Use of molecular methods for diagnostics of infectious diseases Tiit Talpsep

1
Use of molecular methods for diagnostics of
infectious diseasesTiit Talpsep

• The 7th Baltic Congress
• in Laboratory Medicine
• Pärnu, September 9 - 11, 2004

2
(No Transcript)
3
Diagnostic methods in microbiology
Task of the method to make the microorganism
visible and measureable

• Microscopy
• Cultivation
• Bio-testing
• Immunological methods
• Biochemical methods
• Molecular methods

The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
4
Topics to be discussed

• What is molecular diagnostics ?
• Why to use molecular diagnostics ?
• In-house or commercial PCR ?

4
The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
5
Molecular methods are necessary if the
traditional methods provide poor results

• Microscopy gives false positive results -
• - T.vaginalis, N.gonorrhoeae
• Intracellular pathogens viruses, M.genitalium
  
• Low sensitivity Chlamydia sp.,Neisseria
  sp.
• Seropositivity is common Chlamydia sp.
• Subtyping is mandatory HSV, HPV, HCV
• Microbial growth is slow M. tuberculosis

The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
6
Diagnostic methods for detection of Chlamydia
trachomatis - the most common STD in Europe
WHO - sensitivity gt 90 specificity gt 99
- serology for scientific purpose
only
Method Sensitivity Specificity Price()
Comments Cell culture 40-85 100
6,3 Low sensitivity Immunofl.
50-90 85-95 5,2 Needs
expertise Gen-Probe 70-85 95-97
10,9 Low sensitivity PCR 70-95
97-100 10,4 ?Contamination!
The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
7
Molecular diagnostics how it works?

• Every organism contains some unique,
• species specific DNA sequences
• Molecular diagnostics makes the species specific
  DNA visible

The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
8
Molecular diagnostics is a set of methods to
study primary structure (sequence) of DNA

• Hybridization with complementary sequences

-A-A-T-T-C-G-C-G-A-T-G-
- T-T-A-A-G-C-G-C-T-A-C-

• Amplification (synthesis) of species specific
  sequences
• PCR polymerase chain reaction

-A-A-T-T-C-G-C-G-A-T-G-
-A-A-T-T-C-G-C-G-A-T-G-
-A-A-T-T-C-G-C-G-A-T-G-
-A-A-T-T-C-G-C-G-A-T-G-
-A-A-T-T-C-G-C-G-A-T-G-
The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
9

Key issues
1. place who where, what how 2. price
how much does it cost 3. proficiency - how
much high quality information it
provides
The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
10
PCR laboratory
QC QA Quality control assurance
Sample handling DNA preparation
No alternative
Laboratory Mixing site
Detection Documentation
Thermocycler Amplification
R D (Research and development)
Clean room Stock solutions
Alternatives - commercial kits - robots kits
11

Quality Control is expensive

• Quality management
• Validation
• Regular examination of instruments and reagents
• Proficiency testing by interlaboratory
  comparisons
• - Labquality - 90
• - Instand - 150
• - QCMD - 590

Estonia Molecular diagnostics of infect. dis.
15 ? labs Accrediated according to ISO 15189
1 ? lab
The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
12
Hard choice - what is the best

• In-house (home-brew) PCR or commercial PCR kits
• Simple thermocycler or fancy robot
• Ordinary PCR or real-time PCR

Cost Quality?!
The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
13
Cost of one analysis () (excluding human
resources, infrastructure costs, etc.)
Estonian Health Insurance Fund 10,4
Method Consumables Equipment PCR kit
15-19 0,3 PCR kit (RU)
0,7 0,1 Real-time 16-21 0,6 In-house
8 10 (all costs, incl. RD QCQAetc.)
The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
14
QCMD proficiency panel- Participants -
in-house - commercial - gen-probe
N. gonorrhoeae EST-1 SWE-1 FIN-0 LI-0 LT-0
M. tuberculosis EST-1 SWE-2 FIN-1 LI-0 LT-0
12
14
36
36
47
Herpes simplex virus EST-1 SWE-3 FIN-2 LI-0
LT-0
Hepatitis C virus EST-3 SWE-2 FIN-1 LI-1 LT-0
12
29
95
85
The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
15

QCMD proficiency panel - Correct
N. gonorrhoeae In-house 90,0 Commercial
81,5
HCV In-house 89,5 Commercial 95,0
M. tuberculosis In-house 86,4 Commercial
82,0 Genprobe 80,7
HSV In-house 86,1 Commercial 76,2
The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
16
Advantages
Molecular methods

• High sensitivity and specificity
• Detects pathogen, not immune response
• Quick results
• High transport toleration

In-house (home-brew) PCR methods

• Cost effective
• High sensitivity
• High quality
• Fast implementation of scientific discoveries
• Customer friendly

RD is absolutely necessary
The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
17
Bottlenecks in Estonia

• QC QA is not yet everyday practice
• Poor cooperation between laboratories
• Insufficient communication with doctors
• Nonsense investments into fancy equipment
• robots give money back if you run
• 50 000 200 000 analysis per year

The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
18
What can we do better

• Create networking between laboratories
• Take second opinion
• Honest dialogue with doctors
• Education
• Concentration into specialized laboratories
• QC QC QC to build up the trust

The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
19
Some people do not believe into the advantages
of PCR
I think I may say without contradiction that
when the Paris Exhibition closes, electric light
will close with it, and no more will be heard of
it Prof. Erasmus Wilson Oxford
University, 1878
The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
20
Compliments to

• Kaido Beljaev
• Paul Naaber
• Katrin Reimand
• Milvi Topman
• Rain Lehtme

• Kai Jõers
• Raili Randoja
• Kärt Denks

• Kadri Raudsep
• Avo Karus

The 7th Baltic Congress in Laboratory Medicine,
Pärnu 11.09.2004
21
Thank you for your attention!