTANCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PSEUDOMONAS; PYROSEQUENCING; REVIEW; STRAIN DIFFERENCE;

ACINETOBACTER; ANTI-BACTERIAL AGENTS; DRUG RESISTANCE, MULTIPLE, BACTERIAL; ENTEROBACTERIACEAE; GENOMICS; GRAM-NEGATIVE BACTERIA; GRAM-NEGATIVE BACTERIAL INFECTIONS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PHYLOGENY; PSEUDOMONAS; SEQUENCE ANALYSIS, DNA;

EID: 84874586090     PISSN: 14787210     EISSN: 17448336     Source Type: Journal    
DOI: 10.1586/eri.13.1     Document Type: Review

References (102)

1. Bissett L. ESBL-producing Enterobacte-riaceae: controlling the spread of infection. Br. J. Nurs. 16(11), 644-647 (2007).
2. Higgins PG, Dammhayn C, Hackel M, Seifert H. Global spread of carbapenem-resistant Acinetobacter baumannii. J. Antimicrob. Chemother. 65(2), 233-238 (2010).
3. Paterson DL. Extended-spectrum β-lactamases: the European experience. Curr. Opin. Infect. Dis. 14(6), 697-701 (2001).
4. Bush K, Courvalin P, Dantas G et al. Tackling antibiotic resistance. Nat. Rev. Microbiol. 9(12), 894-896 (2011).
5. Cosgrove SE. The relationship between antimicrobial resistance and patient outcomes: mortality, length of hospital stay, and health care costs. Clin. Infect. Dis. 42(Suppl. 2), S82-S89 (2006).
6. Schwaber MJ, Navon-Venezia S, Kaye KS, Ben-Ami R, Schwartz D, Carmeli Y. Clinical and economic impact of bactere-mia with extended-spectrum-β- lactamase-producing Enterobacteriaceae. Antimicrob. Agents Chemother. 50(4), 1257-1262 (2006).
7. Kunz AN, Brook I. Emerging resistant Gram-negative aerobic bacilli in hospital-acquired infections. Chemotherapy 56(6), 492-500 (2010).
8. Boucher H W, Talbot GH, Bradley JS et al. Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America. Clin. Infect. Dis. 48(1), 1-12 (2009).
9. Tumbarello M, Sanguinetti M, Montuori E et al. Predictors of mortality in patients with bloodstream infections caused by extended-spectrum-β- lactamase-producing Enterobacteriaceae: importance of inadequate initial antimicrobial treatment. Antimicrob. Agents Chemother. 51(6), 1987-1994 (2007).
10. Chastre J, Fagon JY. Ventilator-associated pneumonia. Am. J. Respir. Crit. Care Med. 165(7), 867-903 (2002).
11. Chastre J, Trouillet JL. Problem pathogens (Pseudomonas aeruginosa and Acinetobac-ter). Semin. Respir. Infect. 15(4), 287-298 (2000).
12. Oncül O, Keskin O, Acar HV et al. Hospital-acquired infections following the 1999 Marmara earthquake. J. Hosp. Infect. 51(1), 47-51 (2002).
13. Scott P, Deye G, Srinivasan A et al. An outbreak of multidrug-resistant Acinetobacter baumannii-calcoaceticus complex infection in the US military health care system associated with military operations in Iraq. Clin. Infect. Dis. 44 (12), 1577-1584 (2007).
14. Davies J. Inactivation of antibiotics and the dissemination of resistance genes. Science 264(5157), 375-382 (1994).
15. Georgiades K. Genomics of epidemic pathogens. Clin. Microbiol. Infect. 18 (3), 213-217 (2012).
16. Merhej V, Royer-Carenzi M, Pontarotti P, Raoult D. Massive comparative genomic analysis reveals convergent evolution of specialized bacteria. Biol. Direct 4, 13 (2009).
17. Wright GD, Sutherland AD. New strategies for combating multidrug-resist-ant bacteria. Trends Mol. Med. 13(6), 260-267 (2007).
18. Neu HC. The emergence of bacterial resistance and its infuence on empiric therapy. Rev. Infect. Dis. 5(Suppl. 1), S9-S20 (1983).
