title: Modern clinical microbiology: new challenges and solutions.
abstract: In the twenty-first century, the clinical microbiology laboratory plays a central part in optimizing the management of infectious diseases and surveying local and global epidemiology. This pivotal role is made possible by the adoption of rational sampling, point-of-care tests, extended automation and new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and versatile and permissive culture systems. When balanced with cost, these developments can improve the workflow and output of clinical microbiology laboratories and, by identifying and characterizing microbial pathogens, provide significant input to scientific discovery.
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Marseille, France.
authors.forename: Pierre-Edouard
authors.initials: PE
authors.lastname: Fournier
authors.forename: Michel
authors.initials: M
authors.lastname: Drancourt
authors.forename: Philippe
authors.initials: P
authors.lastname: Colson
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Rolain
authors.forename: Bernard
authors.initials: B
authors.lastname: La Scola
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D057205:Automation, Laboratory / Q000379:methods*; D001419:Bacteria / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification; D003141:Communicable Diseases / Q000175:diagnosis* / Q000188:drug therapy; D018563:Disease Notification; D024881:Drug Resistance, Bacterial; D006801:Humans; D008828:Microbiological Techniques / Q000295:instrumentation / Q000379:methods*; D011786:Quality Control; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods; D014780:Viruses / Q000235:genetics / Q000302:isolation & purification
chemical_list: D000900:Anti-Bacterial Agents
references.citation: Ann Lab Med. 2013 Jan;33(1):14-27
references.pmid: 23301218
references.citation: N Engl J Med. 2011 Aug 25;365(8):718-24
references.pmid: 21793736
references.citation: Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4371-6
references.pmid: 20142485
references.citation: Nature. 2009 Jun 25;459(7250):1122-5
references.pmid: 19516283
references.citation: PLoS Pathog. 2012;8(8):e1002824
references.pmid: 22876174
references.citation: J Clin Microbiol. 2010 May;48(5):1549-54
references.pmid: 20220166
references.citation: Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14250-5
references.pmid: 12384570
references.citation: Lancet. 2003 Aug 9;362(9382):447-9
references.pmid: 12927433
references.citation: Clin Microbiol Rev. 1988 Jan;1(1):40-53
references.pmid: 3060244
references.citation: Nucleic Acids Res. 1990 Dec 25;18(24):7213-8
references.pmid: 2259619
references.citation: J Clin Microbiol. 1994 Aug;32(8):1970-5
references.pmid: 7989551
references.citation: J Emerg Med. 2010 Oct;39(4):501; author reply 501-2
references.pmid: 20456899
references.citation: Nucleic Acids Res. 1995 Nov 11;23(21):4407-14
references.pmid: 7501463
references.citation: PLoS One. 2011;6(7):e22403
references.pmid: 21811599
references.citation: Nature. 2008 Feb 21;451(7181):990-3
references.pmid: 18288193
references.citation: J Infect. 2012 Oct;65(4):302-9
references.pmid: 22728132
references.citation: Infect Genet Evol. 2010 Oct;10(7):866-75
references.pmid: 20692376
references.citation: PLoS One. 2009 Nov 25;4(11):e8041
references.pmid: 19946369
references.citation: J Clin Microbiol. 2007 Sep;45(9):2761-4
references.pmid: 17626177
references.citation: Appl Environ Microbiol. 2012 Jun;78(12):4065-73
references.pmid: 22504816
references.citation: Lancet Infect Dis. 2007 Nov;7(11):711-23
references.pmid: 17961857
references.citation: Nat Rev Microbiol. 2013 Jan;11(1):1
references.pmid: 23367520
references.citation: Clin Microbiol Infect. 2012 Dec;18(12):1185-93
references.pmid: 23033984
references.citation: Eur J Clin Invest. 2011 Jan;41(1):52-8
references.pmid: 20840375
references.citation: N Engl J Med. 2011 Feb 24;364(8):730-9
references.pmid: 21345102
references.citation: N Engl J Med. 2011 Jan 6;364(1):33-42
references.pmid: 21142692
references.citation: Nutr Rev. 2012 Aug;70 Suppl 1:S2-9
references.pmid: 22861804
