Microbial strain typing in surveillance and outbreak investigationMatthew O'Sullivan

Staff Specialist in Infectious Diseases and Clinical Microbiology

Senior Lecturer, Sydney Medical School

SYDNEY MEDICAL SCHOOL

CENTRE FOR INFECTIOUS DISEASES & MICROBIOLOGY, WESTMEAD HOSPITAL,

Overview

› What is strain typing?

› Why do strain typing?

› Strain Typing in Infection Control

› Strain Typing Methods

› Typing Method Characteristics

› Strain Typing Interpretation

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What is strain typing?

Taxonomic Classifications

3

What is strain typing?

4

What is strain typing?

› Phenotype

Much variation is evident even within species

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What is strain typing?

› Phenotype

Much variation is evident even within species

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What is strain typing?

› Genotype

Much variation is evident even within species

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What is strain typing?

› Dividing organisms into groups below species level

- Using phenotypic or genotypic methods

What is strain typing?

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Why Do Strain Typing?

1. Study the evolution and population genetics

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Why Do Strain Typing?

1. Study the evolution and population genetics

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Why Do Strain Typing?

› Eg: Clostridium difficile ribotype 027

2. Detect strains of increased virulence

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EID 2012 17(6):976

Why Do Strain Typing?

3.Identify source of infection

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Strain typing in infection control

› Incidence of organism

- A patient develops MRSA bacteraemia in the ICU 5 days after admission to

hospital after one negative MRSA screen. The prevalence of MRSA colonisation

in ICU patients is 25%

- A patient develops bacteraemia with KPC-producing Klebsiella pneumoniae 5

Is strain typing required to identify source of infection?

- A patient develops bacteraemia with KPC-producing Klebsiella pneumoniae 5

days after admission to hospital. The patient in the adjacent bed is known to be

colonised with KPC-producing Klebsiella pneumoniae. KPC producing organisms

have never been identified at the hospital before.

› Other characteristic markers?

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Strain Typing in Infection Control

Approaches

Retrospective

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Prospective

Retrospective Strain Typing

Traditional way of utilising strain

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utilising strain typing in infection control

Strain Typing

Case Definition

› Diagnosis

› Time

› Place

› Epidemiologic Parameters

› Strain type

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Prospective Strain Typing

Strain Typing

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Prospective typing increasingly utilised

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New MRSA isolates per day for hospital inpatients

Prospective Strain Typing

0

2

4

6

8

10

12

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New MRSA isolates per day for hospital inpatients

Prospective Strain Typing

0

2

4

6

8

10

12

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New Strain A MRSA isolates per day for hospital inpatients

Prospective Strain Typing

0

2

4

6

8

10

12

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New Strain G MRSA isolates per day for hospital inpatients

Prospective Strain Typing

0

2

4

6

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Strain typing methods

› Phenotypic

- Serotyping

- Streptococcus pneumoniae

- Phage typing

- Salmonella enterica

› Genotypic

- Pulse-field gel electrophoresis (PFGE)

- Many organisms (MRSA, VRE, MRAB)- Many organisms (MRSA, VRE, MRAB)

- PCR-ribotyping

- Clostridium difficile

- Multilocus variable number of tandem repeats analysis (MLVA)

- Salmonella enterica

- Binary typing

- Staphylococcus aureus

- Single locus sequence typing

- Stapylococcus aureus (spa)

- Multilocus sequence typing (MLST)

- Many organisms

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Typing Method Characteristics

› Discriminatory power

› Reproducibility

› Stability

› Typeability

› Ease of interpretation

› Ease of use

› Portability of results

› Turnaround time

› Throughput

› Cost

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Interpreting Strain Typing Results

A. Yes

B. No

Typing Results: All Part of Outbreak?

Maybe: Depends on discriminatory

power of typing system,

background prevalence of the strain

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background prevalence of the strain

type

Maybe: Depends on stability of the

typing system, how ‘different’ are

the strains

A. Yes

B. No

Interpreting Strain Typing Results

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Interpreting Strain Typing Results

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Transmissible Resistance

Need to consider typing transmissible element as well as the ‘host’

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Conclusions

› Strain typing not necessary for infection control surveillance for all organisms

› Strain typing in infection control may be retrospective or prospective

› Characteristics of the available typing method must be considered before deciding to perform typingdeciding to perform typing

› Characteristics of the typing method must be considered in interpreting the results

› Typing does not provide a ‘Yes’ – ‘No’ answer, but a likelihood

› Transmissible resistance requires a different approach

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