19. Iannini PB, Eickhoff TC, LaForce FM. Multidrug-resistant Proteus rettgeri: an emerging problem. Ann. Intern. Med. 85(2), 161-164 (1976).
20. Acar JF. Problems and changing patterns of resistance with Gram-negative bacteria. Rev. Infect. Dis. 7(Suppl. 4), S545-S551 (1985).
21. Lambert T, Gerbaud G, Courvalin P. Transferable amikacin resistance in Acinetobacter spp. due to a new type of 3́-aminoglycoside phosphotransferase. Antimicrob. Agents Chemother. 32(1), 15-19 (1988).
22. Hedges RW, Matthew M, Smith DI, Cresswell JM, Jacob AE. Properties of a transposon conferring resistance to penicillins and streptomycin. Gene 1(3-4), 241-253 (1977).
23. Mazel D. Integrons: agents of bacterial evolution. Nat. Rev. Microbiol. 4(8), 608-620 (2006).
24. Wright GD. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat. Rev. Microbiol. 5(3), 175-186 (2007).
25. Villa L, Poirel L, Nordmann P, Carta C, Carattoli A. Complete sequencing of an IncH plasmid carrying the blaNDM-1, blaC TX-M-15 and qnrB1 genes. J. Antimicrob. Chemother. 67(7), 1645-1650 (2012).
26. Hassan WM, Hashim A, Domany R. Plasmid mediated quinolone resistance determinants qnr, aac(6)-Ib-cr, and qep in ESBL-producing Escherichia coli clinical isolates from Egypt. Indian J. Med. Microbiol. 30(4), 442-447 (2012).
27. Liou GF, Yoshizawa S, Courvalin P, Galimand M. Aminoglycoside resistance by ArmA-mediated ribosomal 16S methyla-tion in human bacterial pathogens. J. Mol. Biol. 359(2), 358-364 (2006).
28. Hopkins KL, Davies RH, Threlfall EJ. Mechanisms of quinolone resistance in Escherichia coli and Salmonella: recent developments. Int. J. Antimicrob. Agents 25(5), 358-373 (2005).
29. Barrow K, Kwon DH. Alterations in two-component regulatory systems of phoPQ and pmrAB are associated with polymyxin B resistance in clinical isolates of Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 53 (12), 5150-5154 (2009).
30. Giannouli M, Di Popolo A, Durante-Man-goni E et al. Molecular epidemiology and mechanisms of rifampicin resistance in Acinetobacter baumannii isolates from Italy. Int. J. Antimicrob. Agents 39(1), 58-63 (2012).
31. D'Costa VM, King CE, Kalan L et al. Antibiotic resistance is ancient. Nature 477(7365), 457-461 (2011).
32. Rolain JM, Canton R, Cornaglia G. Emergence of antibiotic resistance: need for a new paradigm. Clin. Microbiol. Infect. 18 (7), 615-616 (2012).
33. Fleischmann RD, Adams MD, White O et al. Whole-genome random sequencing and assembly of Haemophilus infuenzae Rd. Science 269(5223), 496-512 (1995).
34. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA 74(12), 5463-5467 (1977).
35. Margulies M, Egholm M, Altman WE et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057), 376-380 (2005).
36. Sahl J W, Johnson JK, Harris AD et al. Genomic comparison of multi-drug resistant invasive and colonizing Acineto-bacter baumannii isolated from diverse human body sites reveals genomic pla s ticit y. BMC Genomics 12, 291 (2011).
37. Rasko DA, Webster DR, Sahl JW et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N. Engl. J. Med. 365(8), 709-717 (2011).
38. Hall N. Advanced sequencing technologies and their wider impact in microbiology. J. Exp. Biol. 210(Pt 9), 1518-1525 (2007).
39. Fournier PE, Drancourt M, Raoult D. Bacterial genome sequencing and its use in infectious diseases. Lancet Infect. Dis. 7(11), 711-723 (2007).
40. Shendure J, Porreca GJ, Reppas NB et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309(5741), 1728-1732 (2005).
41. Bennett S. Solexa Ltd. Pharmacogenomics 5(4), 433-438 (2004).
42. Madabhushi RS. Separation of 4-color DNA sequencing extension products in noncovalently coated capillaries using low viscosity polymer solutions. Electrophoresis 19(2), 224-230 (1998).