references.citation: J Antimicrob Chemother. 2012 Oct;67(10):2307-8
references.pmid: 22729921
references.citation: Clin Microbiol Infect. 2011 May;17(5):651-4
references.pmid: 21521408
references.citation: J Clin Microbiol. 2013 Apr;51(4):1272-7
references.pmid: 23345298
references.citation: Nat Rev Genet. 2012 Sep;13(9):601-612
references.pmid: 22868263
references.citation: J Clin Microbiol. 2010 Jun;48(6):2110-5
references.pmid: 20392910
references.citation: J Clin Microbiol. 2011 Sep;49(9):3222-7
references.pmid: 21775535
references.citation: PLoS Pathog. 2009 May;5(5):e1000455
references.pmid: 19478873
references.citation: FEMS Microbiol Rev. 2012 Mar;36(2):380-407
references.pmid: 22092265
references.citation: Future Microbiol. 2010 Nov;5(11):1733-54
references.pmid: 21133692
references.citation: N Engl J Med. 1992 Jul 30;327(5):293-301
references.pmid: 1377787
references.citation: Microbiology (Reading). 2009 Jul;155(Pt 7):2384-2389
references.pmid: 19389783
references.citation: J Clin Microbiol. 2004 May;42(5):1875-84
references.pmid: 15131143
references.citation: N Engl J Med. 1990 Dec 6;323(23):1573-80
references.pmid: 2233945
references.citation: Curr Opin Infect Dis. 2013 Feb;26(1):73-9
references.pmid: 23242343
references.citation: Clin Microbiol Infect. 2009 Dec;15 Suppl 2:173-5
references.pmid: 19548995
references.citation: Curr Microbiol. 2012 Jul;65(1):44-53
references.pmid: 22526571
references.citation: Methods Mol Biol. 2013;943:49-79
references.pmid: 23104281
references.citation: PLoS Negl Trop Dis. 2007 Nov 28;1(2):e83
references.pmid: 18060087
references.citation: PLoS One. 2011;6(7):e22751
references.pmid: 21799941
references.citation: Clin Microbiol Infect. 2011 Mar;17(3):349-57
references.pmid: 20384709
references.citation: Lancet. 1994 Jan 22;343(8891):242
references.pmid: 7904703
references.citation: BMJ Open. 2012 Jun 06;2(3):
references.pmid: 22674929
references.citation: Int J Antimicrob Agents. 2011 Jun;37(6):544-6
references.pmid: 21497063
references.citation: J Clin Microbiol. 2012 Jun;50(6):2069-71
references.pmid: 22493334
references.citation: FEMS Microbiol Rev. 2009 Sep;33(5):892-916
references.pmid: 19453749
references.citation: Clin Microbiol Infect. 1998 Jul;4(7):401-404
references.pmid: 11864356
references.citation: J Antimicrob Chemother. 2006 May;57(5):825-31
references.pmid: 16547071
references.citation: PLoS Negl Trop Dis. 2013;7(1):e1999
references.pmid: 23350001
references.citation: New Microbiol. 2008 Oct;31(4):501-5
references.pmid: 19123305
references.citation: Trends Microbiol. 2013 Feb;21(2):92-9
references.pmid: 23182864
references.citation: Science. 1995 Oct 20;270(5235):467-70
references.pmid: 7569999
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4430-4
references.pmid: 19246385
references.citation: Curr Opin Microbiol. 2002 Jun;5(3):240-5
references.pmid: 12057676
references.citation: FEMS Immunol Med Microbiol. 2007 Feb;49(1):22-7
references.pmid: 17266711
references.citation: Future Microbiol. 2011 Sep;6(9):991-7
references.pmid: 21958140
references.citation: BMJ Open. 2013 Jan 09;3(1):
references.pmid: 23306006
references.citation: Arch Pathol Lab Med. 2013 Sep;137(9):1247-54
references.pmid: 23216247
references.citation: PLoS One. 2009;4(5):e5470
references.pmid: 19421405
references.citation: J Appl Microbiol. 2010 Feb;108(2):375-85
references.pmid: 19659699
references.citation: Int J Antimicrob Agents. 2006 Feb;27(2):138-51
references.pmid: 16427254
references.citation: J Hosp Infect. 2010 May;75(1):37-41
references.pmid: 20299126
references.citation: PLoS Pathog. 2012 Sep;8(9):e1002924
references.pmid: 23028323
references.citation: J Proteome Res. 2012 Jan 1;11(1):79-84
references.pmid: 22013912
references.citation: PLoS One. 2010 Apr 19;5(4):e10224
references.pmid: 20419105
references.citation: Clin Microbiol Infect. 2012 Apr;18(4):E81-3
references.pmid: 22360446
references.citation: JAMA. 2013 Apr 10;309(14):1531-2
references.pmid: 23571595
references.citation: J Appl Microbiol. 2007 Oct;103(4):1262-71
references.pmid: 17897230
