bacterial+classification.pdf

Classification of Bacteria Microbiology Lecture Objectives 1. Understand how the vocabulary of taxonomy is critical to communicating the science of infectious diseases. 2. Know the taxonomic ranks. 3. Appreciate the growth, biochemical, and genetic characteristics that are used in differentia...

Classification of Bacteria Microbiology Lecture Objectives 1. Understand how the vocabulary of taxonomy is critical to communicating the science of infectious diseases. 2. Know the taxonomic ranks. 3. Appreciate the growth, biochemical, and genetic characteristics that are used in differentiating bacteria. 4. Understand the differences between the Eubacteria, Archaebacteria, and Eukaryotes. Taxonomy: A Vocabulary of Medical Microbiology Understanding Infectious Pathogens The diversity of medical pathogens associated with infectious diseases is vast. Currently, only 10% of pathogens responsible for human disease can be identified. Understanding Infectious Agents Each infectious agent has adapted to a specific mode of transmission, a mechanism to grow in human hosts, and a mechanism to cause disease. Classification, Nomenclature, and Identification 1. Classification - categorizing organisms into taxonomic groups. 2. Nomenclature - The naming of an organism by international rules based on its characteristics. 3. Identification - Practical use of a classification scheme to isolate and distinguish desirable organisms from undesirable ones. Implications of Taxonomy Identification schemes are not classification schemes but can be devised only after a group has been classified. Linnaean taxonomy - Most familiar system for biology, using formal taxonomic ranks of kingdom, phylum, class, order, family, genus, and species.  Linnaean Taxonomy “King Philip Came Over For Good Soup”  Bacterial Classification and Growth on Media 1. Growth on Bacterial Media - Bacterial growth is a key criterion for bacterial classification. - Most bacteria can be isolated on solid agar- containing media - Include agar, a carbon source, and an acid hydrolysate or enzymatically degraded source of biologic material. Bacterial Classification and Growth on Media 2. Types of Media a. Nonselective Media: - Support the growth of many different bacteria (e.g. Blood agar and chocolate agar) b. Selective Media: - Used to eliminate or reduce the large numbers of irrelevant bacteria in certain sampling sites. C. Differential Media: - Different bacteria produce characteristic pigments and can be differentiated based on their complement of extracellular enzymes. Bacterial Classification and Growth on Media 3. Bacterial Microscopy A. Gram stain B. Light microscopy Bacterial Classification and Growth on Media 4. Biochemical Tests A. Oxidase test - Can distinguish organisms based on the presence or absence of a respiratory enzyme, cytochrome C. B. Catalase activity - Can differentiate between gram-positive and gram-negative cocci. Bacterial Classification and Growth on Media 5. Immunologic Tests: Serotypes, Serogroups, and Serovars - "Sero" refers to antibodies reacting with specific bacterial cell structures. - "Serotype," "serogroups," and "serovars" use these antibodies to subdivide strains of a specific bacterial species. Genetic Instability Taxonomic criterion value depends on the biologic group being compared. Traits shared by all or none of a group can define a group. Genetic instability can cause highly variable traits within a biologic group or specific taxonomic group. - antibiotic resistance genes or enzyme-encoding genes on plasmids or bacteriophages. Phylogenetic Classification Suggest shared ancestors among two organisms. Fossil record lacks for bacteria, making it difficult to distinguish between convergent and divergent evolution. Bacteria's genetic properties - gene exchange among distantly related organisms. Bacteria reproduce clonally by binary fission -requiring a complementary set of chromosomes for reproduction. Genetic Diversity Among Bacteria Chemical characterization of bacterial genomic DNA reveals a wide range of nucleotide base compositions. Genetic relatedness of DNA from similar organisms can be used as a measure of taxonomic relatedness. DNA sequencing - more precise method for species delineation. Bergey's Manual of Systematic Bacteriology: Major Categories and Groups of Bacteria A comprehensive work on the taxonomic organization of bacteria. Published in 1923, it categorizes known bacteria into key groups. Bergey's Manual of Determinative Bacteriology - A companion volume - Aids in identifying previously described and cultured bacteria. - Lists major bacteria causing infectious diseases. Eubacteria and Archaebacteria: Two Types of Prokaryotic Organisms Eubacteria Classic bacteria with characteristic lipids, a peptidoglycan cell wall, and selectively inhibitable protein and nucleic acid synthesis machinery. Archaebacteria Lack a classic peptidoglycan cell wall Share characteristics similar to eukaryotic cells. Gram-Negative Eubacteria Heterogeneous group of bacteria with complex cell envelope. Reproduction: 1. Binary fission 2. Budding. Members may be phototrophic or nonphototrophic and include aerobic, anaerobic, facultatively anaerobic, and microaerophilic species. Gram-Positive Eubacteria: Cells have a gram-positive cell wall profile. Cells may be encapsulated and exhibit flagella-mediated motility. Reproduction : Binary fission Some bacteria produce spores as resting forms: - highly resistant to disinfection!  