PHA112 Microbial Classification 2020 PDF

MPharm Programme Microbial Classification Dr Callum Cooper [email protected] Learning Outcomes Describe the differences between cellular and acellular microorganisms Describe the main taxonomic groups of microorganisms and their features Describe how microbes can be classified and provi...

MPharm Programme Microbial Classification Dr Callum Cooper [email protected] Learning Outcomes Describe the differences between cellular and acellular microorganisms Describe the main taxonomic groups of microorganisms and their features Describe how microbes can be classified and provide examples Biological systematics Studies how life changes through time and how living things relate to one another Taxonomy: define systems by shared characteristics Classification: arrange organisms into groups Nomenclature: assign names Classification of Biological entities Biological Entities Cellular Eukarya Acellular Bacteria Archaea The Tree of Life Tree of Life website: tolweb.org/tree/ Development of classification systems: cellular entities Linnaeus Haeckel Chatton Whittaker Woese 1735 1866 1925 1969 1977 2 Kingdoms 3 Kingdoms 2 Empires 5 Kingdoms 3 Kingdoms Not described Protista Prokaryota Monera Bacteria Archaea Protista Vegetablia Plantae Animalia Animalia Eukaryota Plantae Fungi Animalia Eucarya Classification of Biological entities Biological Entities Cellular Eukarya Acellular Bacteria Archaea Viruses Viroids Virusoids Prions Classification systems: Acellular entities Viruses and prions are anomalous entities Non-living Viruses are parasitic (require hosts and resources to reproduce) Viral classification is an ongoing source of debate 2 competing systems; Baltimore system International committee for taxonomy of viruses (ICTV) system Classically based on phenotype and nucleic acid type Prions (PrP) do not reproduce Misfolded proteins Can exist as multiple isoforms By Emw - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=8821061 Taxonomic ranks Domain Eukaryota Bacteria Phylum Chordata Proteobacteria - Class Mammalia γ-proteobacteria - Order Primates Enterobacteriales Caudovirales Family Hominidae Enterobacteriaceae Subfamily Genus - - Homo Escherichia Species H. sapiens E. coli N.B. Genus and species are normally written in italics Podoviridae Autographivirinae Phikmvvirus Pseudomonas virus phiKMV Taxonomic ranks: Species What is a species? A group of living organisms capable of interbreeding, even if geographically isolated; Tigon Liger Panthera tigris Panthera leo WHAT ABOUT ORGANISMS THAT DO NOT REPRODUCE SEXUALLY? (e.g. bacteria) Taxonomic ranks: Species in microbiology Species: collection of strains that share stable properties but differ significantly from other groups of strains Staphylococcus aureus Staphylococcus epidermidis Strain: is a genetic variant or subtype of a bacterial species that varies slightly from other members of the same species Staphylococcus aureus E. coli Nissle 1917 Methicillin resistant Staphylococcus aureus E. coli O157:H7 Taxonomic ranks: Species/Strains in microbiology These organisms are assigned on the basis of phenotype, serotype or genotype; Phenotype: an organism's observable characteristics or traits (e.g morphology, development, biochemical or physiological properties) Serotype: distinct variations in cell surface antigens within a species Genotype: is the part of the genetic makeup of a cell, which determines one of its characteristics Phenotype classification in microbiology Morphology Cell shape (bacilli or cocci) Cell structure (gram staining) Biochemistry Enzyme production Transport proteins activity Life cycle Vegetative or spore forming Phenotype classification in microbiology Ecological niche Temperature Thermophile Psychrophile Interactions with other organisms Susceptibility to bacteriophages Pathogenicity (ability to cause disease) Provides the least detailed information Serotype classification in microbiology Serotype: distinct variations in cell surface antigens within a species A B Salmonella genus has over 2600 different serotypes Kauffman-White classification O antigen: oligosaccharides on the cell surface H antigen: flagellar proteins Vibrio cholerae (cholera causing bacterium) has over 200 serotypes Only 2 cause cholera: O1 and O139 Requires specific antibodies and pure cultures Genotype classification Genotype: part of the genetic makeup of a cell which determines one of its characteristics (phenotype) Genomics PCR Amplification of selected region of interest Base composition (%G/C) Nucleic acid sequencing 16S rRNA Used in phylogenetics due to slow rate of evolution Can also be used in