Transcript - MediPIET

Lab-based surveillance
Introduction to Intervention Epidemiology
Tunis, 3 November 2014
Presented by Nada Ghosn
Ministry of Public Health - Lebanon
[email protected]
Learning objectives
‒ To understand the need of
coordination and communication
‒ To understand specimen collection
procedures: types, timing,
conservation, transportation
‒ To understand the role of
laboratories in surveillance
‒ To know the factors for lab-based
surveillance
‒ To understand the scope of
pathogen surveillance
Learning objectives
‒ To understand the need of
coordination and
communication
‒ The relation between
epidemiology and laboratory
Public Health workforce
Public Health workforce
 Public health is multidisciplinary
•
•
•
•
•
•
•
•
Epidemiologists
Laboratory specialists
Clinicians
Nurses
Veterinarians
Entomologists
Environmental specialists
And more…
• Public health workforce is multidisciplinary
• There is need for coordination to reach common goals
Lab – Epi collaboration
 Epidemiologists and lab specialists need to
work together
 Do they have same?
– Terms of reference
– Competencies: knowledge, skills, and attitudes
– Approach and working habits
Communication and mutual understanding
between Lab and Epi is crucial to the quality
of public health investigations!
Lab – Epi collaboration
What are their TOR?
Epidemiologists:
– …
– …
– …
Microbiologists:
–
–
–
…
…
…
Lab – Epi collaboration
Epidemiologists:
– Run surveillance
– Conduct descriptive &
analytical studies
– Describe cases
– Measure association
between disease &
exposure factors
Microbiologists:
–
–
–
–
Conduct laboratory
confirmation tests
Describe pathogens
Trace back the source of
infection
May conduct surveillance
of pathogens
characteristics
Lab – Epi collaboration
• Close collaboration: is needed between
microbiologists and epidemiologists
• Quality of outbreak investigations: relies
also on communication and mutual
understanding between Lab and Epi
Learning objectives
‒ To understand specimen
collection procedures:
types, timing, conservation,
transportation
Specimen collection procedures
• Why do we need Standard Operating
Procedures SOP?
Specimen collection procedures
• Needs to have Standard Operating Procedures
to specify:
–
–
–
–
–
–
–
–
–
Type of specimens
Required tests
Timing for specimen collection
Materials for collection of samples
Needed transport medium
Methods for specimen collection: packaging, temperature …
Target laboratory: clinical or reference
Laboratory request form accompanying the samples
Procedure of coordination with the lab: inform before arrival
…
Specimen collection:
types
• Clinical specimens
– From humans: patients, contacts, staff (food handlers …)
– From animals: alive or dead
• Environmental specimens
– Food: left over, similar food, ingredients, milk
– Water: drinking, recreational, air-conditioner/cooling
system …
– Vectors: mosquitoes, sand-flies …
– Surfaces
• Isolates: culture of pathogens
Specimen collection:
• How to collect?
• When to collect?
• What test to request?
Specimen collection:
invasive/non-invasive procedures
Examples
Respiratory
Invasive
Broncho-alveolar
lavage
(bronchoscopy)
Digestive
Non-invasive
Naso-pharygeal, throat
swab, sputum
Stool, rectal swab
CNS
Cerebrospinal fluid
(lumbar punction),
tissue (biopsy)
Blood
Blood, serum
Dried blood
Renal
Urine
Other
Conjunctival swab, oral
fluid …
Poliovirus infection
Duration of Fecal Excretion of Wild Polioviruses
Source: WHO
Influenza infection
Source: WHO
Measles infection
Source: WHO
Specimens collection:
timing and tests
Examples
Specimens
Timing
Tests
Polio
Stool
Within 14 days from
onset
Virological culture
Influenza
(before
anti-viral
ttt)
Respiratory specimen
Within 5 days
Virological culture
Respiratory specimen
Within 7 days
PCR
Paired sera
Acute phase +
convalescent phase
Serological testing
Throat swab, urine
Within 5 days from
onset
Virological culture
Dried blood
Within 7 days
PCR
Oral fluid
Within 14 days
PCR
Serum, oral fluid, dried
blood
Within 28 days
Serology IgM
Measles
Specimens collection:
timing and tests
• For direct diagnostics: microscopy,
culture, PCR
– Early phases of disease (<4 days after
onset)
– Before starting antibiotic therapy
– During bouts of fever
• For indirect diagnostics :
– IgM serology: during acute phase and
after 7-14 days
– IgG serology: starting from 3rd week
Specimens collection:
adequate media
• Do we need media for collection?
