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Chapter 4 : Systems for Identification of Bacteria and Fungi*

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Abstract:

This chapter provides an overview of technologies used for identification of bacteria and fungi recovered from clinical specimens. This includes manual and automated approaches based on biochemical, protein, and/or DNA analysis. Matrix-assisted laser desorption ionization–time-of-flight mass spectrometry, which is being rapidly adopted by clinical laboratories, is highlighted. Regardless of the method used, the scientific approach to identify microorganisms, highlighted in this chapter, relies on the same fundamental principles.

Citation: Carroll K, Patel R. 2015. Systems for Identification of Bacteria and Fungi*, p 29-43. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch4
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Image of FIGURE 1
FIGURE 1

MALDI-TOF MS workflow (from ). A colony from a culture plate is placed on a “spot” on a MALDI-TOF MS target plate (a reusable or disposable plate with a number of test spots). One or many isolates is tested at a time. In this example, the Bruker Biotyper system is shown. Cells are treated with formic acid on the target plate. Following drying, the matrix is added ( ). After drying of the matrix, the plate is placed into the mass spectrometer for analysis ( Fig. 2 ). A mass spectrum is generated and compared by the system’s software against a database of mass spectra, resulting in identification of the organism ( in position A4 in the example). Reproduced by permission of Mayo Foundation for Medical Education and Research. All rights reserved. doi:10.1128/9781555817381.ch4.f1

Citation: Carroll K, Patel R. 2015. Systems for Identification of Bacteria and Fungi*, p 29-43. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch4
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Image of FIGURE 2
FIGURE 2

MALDI-TOF MS (from ). The target plate is placed into the mass spectrometer. Spots to be analyzed are shot by a laser, desorbing microbial and matrix molecules from the target plate. Charge is transferred from matrix to microbial molecules, and the ionized molecules are accelerated through a positively charged electrostatic field into the mass analyzer, a tube under vacuum. The ions travel toward an ion detector with the smallest analytes traveling fastest, followed by progressively larger analytes. As ions emerge from the mass analyzer, they run into the ion detector, thereby generating a mass spectrum representing the number of ions hitting the detector over time. Although separation is by mass-to-charge ratio, since the charge is typically single for the described application, separation is by molecular weight. Reproduced by permission of Mayo Foundation for Medical Education and Research. All rights reserved. doi:10.1128/9781555817381.ch4.f2

Citation: Carroll K, Patel R. 2015. Systems for Identification of Bacteria and Fungi*, p 29-43. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch4
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Tables

Generic image for table
TABLE 1

Technologies for microorganism identification

Citation: Carroll K, Patel R. 2015. Systems for Identification of Bacteria and Fungi*, p 29-43. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch4
Generic image for table
TABLE 2

Features of automated systems for identification of bacteria and yeasts

Citation: Carroll K, Patel R. 2015. Systems for Identification of Bacteria and Fungi*, p 29-43. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch4
Generic image for table
TABLE 3

Summary of nonautomated identification systems for bacterial identification available in 2013

Citation: Carroll K, Patel R. 2015. Systems for Identification of Bacteria and Fungi*, p 29-43. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch4
Generic image for table
TABLE 4

Evaluations of MALDI-TOF MS for routine bacterial identification ( )

Citation: Carroll K, Patel R. 2015. Systems for Identification of Bacteria and Fungi*, p 29-43. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch4

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