Classification of infectious agents (part 1) Flashcards
Taxonomy
is the science of classifying organisms
• Shows degree of similarity among organisms
Systematics, or phylogeny
is the study of the
evolutionary history of organisms
1735: Linnaeus
—kingdoms Plantae and Animalia
1800s
Bacteria and fungi put in kingdom Plantae
(Nägeli); Kingdom Protista proposed for bacteria,
protozoa, algae, and fungi (Haeckel)
1937
Prokaryote introduced to distinguish cells
without a nucleus
1968 Murray
—Kingdom Prokaryotae
• 1969: Whittaker—
five-kingdom system
The Three Domains
• Developed by Woese in 1978; based on sequences of nucleotides in rRNA • Eukarya • Animals, plants, fungi • Bacteria • Archaea • Methanogens • Extreme halophiles • Hyperthermophiles
A Phylogenetic Tree
Grouping organisms according to common properties • Fossils • Genomes Groups of organisms evolved from a common ancestor Each species retains some characteristics of its ancestor
In Bergey’s Manual, name of genus…
s at the beginning of each
article
The Taxonomic Hierarchy
A series of subdivisions developed by Linnaeus to
classify plants and animals
Eukaryotic species
a group of closely related
organisms that breed among themselves
3 domain of life
arch,bact eul
how many dif phylums does bacteria have.
24
how many different classes does proteobacteria have
5 defined by 16s rna
Culture
: bacteria grown in laboratory media
Clone
population of cells derived from a single parent
cell
Strain
genetically different cells within a species
• (In biology strain is a low-level taxonomic rank below
the rank of species)
Logical steps in classification
Collection of data. The bacterial strains that are to be classified have to be chosen, and they must be examined for a number of relevant properties (taxonomic characteristics).
• 2. Data must be coded.
• 3. Similarity or resemblance between the strains is calculated. This
yields a table of similarities (similarity matrix) based on the chosen
set of characters.
• 4. Similarities are analyzed for taxonomic structure, to yield the groups
or clusters that are present, and the strains are arranged into phenons
(phenetic groups), which are broadly equated with taxonomic group
(taxa)
• 5. Properties of the phenons can be tabulated and most appropriate
characters (diagnostic characters) can be chosen on which to set up
identification systems that will allow the best identification of additional
strains.
Classification of Viruses
Not a part of any domain; not composed of cells;
require a host cell
Viral species:
population of viruses with similar characteristics that occupies a particular
ecological niche
New ICTV classification system (2019)
New classifciation system - 15 rank
Now classe and phylums are now added
Keep in mind baltimore classification
Herpes Virus in New Classification
Herpes simplex 1 & 2, Varicellovirus (chickenpox)
• Fam: Herpesviridae
• Order: Herpesvirales
• Class: Herviviricetes
• Phylum: Peploviricota
• Kingdom: Heungongvirae
• Realm: Duplodnaviria (dsDNA) (class I of Baltimore classification)
Influenza Virus in New Classification
Influenza A virus • Fam: Orthomyxoviridae • Order: Articulavirales • Class: Insthoviricetes • Phylum:Negarnaviricota ((-) ssRNA) (class V of Baltimore) • Kingdom: Orthonavirae • Realm: Ribioviria (RNA viruses)
Classification
placing organisms in groups of
related species
• Lists of characteristics of known organisms
Identification
matching characteristics of an
“unknown” organism to lists of known organisms
• Clinical lab identification
Bergey’s Manual of Determinative Bacteriology
provides identification schemes for identifying
bacteria and archaea
Approved Lists of Bacterial Names
lists species of
known classification
Transport media
is used to collect and transport
pathogens to a laboratory
how many phylums are pathogenic?
5/24
Morphological characteristics
useful for identifying
eukaryotes; tell little about phylogenetic
relationships
Differential staining:
Gram staining, acid-fast
staining; not useful for bacteria without cell walls
Biochemical tests
determine presence of bacterial enzymes
FAME
Fatty acid methyl esters provide profiles
that are constant for a particular species
DNA fingerprint
Electrophoresis of restriction enzyme digests of an
organism’s DNA
• Comparing fragments from different organisms provides
information on genetic similarities and differences
DNA Chips
A DNA chip (also known as a microarray)
contains DNA probes and detects pathogens by
hybridization between the probe and DNA in the
sample
• Detected by fluorescence
Ribotyping
• Probing bacterial genome with 16S rRNA gene probe
Fluorescent in situ hybridization (FISH)
Fluorescent DNA or RNA probes stain the
microorganisms being targeted
• Determines the identity, abundance, and relative activity
of microorganisms in an environment
Dichotomous keys
Identification keys based on successive questions
Cladograms
Maps that show evolutionary relationships among
organisms; based on rRNA sequences