43. Nagarajan N, Pop M. Sequencing and genome assembly using next-generation technologies. Methods Mol. Biol. 673, 1-17 (2010).
44. Liu L, Li Y, Li S et al. Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012, 251364 (2012).
45. Loman NJ, Misra RV, Dallman TJ et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 30(5), 434-439 (2012).
46. Daigle D, Simen BB, Pochart P. High-throughput sequencing of PCR products tagged with universal primers using 454 life sciences systems. Curr. Protoc. Mol. Biol. Chapter 7, Unit7.5 (2011).
47. Bush K. Antimicrobial agents targeting bacterial cell walls and cell membranes. Rev. Sci. Tech. 31(1), 43-56 (2012).
48. McCoy LS, Xie Y, Tor Y. Antibiotics that target protein synthesis. Wiley Interdiscip. Rev. RNA 2(2), 209-232 (2011).
49. Beauchef-Havard A, Arlet G, Gautier V, Labia R, Grimont P, Philippon A. Molecular and biochemical characterization of a novel class A β-lactamase (HER-1) from Escherichia hermannii. Antimicrob. Agents Chemother. 47(8), 2669-2673 (2003).
50. Fevre C, Passet V, Weill FX, Grimont PA, Brisse S. Variants of the Klebsiella pneumoniae OKP chromosomal β-lactamase are divided into two main groups, OKP-A and OKP-B. Antimicrob. Agents Chemother. 49 (12), 5149-5152 (2005).
51. Haeggman S, Löfdahl S, Paauw A, Verhoef J, Brisse S. Diversity and evolution of the class A chromosomal β-lactamase gene in Klebsiella pneumoniae. Antimicrob. Agents Chemother. 48(7), 2400-2408 (2004).
52. Nordmann P, Poirel L, Walsh TR, Livermore DM. The emerging NDM carbapenemases. Trends Microbiol. 19 (12), 588-595 (2011).
53. Kempf M, Rolain JM. Emergence of resistance to carbapenems in Acinetobacter baumannii in Europe: clinical impact and therapeutic options. Int. J. Antimicrob. Agents 39(2), 105-114 (2012).
54. Nordmann P, Gniadkowski M, Giske CG, Poirel L, Woodford N, Miriagou V; European Network on Carbapenemases. Identifcation and screening of carbapene-mase-producing Enterobacteriaceae. Clin. Microbiol. Infect. 18(5), 432-438 (2012).
55. Chiu CH, Tang P, Chu C et al. The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen. Nucleic Acids Res. 33(5), 1690-1698 (2005).
56. Peleg AY, Seifert H, Paterson DL. Acinetobacter baumannii: emergence of a successful pathogen. Clin. Microbiol. Rev. 21(3), 538-582 (2008).
57. Miyoshi-Akiyama T, Kuwahara T, Tada T, Kitao T, Kirikae T. Complete genome sequence of highly multidrug-resistant Pseudomonas aeruginosa NCGM2.S1, a representative strain of a cluster endemic to Japan. J. Bacteriol. 193 (24), 7010 (2011).
58. Tada T, Kitao T, Miyoshi-Akiyama T, Kirikae T. Genome sequence of multidrug-resistant Pseudomonas aeruginosa NCG M1179. J. Bacteriol. 193(22), 6397 (2011).
59. Biswas S, Brunel JM, Dubus JC, Reynaud-Gaubert M, Rolain JM. Colistin: an update on the antibiotic of the 21st century. Expert Rev. Anti. Infect. Ther. 10(8), 917-934 (2012).
60. Fournier PE, Vallenet D, Barbe V et al. Comparative genomics of multidrug resistance in Acinetobacter baumannii. PLoS Genet. 2(1), e7 (2006).
61. Chen CC, Lin YC, Sheng WH et al. Genome sequence of a dominant, multidrug-resistant Acinetobacter bauman-nii strain, TCDC-AB0715. J. Bacteriol. 193(9), 2361-2362 (2011).
