role of the laboratory in surveillance sources: who laboratory training for field epidemiologists...
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E P I D E M I C A L E R T A N D R E S P O N S E
Role of the laboratory in surveillance
Sources: WHO Laboratory Training for Field EpidemiologistsECDC -EUPHEMRobert Koch InstituteNational Reference Center for Listeriosis, ParisLaboratory for Urgent Response to Biological Threats, Paris
Ph. Dubois, Laboratory for Urgent Response to Biological Threats, Institut Pasteur, Paris
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
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)
E P I D E M I C A L E R T A N D R E S P O N S E
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 disseminatedover a large area, or correlate events (food control-
cluster of human cases).
E P I D E M I C A L E R T A N D R E S P O N S E
Listeria monocytogenesGenoserotyping or PCR Group
Profile PCR Group Serovar
1, 5 IIa 1/2a ou 3a
2, 6, 10 IIb 1/2b ou 3b ou 7
3, 7 IIc 1/2c ou 3c
4, 8, 9 IVb 4b ou 4d ou 4e
11-16 LListeria monocytogenes 4a, 4ab, 4c or
other species of Listeria
ORF2819
lmo0737 1000
800 700 600 500 400 300
M 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
lmo1118
ORF2110
prs
IIa IIcIIb IVb
Doumith et al. JCM, 2004Doumith et al., J Food Protect 2005
Multiplex PCR : simultaneous PCR on 5 different DNA fragments
E P I D E M I C A L E R T A N D R E S P O N S E
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 surveillancerequires good communication between theepidemiologists and the laboratories
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
Laboratory role during outbreaks
For new and emerging pathogens:
•Identify the pathogen
•Develop laboratory tests
•Patient treatment/managementSARS
Courtesy:The University of Hong Kong
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
0
100
200
300
400
500
600
85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 2000
Year
Num
ber o
f cas
es
C
B
A
Unknown
Source : InVS and NRC for N. meningitis, Pasteur Institute, Paris
Invasive meningococcal infection serogroups by year, France, 1985-2000
E P I D E M I C A L E R T A N D R E S P O N S E
IV - Eradication/elimination monitoring
The elimination phase requires more specific tests aspositive predictive value decreases
Laboratory confirmed diagnosis
• Polio surveillance
• Measles
Typing helps identifying the origin
E P I D E M I C A L E R T A N D R E S P O N S E
0
50
100
150
200
250
80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96
Years
Nu
mb
er
of c
ase
s
National immunization day
National immunization day
Cases of polio where wild poliovirus was isolated in children, District X 1980-1996
E P I D E M I C A L E R T A N D R E S P O N S E
Tuberculosis: new cases, treatment completion and cures, District X, 1994-1997
0
500
1000
1500
2000
1994 1995 1996 1997
Years
Num
ber o
f pat
ient
s
Cases
Completion
Cure
Monitoring TB control program to ensure complete treatment and cure
E P I D E M I C A L E R T A N D R E S P O N S E
V - Monitoring seroconversion/susceptibility
Systematic control of immune status for specific diseases
Tuberculin reaction
Toxoplasmosis
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
DNA CHIPSPathogenID® Microarray :
Categories of genes Number of Genes 16S ribosomal RNA 51 Toxins/Pathogen effects 229 Resistance to antibiotics 390 Conserved genes 72 MLST 7
Point mutations 167
ARNr 18S 4 Viruses 42
Total 962
Genre SpeciesAlphavirus Eastern Equine Encephalitits virusAlphavirus Venezuelan equine encephalitis virusAlphavirus Western equine encephalomyelitis virusArenavirus Guanarito virusArenavirus Junin virusArenavirus Lymphocytic choriomeningitis virusArenavirus Machupo virusCoronavirus SARS coronavirus Ebolavirus Reston ebolavirusEbolavirus Zaire virusEphemerovirus Bovine ephemeral fever virusFlavivirus Dengue virus type 2Flavivirus Japanese encephalitis virusFlavivirus Kyasanur forest disease virus strain
W371Flavivirus Tick-borne encephalitis virus
etc…………..
42 virus sequences :26 genders11 families
126 virus sequences :37 genders14 families
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
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 foodmicrobiology
(Private & Public)
Legend :FI, Food IncidentM, Mandatory NotificationS, StrainFQ, Food Questionnaire
M
FQ
Cell Listeria
FI
FI
SFood Information
M
M
FQ
SPatient
information
NRL
E P I D E M I C A L E R T A N D R E S P O N S E
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!
E P I D E M I C A L E R T A N D R E S P O N S E
The result of any laboratory test is only as good as the
sample received in the laboratory
E P I D E M I C A L E R T A N D R E S P O N S E
Packaging infectious substances for shipment
Triple packaging system
Infectious substance (BIOHAZARD) label
Container for the first suspected anthrax letter / Berlin
Prof. Matthias Niedrig, RKI
Packaging Specification Marking example: 4H’’/Class 6.2/94 GB/2470 The packaging marking consists of: The United Nations packaging symbol Type of packaging The text “Class 6.2” The last two digits of the year of
manufacture of the packaging State authority manufacturer’s code
u n
E P I D E M I C A L E R T A N D R E S P O N S E
Sampling module
E P I D E M I C A L E R T A N D R E S P O N S E
Biological Risk ManagementBiological 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)
E P I D E M I C A L E R T A N D R E S P O N S E
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E P I D E M I C A L E R T A N D R E S P O N S E
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E P I D E M I C A L E R T A N D R E S P O N S E
Risk assessmentRisk assessment
E P I D E M I C A L E R T A N D R E S P O N S E
Laboratory Biorisk Management Laboratory Biorisk Management StandardStandard
• 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
E P I D E M I C A L E R T A N D R E S P O N S E
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
E P I D E M I C A L E R T A N D R E S P O N S E
THANK YOU FOR YOUR ATTENTION
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The ENIVD-CLRN project is funded by the ECDC under the Framework Service Contract Ref. No. ECDC/2008/011.