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Role of the laboratory in surveillance Sources: WHO Laboratory Training for Field Epidemiologists ECDC -EUPHEM Robert Koch Institute National Reference.

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Presentation on theme: "Role of the laboratory in surveillance Sources: WHO Laboratory Training for Field Epidemiologists ECDC -EUPHEM Robert Koch Institute National Reference."— Presentation transcript:

1 Role of the laboratory in surveillance Sources: WHO Laboratory Training for Field Epidemiologists ECDC -EUPHEM Robert Koch Institute National Reference Center for Listeriosis, Paris Laboratory for Urgent Response to Biological Threats, Paris Ph. Dubois, Laboratory for Urgent Response to Biological Threats, Institut Pasteur, Paris

2 Learning objectives At the end of the presentation, participants should: Understand how the laboratory contributes to epidemiological surveillance Understand the principles of laboratory-based surveillance Understand some concerns of public health microbiologists

3 Laboratories and disease surveillance Before the outbreak Early warning signals Outbreak detection During the outbreak Outbreak response and management In between outbreaks Trend monitoring Intervention evaluation Monitoring progress towards a control objective

4 Expected results Laboratory: Confirmation of clinical diagnostic: Direct identification of the bug Serology detection Identification of the strain/isolate/subtype Identification of new pathogen Characterization of pathogen sensitivity to antimicrobials Identification of seroconvertants/carriers in populations Collection of data/information from patients with various / different geographic origins Collection of data/information from environmental or animal origin

5 Expected results Surveillance: Early warning Outbreak detection Post-outbreak surveillance Environment and reservoir analyses Surveillance of eradication-elimination of a bug Surveillance of vaccination campaign Surveillance of notifiable diseases Surveillance of national drug treatment efficacy

6 I - Early warning signals Detection of pathogens that have potential to spread Sentinel events requiring early control measures Isolation of a single epidemic prone isolate (e.g. non-typhoidal salmonella isolated from a neonate in a hospital neonatal intensive care unit) Emergence of resistant strains in the hospital or the community (e.g. multi-drug resistant tuberculosis)

7 Outbreak detection by the lab Identification of a cluster of: Infections with an unusual pathogen Specific subtype of a pathogen – Outbreak of antibiotic-resistant strains – Subtypes of a pathogen (e.g. Shigella dysenteriae type I) Reference centres may capture outbreaks disseminated over a large area, or correlate events (food control- cluster of human cases).

8 Listeria monocytogenes Genoserotyping or PCR Group ProfilePCR GroupSerovar 1, 5IIa1/2a ou 3a 2, 6, 10IIb1/2b ou 3b ou 7 3, 7IIc1/2c ou 3c 4, 8, 9IVb4b ou 4d ou 4e 11-16L Listeria monocytogenes 4a, 4ab, 4c or other species of Listeria IIaIIcIIbIVb Doumith et al. JCM, 2004 Doumith et al., J Food Protect 2005 Multiplex PCR : simultaneous PCR on 5 different DNA fragments

9 II - Outbreak confirmation Epidemiologist captures an increased incidence Laboratory: Confirms the diagnosis Allows for a more specific case definition Detects a new pathogen Provides additional details on the pathogen (e.g., phage type) Examples : detection H5N1, detection H1N1 Effective participation of the laboratory in surveillance requires good communication between the epidemiologists and the laboratories

10 Laboratory role during outbreaks Laboratory confirmation of early cases On a subset of cases Identification of new pathogens Typing of the pathogen Link clusters when the epidemiological data is not sufficient Antimicrobial susceptibility testing to guide treatment Post-outbreak surveillance Environmental investigations Detection of carriers

11 Laboratory role during outbreaks For new and emerging pathogens: Identify the pathogen Develop laboratory tests Patient treatment/management SARS Courtesy: The University of Hong Kong

12 III - Monitoring endemic disease trends Confirm diagnosis Case definitions that include laboratory criteria: Monitor resistance patterns Monitor subtypes of a pathogen Detection Flu viruses subtypes, such as H5N1, H1N1

13 Monitoring endemic disease trends Examples: Circulating strains of bacterial meningitis Impact on treatment protocols Impact on immunization policies Antibiotic resistance Methicilin resistant staphylococcus aureus Vancomycin resistant enterococcus Tuberculosis Monitoring of Flu viruses circulation, vaccination policies

14 Source : InVS and NRC for N. meningitis, Pasteur Institute, Paris Invasive meningococcal infection serogroups by year, France,

15 IV - Eradication/elimination monitoring The elimination phase requires more specific tests as positive predictive value decreases Laboratory confirmed diagnosis Polio surveillance Measles Typing helps identifying the origin

16 Cases of polio where wild poliovirus was isolated in children, District X

17 Monitoring TB control program to ensure complete treatment and cure

18 V - Monitoring seroconversion/susceptibility Systematic control of immune status for specific diseases Tuberculin reaction Toxoplasmosis