62. Adams MD, Goglin K, Molyneaux N et al. Comparative genome sequence analysis of multidrug-resistant Acinetobacter bauman-nii. J. Bacteriol. 190(24), 8053-8064 (2008).
63. Zarrilli R, Giannouli M, Rocco F et al. Genome sequences of three Acinetobacter baumannii strains assigned to the multilocus sequence typing genotypes ST2, ST25, and ST78. J. Bacteriol. 193(9), 2359-2360 (2011).
64. Zhou H, Zhang T, Yu D et al. Genomic analysis of the multidrug-resistant Acinetobacter baumannii strain MDR-ZJ06 widely spread in China. Antimicrob. Agents Chemother. 55 (10), 4506-4512 (2011).
65. Galimand M, Courvalin P, Lambert T. Plasmid-mediated high-level resistance to aminoglycosides in Enterobacteriaceae due to 16S rRNA methylation. Antimicrob. Agents Chemother. 47(8), 2565-2571 (2003).
66. Huang H, Yang ZL, Wu XM et al. Complete genome sequence of Acinetobac-ter baumannii MDR-TJ and insights into its mechanism of antibiotic resistance. J. Antimicrob. Chemother. 67(12), 2825-2832 (2012).
67. Rolain JM, Diene SM, Kempf M, Gimenez G, Robert C, Raoult D. Real-time sequencing to decipher the molecular mechanism of resistance of a clinical pan-drug-resistant Acinetobacter baumannii isolate from Marseille, France. Antimicrob. Agents Chemother. 57(1), 592-596 (2013).
68. Imperi F, Antunes LC, Blom J et al. The genomics of Acinetobacter baumannii: insights into genome plasticity, antimicrobial resistance and pathogenicity. IUBMB Life 63(12), 1068-1074 (2011).
69. Hornsey M, Loman N, Wareham DW et al. Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy. J. Antimicrob. Chemother. 66(7), 1499-1503 (2011).
70. Coelho JM, Turton JF, Kaufmann ME et al. Occurrence of carbapenem-resistant Acinetobacter baumannii clones at multiple hospitals in London and Southeast England. J. Clin. Microbiol. 44 (10), 3623-3627 (2006).
71. Iacono M, Villa L, Fortini D et al. Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group. Antimicrob. Agents Chemother. 52(7), 2616-2625 (2008).
72. Poirel L, Marqué S, Héritier C, Segonds C, Chabanon G, Nordmann P. OXA-58, a novel class D {β}-lactamase involved in resistance to carbapenems in Acinetobacter baumannii. Antimicrob. Agents Chemother. 49(1), 202-208 (2005).
73. Barbe V, Vallenet D, Fonknechten N et al. Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucleic Acids Res. 32(19), 5766-5779 (2004).
74. Ramirez MS, Adams MD, Bonomo RA, Centrón D, Tolmasky ME. Genomic analysis of Acinetobacter baumannii A 118 by comparison of optical maps: identifca-tion of structures related to its susceptibility phenotype. Antimicrob. Agents Chemother. 55(4), 1520-1526 (2011).
75. Park JY, Kim S, Kim SM, Cha SH, Lim SK, Kim J. Complete genome sequence of multidrug-resistant Acinetobacter baumannii strain 1656-2, which forms sturdy bioflm. J Bacteriol. 193(22), 6393-6394 (2011).
76. Yong D, Toleman MA, Giske CG et al. Characterization of a new metallo-β-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob. Agents Chemother. 53(12), 5046-5054 (2009).
77. Wolter DJ, Hanson ND, Lister PD. Insertional inactivation of oprD in clinical isolates of Pseudomonas aeruginosa leading to carbapenem resistance. FEMS Microbiol. Lett. 236(1), 137-143 (2004).
78. Savard P, Perl TM. A call for action: managing the emergence of multidrug-resistant Enterobacteriaceae in the acute care settings. Curr. Opin. Infect. Dis. 25(4), 371-377 (2012).
79. Lescat M, Calteau A, Hoede C et al. A module located at a chromosomal integration hot spot is responsible for the multidrug resistance of a reference strain from Escherichia coli clonal group A. Antimicrob. Agents Chemother. 53(6), 2283-2288 (2009).
