Introduction to Medical Microbiology and Microbial Classification

Question 1

What are the aims of sampling?

Answer 1

• Show evidence of infection
  -direct evidence via culture or
  PCR test
  -indirect evidence by looking at
  host response, immunological
  reactivity or histopathological
  manifestation
• Be repeatable or quantitative
  -direct = negative culture
  conversion after therapy
  -indirect = increase in antibody
  titre over time

Question 2

What is the basic techniques of sampling?

Answer 2

• All samples must be labelled
• Transport media must be in date and not leaking/cracked/broken etc.
• Sample quantity must be sufficient
• Sterile sites (blood or CSF) need sterile sample collection eg. cleaning skin with ethanol prior to needle

Question 3

What is required for non-sterile site sampling and why?

Answer 3

• Same day testing or cold storage
• prevent overgrowth of bacterial/fungal flora
• prevent degeneration of test material eg DNA
• reduce viability of fastidious organisms eg anaerobes, Neisseria gonorrhoeae

Question 4

What are the different taxonomic approaches for classifying pathogens?

Answer 4

• Linnaean taxonomy - original scheme of Carl Linnaeus
• Evolutionary taxonomy - hierarchical biological tree of life by Darwin (amphibians, reptiles, dinosaurs, birds)
• Rank based - Kingdom, Phylum Class, Order…
• Nosology - classification of diseases
• Phenetics - ordering into species based on similarity of characteristics
• Phylogenetics - evolutionary heritage (combining with numerical and time-line analysis)

Question 5

What defines a pathogen?

Answer 5

A replicative entity with capacity (virulence) to cause disease (pathogenicity) to its host (transmissibility)

Question 6

What is the phylogenetic based definition of species?

Answer 6

A group of organisms descended from a common evolutionary ancestor exhibiting > 95% pair-wise average nucleotide identity in their genome

Question 7

Why is this definition of species not perfect?

Answer 7

Some viral taxa have only 65 % genome nucleotide identity but identical biological and phenotypic properties
Many viruses use recombination and reassortment among parts of the viral genomes to produces chimeric viruses (polyphyletic genomes).
DNA identification requires 1) pure isolation or 2) knowing the genome sequence beforehand
BUT
99% of all known microbes in the metagenomic world are not as yet culturable
Not all known pathogens can be cultured (intracellular permissive host) e.g. Mycobacterium leprae
Some pathogens do not have DNA (e.g. Prions)

Question 8

Define species

Answer 8

Able to interbreed and create fertile offspring
Distinguished from all other species by unique multiple phenotypic or genotypic set of criteria