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Bacterial Epidemiological


Dr Edet E. Udo
 Define
– Epidemiological markers
– Microbial typing
– What is microbial typing?
– Purposes of typing
– Application of microbial typing in healthcare
 Epidemiological markers
– are biological markers that are used to characterize
microorganisms or discriminate between genomes based
on genetic variation among microbial isolates.

– The ability to discriminate between genomes is essential to

several disciplines of microbiology research including
taxonomy, microbial epidemiology, population genetics and
evolutionary biology
 Epidemiological markers are used for strain typing
Microbial epidemiology
 Microbial typing (fingerprinting)
– are methods used to characterize

 It is used to:
– Classify isolates of microorganisms
– Catalogue genetic variation
– Define relatedness or lack of it between microbial
species or genera.
Qualities of biological markers
 Epidemiological markers should be:
– Generally stable to discriminate between related
and unrelated strains
– Widely available
– Easy to detect
– Common among strains
Application of typing in hospital
Microbial typing can be applied in hospital infection
control to:
– Confirm an outbreak in an institution
– Identify an outbreak in what appears to be sporadic cases of
– Identify risk factors for recent infections or rapidly progressing
– Design intervention in the spread of disease
– Assess the efficacy of the intervention
– Define mode of spread of pathogenic organisms e.g. MRSA,
VRE and ESBL producing organisms
– Track geographical spread of pathogens of public health
Microbial typing
The objective of typing
– is to ascertain if two or more strains are
derived from a single parent organism

– It is usually performed to clarify whether two

isolates from different sources represent the
same strains or distinct ones in order to provide
data for epidemiological purposes
Microbial typing
Typing studies are often initiated:
– When a sudden increase in the incidence of a
particular pathogen in a geographically limited
area is noted ( an outbreak)

– Typing is used to compare if they are clonally

related or unrelated with the goal of short term
control of transmission.
Microbial typing
 Requires:
– Source of the organism to be studied.
– Natural habitat is important to interpret
typing results.
 Microbial isolate or stock
– A collection of cells derived as a monoculture

– A STRAIN represents an isolate or groups of

isolates displaying specific genetic or phenotypic
characteristics that set it apart from other isolates

– A reference strain is a well characterized strain that

is preserved and included in further studies for
comparison purposes

– A clone ( or clonal group) comprises organisms

descending from a common ancestor because of a
direct chain of replication .

– A genetic clone comprises a group of strains that

are completely identical at the DNA level.
Typing systems
Typing procedures are specific for different phenotypic or
genetic parameters and can be applied to any microbial
 Typing should reveal differences not only between strains
belonging to different species but also between strains
belonging to the same species
 Qualities of current typing methods
 1. Should have Optimal typeability
– Refers to the proportion of isolates that can be typed, ideally all
 2. Reproducibility
– The ability to assign the same result on repeat testing
Qualities of current typing methods

 3. Stability
– The ability of clonally derived isolates to express constant markers
over time and generations
 4. Discriminatory power
– it conditions the probability that isolates sharing identical or closely
related types are truly clonal and part of the same chain of
 5. Epidemiologic concordance
– the capacity of a typing system to correctly classify into the same
clone all epidemiologically related isolates from a well described
 6. Technically simple
 7. Availability- Widely available
 8. Not expensive
Different typing methods
 Phenotypic and genotypic methods
 Phenotypic methods
– Biotyping, antimicrobial susceptibility testing (antibiogram)
– Bacteriophage typing, multilocus enzyme electrophoresis,
polycarylamide gel electrophoresis of cellular proteins,
immunoblot fingerprinting
 Disadvantages:
– Poor discrimination between strains,
– labor intensive, long procedures,
– produce variable results, some not available for all
Genotypic (DNA based) methods
 1. Plasmid fingerprinting,
 2. Restriction endonuclease analysis of chromosomal
DNA with conventional electrophoresis
 3. Ribotyping
 4. Pulsed-field gel electrophoresis (PFGE)
 5. Amplification methods- PCR
 6. Mulitlocus sequence typing
 7. Genome sequencing- most reliable method
Genotypic (DNA based) methods
– Stable, avoid problems associated with
gene expression
– Widely applicable to a range of
• Expensive start up cost, labor intensive,
Phenotypic typing methods

Antibiotic sensitivity Phage

testing typing
Genotypic typing methods
Plasmid analysis Ribotyping
REA + Probing

How to answer short notes questions
 Short notes could be general or specific
 Definition (Define the subject)
 Describe process
 Discuss the problem
 Give examples
 State differences
 Give advantages or disadvantages
 Conclude if required
 NOTE: Should not be more than half a page.
Examples for self evaluation
 Write short notes on the following topics:
 1. Functions of bacterial cell envelope
 2. Discuss differences between Gram-positive
and Gram-negative cell walls
 3. Bacterial secretory toxins
 4. Bacterial virulence factors
 5. Clinical importance of bacterial biofilms