Specimens collection:
adequate media
• Transport media
– Allows organisms (pathogens and contaminants) to
survive
– Non-nutritive - does not allow organisms to
proliferate
• Examples:
– Specific media for bacteria
• Amies, Cary Blair…
– Specific media for virus
• Viral transport media
Specimen collection:
Transportation
 How to transport specimen to lab?
Specimen collection:
Transportation
 Local transport
 National legislations
 International transport
 International legislations
 Air: IATA regulations for dangerous goods: pose a risk
during transport
 Category A
 Category B
 Exempt specimens
 Laboratory form
Transport of specimens
Catego
ry
Definitions
Examples
Triple packaging
Shipper profile
A
An infectious substance which
is transported in a form that,
when exposure to it occurs,
is capable of causing
permanent disability, lifethreatening
or fatal disease in otherwise
healthy humans or animals
Poliovirus
(culture),
Ebola virus,
Brucella (culture)
…
Yes, UN2814 or
UN2900,
Packaging
Instruction 620 +
Declaration of
Dangerous Goods
DGD
Trained by IATA
accredited body
B
An infectious substance which
does not meet the criteria for
inclusion in Category A, and
has not been determined to
have a minimal likelihood that
pathogens are present.
Poliovirus clinical
specimens,
Brucella clinical
specimens …
Yes, UN3373,
Packaging
Instruction 650
-
Exempt
Patient specimens for which
there is minimal likelihood that
pathogens are present.
Urine of
athletes…
May be with triple
packaging
-
Category A “602 package”
Labels: UN 2814 UN 2900 Biohazard
Source: WHO
Category B,
“650 package”
UN 3373
No biohazard label
Source: WHO
Learning objectives
‒ To understand the role of
laboratories in surveillance
‒ Role of laboratory for
endemic diseases
‒ Role of laboratory during
outbreaks
Role of laboratory
 What role?
 At what time?
Role of laboratory
 Confirmation
 Diseases: clinical diagnosis
 Environmental contamination: food, water …
 Identify pathogens
 Circulating pathogens: types and subtypes …
 Identify novel pathogens: new agents, new
types/subtypes
 Identify susceptibility/resistance to
antibiotics/antivirals…
Neisseria meningitidis by serogroup and year,
France, 1985-2000
C
600
B
Number of cases
500
A
Unknown
400
300
200
100
0
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
2000
Year
Source : InVS and NRC for N. meningitis, Pasteur Institute, Paris
Source: InVS, France
Influenza surveillance
Source: WHO
Influenza surveillance
Laboratory for endemic pathogens
 During endemic phase
–
–
–
–
–
Case confirmation
Monitoring trends
Identifying and monitoring circulating agents and characteristics
Monitoring antibiotic/antiviral susceptibility/resistance
Guidance for clinical case management: viruses, bacteria …
Laboratory during outbreaks
 Before an outbreak
 Early detection
 During an outbreak:
 Laboratory confirmation: first cases, and during the course
of the outbreak
 Specific case definition
 Identification of pathogen: novel agents, comparison of
strain
 Identification of food and environmental contamination:
identification of the source of infection
 Characterization of antibiotic resistance: guide clinical
management
Ebola virus disease in Liberia,
up to 15 October 2014
Source: WHO
Reported measles cases,
Lebanon, 2013
Source: MOPH, Lebanon
Laboratory during outbreaks
• There is need:
– To inform early the laboratory about the
alert
– To include laboratory specialists in the
outbreak team
 Only if the labs are included in the information
flow will the necessary investigation be
possible.
Outline
‒ To know the factors for labbased surveillance
Laboratory-based surveillance
 How to proceed?
Elements for lab-based surveillance
 Which diseases and pathogens?
 List diseases that require laboratory confirmation
 Determine tests to be performed
 Which laboratories?
 Map laboratory facilities and human resources
 Identify clinical and reference laboratories
 Establish laboratory networking
 How?
 Official texts
 Designation of focal person to coordinate laboratory
activities
 Determine information flow …
Factors for lab-based surveillance
Define roles and responsibilities:
Identify referral system
Develop preparedness plan
Ensure capacity
Train human resources
Provide supplies, logistics,
Prepare guidelines/SOP & forms
Establish communication
 Organize communication
between lab and epi
 Prompt, regular reporting of
results and feedback
Ensure quality
Plan quality assurance
Biosafety and biosecurity
Waste management
Supervise and monitor
Laboratory network
 How is lab network organized?
