Lecture 9 - Bacterial Epidemiological Markers

Bacterial Epidemiological
Markers
Dr Edet E. Udo
Objectives
 Define
– Epidemiological markers
– Microbial typing
– What is microbial typing?
– Purposes of typing
– Application of microbial typing in healthcare
Definitions
 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
microorganisms.
 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
epidemiology
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
infection
– Identify risk factors for recent infections or rapidly progressing
disease
– 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
importance.
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
species
 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
isolates.
 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
transmission
 5. Epidemiologic concordance
– the capacity of a typing system to correctly classify into the same
clone all epidemiologically related isolates from a well described
outbreak.
 6. Technically simple
 7. Availability- Widely available
 8. Not expensive
Different typing methods
 Phenotypic and genotypic methods
 Phenotypic methods
– Biotyping, antimicrobial susceptibility testing (antibiogram)
serotyping
– 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
microorganisms
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
Advantages:
– Stable, avoid problems associated with
gene expression
– Widely applicable to a range of
microorganisms
Disadvantage
• Expensive start up cost, labor intensive,
Phenotypic typing methods
Biotyping
Antibiotic sensitivity Phage

testing typing
Genotypic typing methods
Plasmid analysis Ribotyping
REA + Probing
REA
of
PCR
PFGE
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

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Bacterial Epidemiological

– The ability to discriminate between genomes is essential to

– It is usually performed to clarify whether two

– Typing is used to compare if they are clonally

– A STRAIN represents an isolate or groups of

– A reference strain is a well characterized strain that

– A clone ( or clonal group) comprises organisms

– A genetic clone comprises a group of strains that

Antibiotic sensitivity Phage

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