Eubacteria Lacking Cell Walls Mycoplasmas Enclosed by a plasma membrane. Do not synthesize peptidoglycan precursors Resemble L-forms from many bacteria species Range in size: vesicle-like forms to small and filterable forms Budding, fragmentation, or binary fission. 6 genera Require cholesterol for growth- Mollicutes' membranes Archaebacteria and Their Role in Epidemiology “Extremophiles" Archaebacteria and Their Role in Epidemiology Chemolithotrophs, Heterotrophs, Facultative heterotrophs, Mesophiles Lack of a peptidoglycan cell wall, possession of isoprenoid diether or diglycerol tetraether lipids, and characteristic ribosomal RNA sequences. Share some molecular features with eubacteria! Subtyping and its Application Process of distinguishing among strains of a given species or identifying a particular strain. Accomplished by examining bacterial isolates for characteristics that allow discrimination below the species level. Example: - Identification of over 130 serogroups of Vibrio cholerae based on antigenic differences in their LPS. Serologic Typing Plays an important role in the epidemiology of infectious diseases Especially in the context of common source outbreaks. Biotechnology advancements improved the ability to subtype microorganisms, with monoclonal antibodies against cell surface antigens used to create highly standardized antibody-based subtyping systems. Genotyping Genotyping multilocus enzyme electrophoresis (MLEE) Standard method for studying eukaryotic population genetics and pathogenic microorganisms' genetic diversity and clonal structure. Determines the mobility of soluble enzymes by starch gel electrophoresis, revealing amino acid substitutions in protein sequences and changes in DNA sequences. Helped researchers at the Centers for Disease Control and Prevention identify the HUS pathogen E coli serotype O157:H7. Chemical Fingerprinting Improves isolate identification using physical methods FTIR (Fourier Transform Infrared Spectroscopy) Pyrolysis/mass spectrometry Matrix-assisted laser desorption/ionization Nucleic based taxonomy Since 1975, advancements in nucleic acid isolation, amplification, and sequencing have led to the development of nucleic acid-based subtyping systems, including plasmid profile analysis, restriction endonuclease analysis, and ribotyping. Plasmid analysis Nucleic acid-based technique used to examine outbreaks in bacteria. Involves isolating plasmids from each bacterium and separating them using agarose gel electrophoresis. Plasmids of identical size with different sequences can exist in many bacteria. Restriction endonucleases Most useful for examining outbreaks restricted in time and place, especially when combined with other identification methods. Restriction endonucleases analysis Used to cleave DNA into discrete fragments. Recognize short DNA sequences and cleave double-stranded DNA within or adjacent to these sequences. Recognize short sequences more frequently than those that recognize long sequences. Several subtyping methods use restriction endonuclease digested DNA: Agarose gel electrophoresis Pulsed field gel electroctrophoresis (PFGE). Southern Blot Analysis Used as a subtyping method to identify isolates associated with outbreaks. DNA preparations from bacterial isolates are subjected to restriction endonuclease digestion, and the separated fragments are transferred to a nitrocellulose or nylon membrane. Resulting restriction fragments contain sequences homologous to the probe, and restriction fragment length polymorphisms (RFLPs) are used to identify these loci. Ribotyping and Repetitive Sequences in Microbial Genome Analysis Uses Southern blot analysis to detect polymorphisms of rRNA genes in all bacteria. Ribosomal sequences are highly conserved, allowing detection with a common probe from the 16S and 23S rRNA of eubacterium E coli. Ribotyping is limited for some microorganisms like mycobacteria, which have only a single copy of these genes. Repetitive Sequences in Microbial Genome Sequencing Bioinformatical tools Use DNA sequence information to identify novel targets for pathogen subtyping. Repetitive sequences “Satellite DNA” Have repeating units ranging from 10 to 100 bp. Multiple-locus VNTR analysis (MLVA) Uses PCR to subtype monomorphic species like Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Microbial Forensics Genotyping methods are progressing towards identifying single nucleotide polymorphisms (SNPs) to address epidemiologic and evolutionary questions. Microbial forensics developed in response to bioterrorist attacks in 2001. Nonculture Methods for Identifying Pathogenic Microorganisms Challenges in estimating total numbers of organisms: detection and recovery difficulties incomplete knowledge of obligate microbial associations species concept issues Recent studies suggest that the number of bacterial species in the world is between 107 and 109! Nonculture Methods for Identifying Pathogenic Microorganisms PCR-assisted approach using rRNA Used to identify pathogenic microorganisms in situ. Used to identify previously uncharacterized pathogens, (e.g Whipple-disease– associated rod-shaped bacterium now designated Tropheryma whipplei) Used to identify the etiologic agent of bacillary angiomatosis as Bartonella henselae and to show that the opportunistic pathogen Pneumocystis jiroveci is a member of the fungi.