19 Establishing laboratory support for public health surveillance Identify diseases of public health importance List diseases that require laboratory confirmation Determine tests to be performed Map laboratory facilities and human resources, including reference laboratories Establish laboratory networking Identify a focal person to coordinate laboratory activities Determine information flow

20 How to identify a new subtype? Look for genetic material : broad range of genetic probes and methods Direct isolation : culture on selective media to obtain clonal populations Characterize new serotypes Characterize new chemical or biochemical activities Characterize new toxins

21 Pulsed-field gel electrophoresis (PFGE) RFLPs of VRE isolates as determined by PFGE; all appear identical RFLPs of two strains (B & C) from a patient as determined by PFGE; both different implying mixed infection; lane A is marker RFLPs of MRSA isolates with similar ABT ST profile as determined by PFGE; only isolates B & C are identical

22 How to identify a new resistance to antibiotics Look for genetic material : broad range of genetic probes and methods for identification of resistance genes. Direct isolation : Culture on selective media to obtain clonal populations Grow isolates on different antibiotics, and determine dose-response curves

23 How to identify a new pathogen ? Good question !!!!! What if totally unknown, no clue from clinicians, or classical lab techniques ? Look for genetic material : broad range of genetic probes and methods Direct examination : light microscopy, electronic microscopy Direct isolation : culture on a whole spectrum of bacteriology media and conditions Culture on a whole spectrum of cell lines permissive for most known viruses

24 DNA CHIPS PathogenID® Microarray : Categories of genesNumber of Genes 16S ribosomal RNA51 Toxins/Pathogen effects229 Resistance to antibiotics390 Conserved genes72 MLST7 Point mutations167 ARNr 18S4 Viruses42 Total962 GenreSpecies AlphavirusEastern Equine Encephalitits virus AlphavirusVenezuelan equine encephalitis virus AlphavirusWestern equine encephalomyelitis virus ArenavirusGuanarito virus ArenavirusJunin virus ArenavirusLymphocytic choriomeningitis virus ArenavirusMachupo virus CoronavirusSARS coronavirus EbolavirusReston ebolavirus EbolavirusZaire virus EphemerovirusBovine ephemeral fever virus FlavivirusDengue virus type 2 FlavivirusJapanese encephalitis virus FlavivirusKyasanur forest disease virus strain W371 FlavivirusTick-borne encephalitis virus etc………….. 42 virus sequences : 26 genders 11 families 126 virus sequences : 37 genders 14 families

25 Surveillance: Lab functions Confirmation of etiology to resolve syndromic presentation Data intelligence for: Antimicrobial resistance monitoring Emergence of unusual isolates Detection of new pathogens Sero-surveillance

26 French surveillance system of listeriosis Laboratory of medical microbiology (Private & Public) Patient Clinician Regional Agency of Ministry of Health ( ANRS) Ministry of Economy ( DGCCRF) Ministry of Agriculture (DGAl) NRC Public Health Agency (InVS) Ministry of Health (DGS) Regional Agency of Ministry of Economy (DDCCRF) Regional Agency of Ministry of Agriculture ( DDPP) Laboratory of food microbiology (Private & Public) Legend : FI, Food Incident M, Mandatory Notification S, Strain FQ, Food Questionnaire M FQ Cell Listeria FI S Food Information M M FQ S Patient information NRL

27 Samples from the field to the lab What samples should you take? And how? Blood, stools, swabs, water, food items, etc… How should you ship the samples? High risk material? Cooling necessary? Box in a box in a box principle Ask the lab and inform that samples are arriving!

28 The result of any laboratory test is only as good as the sample received in the laboratory

29 Packaging infectious substances for shipment Triple packaging system Infectious substance (BIOHAZARD) label Container for the first suspected anthrax letter / Berlin Prof. Matthias Niedrig, RKI

30 Sampling module

31 Biological Risk Management Laboratory biosafety: containment principles, technologies, and practices implemented to prevent unintentional exposure to pathogens and toxins, or their unintentional release Laboratory biosecurity: institutional and personal security measures designed to prevent the loss, theft, misuse, diversion, or intentional release of pathogens and toxins 1Laboratory biosafety manual, Third edition, World Health Organization, 2004)

32 Risk Graph Likelihood Very High Consequences Very Low Moderate High

33 High Risk Likelihood Very High Consequences Very Low Moderate High

34 Low risk ? Likelihood Very High Consequences Very Low Moderate High

35 Low Risk Likelihood Very High Consequences Very Low Moderate High

36 Risk assessment

37 Laboratory Biorisk Management Standard System or process to control safety and security risks associated with the handling or storage and disposal of biological agents and toxins in laboratories and facilities CWA 15793:2008

38 Developed by the Department of Epidemic and Pandemic Alert and Response of the World Health Organization with assistance from: European Program for Intervention Epidemiology Training Canadian Field Epidemiology Program Thailand Ministry of Health Institut Pasteur Role of laboratory in surveillance

39 THANK YOU FOR YOUR ATTENTION The ENIVD-CLRN project is funded by the ECDC under the Framework Service Contract Ref. No. ECDC/2008/011.

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