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Chapter 31 : Diagnostics, Typing, and Taxonomy

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Diagnostics, Typing, and Taxonomy, Page 1 of 2

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Abstract:

Speciation in bacterial systematics is based on a comparison of organismal characteristics in order to arrange microorganisms in groups sharing common properties. The purpose of speciation is identification of a microorganism as belonging to a basic taxon, which, for example, has a particular ecological or clinical significance. In general, the purpose of typing is the study of population dynamics and the spread of microorganisms that undergo clonal (nonsexual) reproduction. Thus typing is an important tool of epidemiology for tracing the spread of particular strains and discovering routes of transmission and reservoirs. Clumping factor causes agglutination in the presence of human plasma and is therefore very easy to detect. The accuracy of commercial slide agglutination tests has recently been improved by the addition of antibodies against capsular antigens, which provides sufficient sensitivity for speciation of methicillin-resistant (MRSA). The chapter talks about requirements for typing systems, and discusses phenotypic typing methods and genotyping methods applied to . Polymorphisms detected by PCR can be based on genetic events taking place between the location of primer binding sequences, thus leading to different length of amplimers. Multilocus sequence typing (MLST) requires the highest workload and is not discriminatory enough for epidemiological typing, but is highly predicative in analysis of evolutionary relationships. Finally, the chapter discusses combined use of different molecular typing methods, and compares different genotypic typing systems.

Citation: Novick R, Witte W, Strommenger B, Werner G. 2006. Diagnostics, Typing, and Taxonomy, p 371-380. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch31

Key Concept Ranking

Restriction Fragment Length Polymorphism
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Random Amplified Polymorphic DNA
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Genetic Elements
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Pulsed-Field Gel Electrophoresis
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Figures

Image of FIGURE 1
FIGURE 1

Phylogenetic relations among staphylococcal species as deduced from DNA-DNA hybridization. (Reprinted with permission from reference .)

Citation: Novick R, Witte W, Strommenger B, Werner G. 2006. Diagnostics, Typing, and Taxonomy, p 371-380. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch31
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Image of FIGURE 2
FIGURE 2

Phylogenetic relationship of staphylococci reflected by the 16S rRNA-based tree. (Reprinted from reference , with permission.)

Citation: Novick R, Witte W, Strommenger B, Werner G. 2006. Diagnostics, Typing, and Taxonomy, p 371-380. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch31
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Image of FIGURE 3
FIGURE 3

Examples of BURST analysis according to Feil et al. ( ). (A) Clonal lineages derived from ancestor lineage ST30; ST36 is EMRSA (epidemic MRSA) 16 in United Kingdom. (B) Clonal lineages derived from ancestor ST51.

Citation: Novick R, Witte W, Strommenger B, Werner G. 2006. Diagnostics, Typing, and Taxonomy, p 371-380. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch31
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Image of FIGURE 4
FIGURE 4

Representation of the gene coding for protein A. Five and 12 repeats have been indicated in the Fc-binding region and the X region, respectively. The locations of the forward and reverse primers, used to amplify and sequence the X region, are shown.

Citation: Novick R, Witte W, Strommenger B, Werner G. 2006. Diagnostics, Typing, and Taxonomy, p 371-380. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch31
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Image of FIGURE 5
FIGURE 5

() Different types of SCC elements demonstrated in MRSA orf X, open reading frame X of the chromosome. (Adapted with permission from references and .)

Citation: Novick R, Witte W, Strommenger B, Werner G. 2006. Diagnostics, Typing, and Taxonomy, p 371-380. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch31
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References

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Tables

Generic image for table
TABLE 1

Characteristics of the genus in comparison to other genera classified as members of the family

ND, not determined.

Citation: Novick R, Witte W, Strommenger B, Werner G. 2006. Diagnostics, Typing, and Taxonomy, p 371-380. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch31
Generic image for table
TABLE 2

Example of numerical coding of types

Reprinted with permission from reference .

Citation: Novick R, Witte W, Strommenger B, Werner G. 2006. Diagnostics, Typing, and Taxonomy, p 371-380. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch31
Generic image for table
TABLE 3

Epidemic MRSA with wide geographical dissemination

Community-acquired MRSA.

Citation: Novick R, Witte W, Strommenger B, Werner G. 2006. Diagnostics, Typing, and Taxonomy, p 371-380. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch31
Generic image for table
TABLE 4

Comparison of genotyping systems applied to

Citation: Novick R, Witte W, Strommenger B, Werner G. 2006. Diagnostics, Typing, and Taxonomy, p 371-380. In Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J (ed), Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816513.ch31

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