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Chapter 3.16 : Guidelines for Biochemical Identification of Aerobic Bacteria

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Guidelines for Biochemical Identification of Aerobic Bacteria, Page 1 of 2

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Abstract:

Clinical microbiology practice is rapidly moving away from the primary use of conventional biochemical tests for the identification of aerobic bacteria and towards the use of nonphenotypic identification methods. Analysis of the protein composition of a bacterial cell using matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry is being widely implemented into routine practice worldwide. MALDI-TOF mass spectrometry rapidly identifies a wide range of bacterial pathogens, including nonfermenting Gram-negative bacilli, staphylococci, corynebacteria, and anaerobes ( ). Molecular methods are also being implemented either as laboratory-developed assays or as part of a commercial platform for rapid identification of specific pathogens by various methods, including real-time PCR, partial DNA target sequencing, or microarrays ( ). Referral or reference laboratories may also routinely perform in-house partial 16S rRNA gene sequencing of fastidious or unusual bacterial isolates that cannot be definitively identified by other means ( ).

Citation: Church D. 2016. Guidelines for Biochemical Identification of Aerobic Bacteria, p 3.16.1-3.16.5. In Leber A (ed), Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.16
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References

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1. Carbonnelle E, Beretti JL, Cottyn S, Quesne G, Berche P, Nassif X, Ferroni A. 2007. Rapid identification of staphylococci isolated in clinical microbiology laboratories by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 45:21562161.
2. Degand N, Carbonnelle E, Dauphin B, Beretti JL, Le Bourgeois M, Sermet-Gaudelus I, Segonds C, Berche P, Nassif X, Ferroni A. 2008. Matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis patients. J Clin Microbiol 46:33613367.
3. Stingu CS, Rodloff AC, Jentsch H, Schaumann R, Eschrich K. 2008. Rapid identification of oral anaerobic bacteria cultivated from subgingival biofilm by MALDI-TOFMS. Oral Microbiol Immunol 23:372376.
4. Nagy E, Maier T, Urban E, Terhes G, Kostrzewa M. 2009. Species identification of clinical isolates of Bacteroides by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry. Clin Microbiol Infect 15:796802.
5. La Scola B, Fournier PE, Raoult D. 2011. Burden of emerging anaerobes in the MALDI-TOF and 16S rRNA gene sequencing era. Anaerobe 17:106112.
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7. Sibley CD, Peirano G, Church DL. 2012. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. Infect Gen Evol 12:505521.
8. CLSI. 2008. Interpretive Criteria for Identification of Bacteria and Fungi by DNA Target Sequencing. CLSI, Wayne, PA.
9. Carroll KC, Weinstein WP. 2007. Manual and automated systems for detection and identification of microorganisms, p 192211. In Murray PR, Baron EJ, Jorgensen JH, Landry ML, Pfaller MA (ed), Manual of Clinical Microbiology, 9th ed, vol 1. ASM Press, Washington, DC.
10. O’Hara CM. 2005. Manual and automated instrumentation for identification of Enterobacteriaceae and other aerobic gram-negative bacilli. Clin Microbiol Rev 18:147162.
11. Rennie RP, Brosnikoff C, Turnbull I, Reller IB, Mirrett S, Janda W, Ristow K, Krilcich A. 2008. Multicenter evaluation of the Vitek 2 anaerobe and Corynebacterium identification card. J Clin Microbiol 46:26462651.
1. McFarland J. 1907. Nephelometer: an instrument for estimating the number of bacteria in suspensions used for calculating the opsonic index and for vaccines. JAMA 49:11761178.
2. CLSI. 2011. Performance Standards for Antimicrobial Disk Susceptibility Tests, 11th ed. Approved standard M02-A11. CLSI, Wayne, PA.
3. Baron EJ, Peterson L, Finegold SM. 1994. Bailey and Scott’s Diagnostic Microbiology, 9th ed, p 170171. Mosby, St. Louis, MO.

Tables

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Table 3.16–1

Summary of commonly used commercial manual and automated bacterial identification systems

Citation: Church D. 2016. Guidelines for Biochemical Identification of Aerobic Bacteria, p 3.16.1-3.16.5. In Leber A (ed), Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.16
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Untitled

Citation: Church D. 2016. Guidelines for Biochemical Identification of Aerobic Bacteria, p 3.16.1-3.16.5. In Leber A (ed), Clinical Microbiology Procedures Handbook, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818814.ch3.16

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