 Who is in charge of which disease?
 Who do you contact in which case?
‒
‒
‒
‒
‒
Local labs
Regional labs
Hospital labs
Reference labs
International lab networks
Organization of laboratory network
 Where do you test for the following
diseases?






Poliovirus
Measles
VHA
VHB
Ebola
MERS-CoV
Organization of laboratory network
Collection of samples,
microscopy, transport
P
P
P
P
P
Periphery
Confirmatory testing,
culture, transport
I
I
Intermediate
Specialized tests:
serology, immunofluorescence, PCR
C
Central
Highly specialized tests
International
laboratories
P
Different types of organizations
35
Laboratory testing complexity
30
25
20
15
10
5
0
Country A
(High-income)
Periphery
Country B
(Middle-income )
National
Country C
(Low-income)
Supra-national
Limitations
• Lack of:
– Laboratory facilities,
– Equipment, material and reagents
– Trained staff
 Essential to have:
 Sample collection system
 Packaging and transport logistics
 Communication with pre-identified national and
international laboratories
Learning objectives
‒ To understand the scope of
pathogen surveillance
Molecular surveillance
 Pathogens have their own heterogeneity
 Various phenotypes due to:
• Resistance profiles
• Biochemical profiles
• Protein/lipid profiles
 Various genotypes
• DNA Sequencing
– One gene: Single-Gene Sequencing
– Many genes: Multi-Locus Sequence Typing (MLST)
– Complete genome: Whole-Genome Sequencing (WGS)
• Not DNA sequencing
– PFGE – DNA Fragment separation
Learning objectives
‒ To understand the scope of
pathogen surveillance
‒ PFGE
Example of an outbreak
Outbreak in Mount Lebanon, September 2011
12 samples processed: 10 patient samples and 2 Arabic sweet samples
Patient stool culture:
8 Salmonella spp.,
1 Morganella morganii
2 Arabic sweet samples:
Salmonella spp.
Serotyping in PulseNet Lab-AUB:
8 patient samples are Salmonella Enteritidis
2 Arabic sweet samples are Salmonella Enteritidis
Do we need more?
Source: MOPH & AUB, Lebanon
PFGE: From serotyping to genotyping:
• Salmonella:
– Phenotypic characterization of strains based on the immunologic
reactivity of two surface structures:
1. Lipopolysaccharide (O antigen)
2. Flagellin protein (H antigen)
Lipopolysaccharide (LPS)
Flagella
Y
PFGE: From serotyping to genotyping:
• Salmonella:
• Molectular genotyping: perform DNA "fingerprinting" by
pulsed-field gel electrophoresis (PFGE).
• PFGE is a subtyping method that detects polymorphism
in restriction fragments of genomic DNA
(macrorestriction).
• PFGE patterns generated, dendograms or bacteria family
tree are produced.
• The dendogram finds all the bacteria that are closely
related using their PFGE fingerprints
PFGE
Pulsed Field Gel Electroforesis
Same strain
Different strain
Example of an outbreak
Outbreak in Mount Lebanon, September 2011
Source: MOPH & AUB, Lebanon
Example of an outbreak
Outbreak in Mount Lebanon, September 2011
12 samples processed: 10 patient samples and 2 Arabic sweet samples
Patient stool culture:
8 Salmonella spp.,
1 Morganella morganii
2 Arabic sweet samples:
Salmonella spp.
Serotyping in PulseNet Lab-AUB:
8 patient samples are Salmonella Enteritidis
2 Arabic sweet samples are Salmonella Enteritidis
PFGE type in PulseNet Lab-AUB:
JEGX01.001 for Salmonella Enteritidis patient samples
JEGX01.001 for Salmonella Enteritidis Arabic sweet samples
Source: MOPH & AUB, Lebanon
PulseNet International
• A network of laboratory networks started in 1996
dedicated to foodborne infections world-wide. It
includes more than 82 countries.
• Subtyping foodborne bacterial pathogens through
standardized process of pulsed-field gel electrophoresis
(PFGE).
• Roles:
– Detect foodborne disease case clusters
– Real-time sharing of information (human strain, food strain and
animal strain),
– Separate outbreak-associated cases from sporadic cases,
– Assist in identifying and confirming the source of the outbreak.