80. Fricke WF, Wright MS, Lindell AH et al. Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5. J. Bacteriol. 190(20), 6779-6794 (2008).
81. Forgetta V, Rempel H, Malouin F et al. Pathogenic and multidrug-resistant Escherichia fergusonii from broiler chicken. Poult. Sci. 91(2), 512-525 (2012).
82. Paterson DL, Ko WC, Von Gottberg A et al. International prospective study of Klebsiella pneumoniae bacteremia: implications of extended-spectrum β-lactamase production in nosocomial Infections. Ann. Intern. Med. 140(1), 26-32 (2004).
83. Paterson DL. Resistance in Gram-negative bacteria: Enterobacteriaceae. Am. J. Infect. Control 34(5 Suppl. 1), S20-S28; discussion S64 (2006).
84. Kumar V, Sun P, Vamathevan J et al. Comparative genomics of Klebsiella pneumoniae strains with different antibiotic resistance profles. Antimicrob. Agents Chemother. 55(9), 4267-4276 (2011).
85. Liu P, Li P, Jiang X et al. Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum. J. Bacteriol. 194(7), 1841-1842 (2012).
86. Michael GB, Kadlec K, Sweeney MT et al. ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer. J. Antimicrob. Chemother. 67(1), 91-100 (2012).
87. Seth-Smith HM, Fookes MC, Okoro CK et al. Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae. J. Bacteriol. 194(6), 1494-1504 (2012).
88. Izumiya H, Sekizuka T, Nakaya H et al. Whole-genome analysis of Salmonella enterica serovar Typhimurium T000240 reveals the acquisition of a genomic island involved in multidrug resistance via IS1 derivatives on the chromosome. Antimicrob. Agents Chemother. 55(2), 623-630 (2011).
89. Diene SM, Merhej V, Henry M et al. The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new 'killer bugs' are created because of a sympatric lifestyle. Mol. Biol. Evol. 30(2), 369-383 (2012).
90. Sun S, Negrea A, Rhen M, Andersson DI. Genetic analysis of colistin resistance in Salmonella enterica serovar Typhimurium. Antimicrob. Agents Chemother. 53(6), 2298-2305 (2009).
91. Ye C, Lan R, Xia S et al. Emergence of a new multidrug-resistant serotype X variant in an epidemic clone of Shigella fexneri. J. Clin. Microbiol. 48(2), 419-426 (2010).
92. Clifford RJ, Hang J, Riley MC et al. Complete genome sequence of Providencia stuartii clinical isolate MRSN 2154. J. Bacteriol. 194(14), 3736-3737 (2012).
93. McGann P, Hang J, Clifford RJ et al. Complete sequence of a novel 178-kilobase plasmid carrying bla(NDM-1) in a Providencia stuartii strain isolated in Afghanistan. Antimicrob. Agents Chemother. 56 (4), 1673-1679 (2012).
94. Sommer MO, Dantas G, Church GM. Functional characterization of the antibiotic resistance reservoir in the human microfora. Science 325 (5944), 1128-1131 (2009).
95. Liu B, Pop M. ARDB-Antibiotic Resistance Genes Database. Nucleic Acids Res. 37(Database issue), D443-D447 (2009).
96. Zankari E, Hasman H, Cosentino S et al. Identifcation of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67(11), 2640-2644 (2012).
97. Tsafnat G, Copty J, Partridge SR. RAC: repository of antibiotic resistance cassettes. Database (Oxford) 2011, bar054 (2011).
98. Scaria J, Chandramouli U, Verma SK. Antibiotic Resistance Genes Online (ARGO): a database on vancomycin and β-lactam resistance genes. Bioinformation 1(1), 5-7 (2005).
99. Hu Y, Zhang W, Liang H et al. Whole-genome sequence of a multidrug-resistant clinical isolate of Acinetobacter lwoffi. J. Bacteriol. 193 (19), 5549-5550 (2011).
100. Loman NJ, Misra RV, Dallman TJ et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat.Biotechnol. 30(5), 434-439 (2012).
101. Liu L, Li Y, Li S. Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012, 251364 (2009).
102. Nagarajan N, Pop M. Sequencing and genome assembly using next-generation technologies. Methods Mol.Biol. 673, 1-17 (2010).