references.citation: Expert Rev Mol Diagn. 2011 Apr;11(3):287-98
references.pmid: 21463238
references.citation: Clin Microbiol Infect. 2010 Aug;16(8):1054-61
references.pmid: 20670287
references.citation: J Microbiol Methods. 2005 Jul;62(1):113-20
references.pmid: 15823399
references.citation: J Clin Microbiol. 2013 May;51(5):1617-21
references.pmid: 23363834
references.citation: Medicine (Baltimore). 2008 May;87(3):167-176
references.pmid: 18520326
references.citation: Nat Genet. 2013 Jan;45(1):109-13
references.pmid: 23222960
references.citation: Nature. 2007 Oct 18;449(7164):804-10
references.pmid: 17943116
references.citation: Genome Res. 1996 Oct;6(10):986-94
references.pmid: 8908518
references.citation: Eur J Clin Microbiol Infect Dis. 2012 Sep;31(9):2445-52
references.pmid: 22395261
references.citation: Methods Mol Biol. 2012;903:103-12
references.pmid: 22782813
references.citation: J Clin Microbiol. 1999 Jun;37(6):1899-905
references.pmid: 10325344
references.citation: Curr Opin Infect Dis. 2000 Feb;13(1):29-36
references.pmid: 11964770
references.citation: J Med Microbiol. 2013 Jun;62(Pt 6):864-874
references.pmid: 23449879
references.citation: Intervirology. 2010;53(5):344-53
references.pmid: 20551686
references.citation: Sci Rep. 2013;3:1902
references.pmid: 23712667
references.citation: Curr Opin Microbiol. 2010 Oct;13(5):640-5
references.pmid: 20846899
references.citation: J Clin Microbiol. 2011 Sep;49(9):3321-4
references.pmid: 21795515
references.citation: Nat Rev Microbiol. 2008 Jul;6(7):553-8
references.pmid: 18521073
references.citation: J Clin Microbiol. 2012 Jul;50(7):2441-3
references.pmid: 22553235
references.citation: J Clin Microbiol. 2005 Oct;43(10):4993-5002
references.pmid: 16207953
references.citation: Genome Res. 2013 May;23(5):855-66
references.pmid: 23525359
references.citation: Emerg Infect Dis. 2001 Jan-Feb;7(1):73-81
references.pmid: 11266297
references.citation: Clin Microbiol Infect. 2011 May;17(5):655-60
references.pmid: 21521409
references.citation: Clin Microbiol Infect. 2011 Dec;17(12):1890-4
references.pmid: 21848972
references.citation: Eur J Clin Microbiol Infect Dis. 2012 Aug;31(8):1719-26
references.pmid: 22678348
references.citation: Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19781-5
references.pmid: 23129646
references.citation: Clin Infect Dis. 2010 Jul 15;51(2):131-40
references.pmid: 20540619
references.citation: Nat Rev Microbiol. 2004 Feb;2(2):161-6
references.pmid: 15040263
references.citation: Annu Rev Microbiol. 2011;65:169-88
references.pmid: 21639792
references.citation: Emerg Infect Dis. 2011 Oct;17(10):1906-9
references.pmid: 22000368
references.citation: N Engl J Med. 2008 Mar 6;358(10):991-8
references.pmid: 18256387
references.citation: Clin Microbiol Infect. 2010 Jul;16(7):809-20
references.pmid: 20880410
references.citation: J Clin Microbiol. 2010 May;48(5):1542-8
references.pmid: 20237092
references.citation: Sci Transl Med. 2012 Aug 22;4(148):148ra116
references.pmid: 22914622
references.citation: Clin Infect Dis. 2009 Aug 15;49(4):543-51
references.pmid: 19583519
references.citation: Nat Rev Microbiol. 2004 Feb;2(2):151-9
references.pmid: 15040262
references.citation: Clin Infect Dis. 1997 Apr;24(4):584-602
references.pmid: 9145732
references.citation: BMC Microbiol. 2010 Dec 03;10:310
references.pmid: 21129171
references.citation: Science. 2003 May 30;300(5624):1399-404
references.pmid: 12730501
references.citation: Eur J Clin Microbiol Infect Dis. 2013 May;32(5):637-45
references.pmid: 23291779
references.citation: J Clin Microbiol. 2012 Oct;50(10):3324-8
references.pmid: 22875888
references.citation: Genome Res. 2009 Jul;19(7):1214-23
references.pmid: 19351617
references.citation: Science. 2005 Jun 10;308(5728):1635-8
references.pmid: 15831718
references.citation: Clin Infect Dis. 1998 Feb;26(2):502-3
references.pmid: 9502483
references.citation: BMC Microbiol. 2012 Apr 04;12:52
references.pmid: 22475029
references.citation: Eur J Clin Microbiol Infect Dis. 2012 Nov;31(11):2919-28
references.pmid: 22644055
references.citation: N Engl J Med. 2000 Mar 2;342(9):620-5
references.pmid: 10699161