diagnosis Whole genome sequencing Bacterial species definition: genomes sequences are at least 95% identical Taxonomy based on genetics can be confused by horizontal gene transfer Vertical & Horizontal Gene Transfer Time Vertical transmission: passage of genetic information from parent to offspring Horizontal transmission: the acquisition of genetic information by transfer from an organism that is not its parent Whole genome sequencing Whole genome sequencing: determines the complete DNA sequence of an organism at a single time How can we characterise with this information? Presence/absence of genes mecA gene in Staphylococcus aureus Gene mutations Point mutations (SNPs) Can change protein encoding Normal SNP DNA TTC TCC RNA AAG AGG Protein Lysine Gene insertions/deletions Acquired genes from horizontal transfer Phylogenetics Arginine Visualising Genotypes: Phylogenetics Phylogenetics: the study of evolutionary relationships among biological entities (within species) Produces clusters (clades) of similar organisms based on DNA or protein sequences For 2 or more sequences, multiple sequence alignments (MSA can be produced) More closely related = more similar the genetic sequences Close Relatives Bacterial Strain 1 2 3 4 5 Sequence ACCTGCAGTA ACGGGTAGTA AACTTGAGCA ACCTGCACTA GCGCGTAAAA Distant Relatives Visualising Genotypes: Phylogenetics MSA converted into genetic distance (% similarity) Summarises % similarity between each pair of sequences Bacterial Strain 1 2 3 4 5 Sequence ACCTGCAGTA ACGGGTAGTA AACTTGAGCA ACCTGCACTA GCGCGTAAAA 1 100 2 70 100 3 60 40 100 4 90 40 60 50 100 40 40 100 1 2 20 3 4 5 5 Visualising Genotypes: Phylogenetic Trees Tree of Life website: tolweb.org/tree/ Visualising Genotypes: Phylogenetic Trees Phylogenetic trees visualise evolutionary relationships between organisms Rooted: each node is based upon inferred most recent ancestor Unrooted: only how each leaf relates to others (no inference on ancestry) Where does classification have a practical application? OR How to work with dangerous bugs and not catch something How to work with dangerous bugs and not catch something Microorganisms are categorised by the Advisory committee on Dangerous Pathogens (ACDP) 4 classification levels Pathogens classified on severity of disease and availability of treatment List available online: http://www.hse.gov.uk/biosafety/information.htm Impacts upon laboratory facilities required Facilities categorised on Biosafety level (BSL) General rule of thumb: BSL ≥ ACDP level Some exceptions and dispensations Biosafety ACDP Category 1 organisms Pose minimal levels of hazard to personnel or the environment Generally non-pathogenic e.g. B. subtilis, E. coli, Saccharomyces cerevisiae BSL-1 facilities General protective equipment only Wash hands on entry and exit Sterilise all potentially infectious material Biosafety ACDP Category 2 organisms Can cause human disease and may be hazardous to the environment Unlikely to spread through the local population Effective prophylaxis, treatment or vaccination available e.g Staphylococcus aureus, Pseudomonas aeruginosa, E.coli BSL-2 facilities All conditions for BSL-1 with the following; Highly regulated design and procedures Specific training Restricted access to laboratory Work can be performed in Biosafety (BSL) cabinets Biosafety ACDP Category 3 organisms Can cause severe human disease and may be severely hazardous to the environment Potential to spread through the local population Effective prophylaxis, treatment or vaccination available e.g B. anthracis, Mycobacterium tuberculosis, Rabies virus Some pathogens require additional approvals BSL-3 facilities All conditions for BSL-1 and BSL-2 with the following; Highly regulated design and procedures All procedures done within BSL Laboratory specific PPE (or disposable) Under negative air pressure All personnel offered available vaccinations Biosafety ACDP Category 4 organisms Causes severe human disease (usually death) and may be severely hazardous to the environment High risk of spread through the local population No effective prophylaxis, treatment or vaccination available e.g Ebola virus, Variola virus BSL-4 facilities All conditions for BSL-1 and BSL-2 with the following; Personnel wear pressurised suits with separate air supply Highly trained personnel only Highly regulated lab design and procedures Organisms handled in class 3 cabinet Summary Describe the main taxonomic groups of microorganisms and their features How microbes can be classified Phenotype Serotype Genotype Practical application of classification Biosafety level Extra reading Prescott's Microbiology: Part V Sections 17,21,22