Learning objectives
‒ To understand the scope of
pathogen surveillance
‒ Virus genotyping
Virus genotyping
•Methods
– PCR
– Restricted Enzyme Digestion
– Sequencing
•Utility:
–Identify circulating pathogens
–Identify novel pathogens
–Trace back importation
–Guide public health measures
Poliovirus types, World, 2001-2009
Wild poliovirus cases, 2001-2009*
WPV1
WPV3
3000
2500
2000
1500
1000
500
2009
2008
2007
2006
2005
2004
2003
2002
2001
0
There are 3 types for poliovirus: 1, 2 and 3.
Source: WHO
Poliovirus types
‒ Poliovirus type 2 was eradicated in 1999.
‒ Is there any implication in public health measures?
Measles genotypes
•WHO currently recognizes 8 clades: A, B, C, D, E, F, G, and H
•Within these clades, there are 23 recognized genotypes:
–A
–B1, B2, B3
–C1, C2
–D1, D2, D3, D4, D5, D6, D7, D8, D9, D10
–E
–F
–G1, G2, G3
–H1, and H2
Global distribution of measles genotypes and measles incidence in 2009.
Rota P A et al. J Infect Dis. 2011;204:S514-S523
Measles in Lebanon
•Annual outbreaks in 2003-2007: D4
•7 years after, national outbreak in 2013:
– Mainly D8,
– and one isolate B3
Measles genotypes
•3 patterns of measles genotype distribution
–In countries with endemic transmission: majority of cases are caused by
one or several endemic genotypes that are distributed geographically.
– In countries that have eliminated measles: small numbers of cases
caused by different genotypes
•reflecting various sources of imported virus
•and suggesting the lack of sustained transmission.
–Countries or regions with very good measles control but are experiencing
increase in numbers of susceptible because of failure to maintain high
vaccination coverage rates: reintroduction of measles usually results in
outbreaks
•that are associated with a single genotype of virus with nearly
identical sequences.
Learning objectives
‒ To understand the scope of
pathogen surveillance
‒ AMR surveillance
Acinetobacter baumannii Isolates
# Acinetobacter isolates
(first isolate, one per patient)
14
Start date*: 6/1/05
End date*: 8/1/05
12
10
8
6
4
2
0
*Dates are fictitious
Source: WHO collaborating center for AMR
Acinetobacter baumannii
Suspicious Susceptibility Pattern
# Acinetobacter isolates
(first isolate, one per patient)
14
12
Start*: 6/1/05
End*: 7/28/05
10
*Dates are fictitious
8
6
4
2
0
Non-susceptible to 7 antibiotics: Ampicillin, Cefotaxime, Ceftazidime, Levofloxacin,
Nitrofurantoin, Gentamicin, Trimethoprim/Sulfamethoxazole
Source: WHO collaborating center for AMR
Use of microbiology data
• Laboratory quality improvement
– Utilization of laboratory services by clinical staff
• Infection control and outbreak preparedness
– Identification of new and problem pathogens
– Identification and investigation of outbreaks
• Antimicrobial policy
– Trends in infections and resistance
– Characterization of cross-resistance
– Development of treatment guidelines
• Research
– New resistance mechanisms
– Risk factors for resistance
• Evaluation of interventions
Source: WHO collaborating center for AMR
Why AMR?
• Better treatment:
– Treatment guidelines
• Better infection control:
– Control of nosocomial infections
• Monitoring the impact of interventions to improve
antimicrobial use and control spread of infection
WHONET: A Microbiology
Data Management Tool
• Free of charge from WHO
– www.whonet.org
• Enhance the use of locally-generated data
– Antimicrobial policy, infection control
– Laboratory quality assurance
• Promote collaborations
– National and international networks
• The software includes 20 languages
WHONET: data entry screen
WHONET: line listing
List of patients with MRSA
Source: WHO collaborating center for AMR
Learning objectives
‒ In conclusion
Conclusions
 Laboratory testing is essential for epidemiology
– Epidemiological surveillance
– Outbreak investigation
 Collaboration between epidemiologists and microbiologists
is crucial
–
–
–
–
Identify common goals
Understand that there are different perspectives
Recognize different skills
Communicate expectations
 Adequate sample collection, packaging, and transport is
essential to ensure the identification of the pathogen
THANK YOU
Introduction to Intervention Epidemiology
Tunis, 3 November 2014
Nada Ghosn
Ministry of Public Health - Lebanon
[email protected]