Microbial typing

Dr Vinodh Kumar,O.RDivision of Epidemiology

ICAR-Indian Veterinary Research InstituteIzatnagar, Uttar Pradesh, India

Analyse multiple isolates within a given species

Study the small differences between the same species.

In epidemiological studies, and to study the pathogenesis of infection.

The process of differentiating strains based on their phenotypic and genotypic differences is known as 'typing'.

Phenotypic techniquesdetect characteristics expressed by the

microorganism

Genotypic techniquesdirect DNA-based analysis of chromosomal or

extrachromosomal genetic elements

Based on size, staining properties, biochemical properties and antigenic properties

BiotypingPhage typingBacteriocine typingSerotypingAntimicrobial Susceptibility Typing

(Antibiogram):Protein typingMultilocus Enzyme Electrophoresis (MLEE)

Based on study of the microbial DNA, the chromosome and plasmid, their composition, homology and presence or absence of specific genes

Plasmid analysisRestriction Endonuclease AnalysisPFGE of Chromosomal DNASouthern blot analysisNucleotide Sequence Analysis

Metabolic activities expressed by an isolate, colonial morphology and environmental tolerances

Manual or automated referred as ‘biotypes’

Based on the pattern of resistance or susceptibility to a standard set of bacteriophages

referred as ‘phage types’

Based on the susceptibility to a set of bacterial peptides (bacteriocine) produced by certain bacteria.

Bacterocines produced by a particular strain are usually only active against other strains of the same species.

Based on antigenic determinants expressed on the cell surface

referred as ‘Serotypes’

Based on comparison of different isolates to a set of antibiotics

Based on major or minor differences in the range of proteins made by different strains

comparisons among multiple strains are difficult

The isolates are analysed for differences in the eletrophoretic mobilities of a set of metablolic enzymes

referred to as ‘electromorph’

Based on the number and sizes of plasmids carried by an isolate

Can be determined by preparing a plasmid extract and subjecting to gel electrophoresis

A restriction endonuclease enzymatically cuts DNA at a specific nucleotide recognition sequence

Bacterial DNA is digested with endonucleases that have relatively frequent restriction sites

A variation of agarose gel electrophoresisThe orientation of the electric field across the

gel is changed periodicallyLarge fragments can be effectively separated

by size

Detect only the particular restriction fragment

fragments transferred to nitrocellulose membranes and detected by labelled DNA probes

Variations in the number and sizes of the fragments

Ribotyping: Blotting of restriction enzyme digestion of rRNA, and one or more tRNAs

Genotype informationAutomated techniques to sequencePossible to compare multiple isolates.