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Chapter 10: Methods for Classifying and Identifying Microorganisms

Chapter 10: Methods for Classifying and Identifying Microorganisms. Phylogenetic Relationships. Taxonomy The science of classifying organisms Provides universal names for organisms Based on phylogenetic studies Phylogeny: the study of the evolutionary relatedness among organisms.

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Chapter 10: Methods for Classifying and Identifying Microorganisms

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  1. Chapter 10:Methods for Classifying and Identifying Microorganisms

  2. Phylogenetic Relationships • Taxonomy • The science of classifying organisms • Provides universal names for organisms • Based on phylogenetic studies • Phylogeny: the study of the evolutionary relatedness among organisms

  3. The Three-Domain System:Classification Based on Cell Type • Bacteria • Archaea • Eukarya • Cell types differ in properties including rRNA sequences, membrane lipid structure, tRNA molecules, sensitivity to antibiotics, cell wall structure • rRNA sequences: primary means of determining phylogenetic relationships (especially for microorganisms) Table 10.1

  4. Applying Classification Strategies:Cladograms • Reflect evolutionary relatedness • Determined by rRNA sequences • The length of a shared line corresponds to the degree of similarity • Each branch point (fork) indicates the evolution of a novel property used to separate one group/organism from another Figure 10.18.2

  5. Species Definition • Eukaryotic species: • A group of closely related organisms that breed among themselves • Prokaryotic species: • A population of cells with similar characteristics • Clone: Population of cells derived from a single cell • Strain: Group of cells within the same species that have a distinct characteristic from others in the species

  6. Classification vs. Identification • Classification: based on phylogenetic/evolutionary relationships • Groups similar organisms together • Largely based on rRNA sequences (microorganisms) • Identification: utilizing observations and tests to identify an unknown organism • Clinical settings—for diagnosis, disease treatment scheme, etc. • Needs to be efficient

  7. Microorganism Identification Methods • Bergey’s Manual of Determinative Bacteriology: identification scheme reference • Morphological characteristics: Shape/structure; useful for identifying eukaryotes • Differential staining: Gram staining, acid-fast staining • Serology: Relies on pathogen-specific antibodies for identification • DNA-based Strategies • Biochemical tests: Determines presence of bacterial enzymes Figure 10.8

  8. Microorganism Identification Methods:Serology • Serology utilizes pathogen-specific antibodiesas a tool for identification • Example: Slide agglutination Known antiserum + unknown bacteriumreaction? Positive test Negative test Figure 10.10

  9. Serology:ELISA • Enzyme-linked Immunosorbent Assay (ELISA) • Antibody detection of specific pathogenic antigens Pathogen-specific antibody Patient sample http://www.komabiotech.com

  10. Microorganism Identification Methods:Phage Typing • Phage typing: tests which bacteriophages a bacterium is susceptible to • Phages are specific to a particular species or strain of bacteria • Many phages cause lysis of the cells they infect • Areas of clearing/ plaques • Can be used for comparisons (i.e. of two individuals’ infections) Figure 10.13

  11. Microorganism Identification Methods:DNA Strategies Patient sample Known bacteria: B E C D F G A • DNA fingerprinting • DNA of known microbe or unknown sample is digested with restriction enzymes • DNA fragments separated and patterns are compared • Polymerase Chain Reaction (PCR) • Amplification of a microbe-specific DNA fragment to detectable levels  identification Figure 10.14, modified

  12. Microorganism Identification Methods:DNA Strategies • Nucleic Acid Hybridization • Strands may be separated with heat • Complimentary sequences hybridize (bind) to one another Figure 10.15

  13. Microorganism Identification Methods:Biochemical Tests • Test for the presence of specific bacterial enzymes • Develop a biochemical/enzymatic profile for an unknown organism  identify the organism based on this profile

  14. Microorganism Identification Methods:Numerical Identification (Biochemical) • Rapid identification of medically important bacteria • Enterics (Enterotube) • Several biochemical tests simultaneously Figure 10.9

  15. Applying Identification Method Results:Biochemical Tests & Dichotomous Keys

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