Transcript Slide 1 - ECDC - Europa - European Centre for Disease Prevention

Public health microbiology
Disciplines and laboratory methods
Ones upon the time there was a microbiologist
Epidemiologist?????
Which one?????
And she found a way; PH microbiologist
Objectives of the lecture
Define public health microbiology (PHM)
Explain role of PHM
Give example of PHM disciplines
Understand basic methods of characterization
of the microorganisms
What is Public Health Microbiology
(PHM)?
“Microbiology is the study of microorganisms, including viruses, fungi,
parasites and bacteria including immunity to these microorganisms.
Public health microbiology refers to a cross-cutting area that spans the
fields of human, animal, food, water, and environmental microbiology, with
a focus on human health and disease.
Public health microbiology laboratories play a central role in detection,
monitoring, outbreak response, and providing scientific evidence to
prevent and control infectious diseases.
Public health microbiology requires laboratory scientists with ability to
work effectively across disciplines, particularly with epidemiologists
and clinicians.”
Consensus definition for PHM laid out by the group of microbiologists representing
the member states of the EU within the ECDC National Microbiology Focal Point Network
Why focus on this?
Public health is multidisciplinary
•Epidemiologists
•Laboratory specialists
•Clinicians
•Veterinarians
•Environmental specialists
Activities must be
•Nurses
coordinated to reach
•And more…
common goals!
The Lab – Epi challenge
Epidemiologists and lab specialists are infectious disease
experts with different:
• Perspective and approach
• Skills and knowledge
• Working habits
“The two sides of the same medal”
Communication and understanding between Lab and Epi is
crucial to the quality of public health investigations!
Epi and lab – room for synergy?
Infecious disease epidemiology
– Hypothesis -> risk factors ->
methods to make conlusions from
incomplete data
Veterinary data
Clinical microbiology
– Evidence of the presence of
pathogen, but not everyone can be
sampled and the problems don’t stop
there...
Environmental data
Different laboratories...
...with different roles
•Primary health care laboratories
•Hospital laboratories
•Independent diagnostic laboratories (state,
regional or private)
•Academic research laboratories
•Veterinary Laboratories
•Environmental Laboratories
•Reference laboratories
•Public health laboratories
Some important PH Laboratory tasks
1. Confirm diagnosis for targeted interventions (detection, monitoring,
outbreak response, and providing scientific evidence)
2. Identify (new) types of pathogens
•
Population-dynamics
•
Virulence, persistence, resistance
•
Implications for control measures
3. Microbiological safety of food and water
4. Quality assurance of diagnostic results
5. Information management, communication and coordination
6. Biosafety
7. Develop new tests/ Optimize existing tests
8. Basic/applied research for new insights and innovative solutions to health
problems (vaccine and antibiotic development)
Where to find a public health
microbiology laboratory regime
•Only integrated into the national PH institute, depending on
size and development of country (eg. Netherlands)
•In a separate institution collaborating with the national PH
institute (eg. France, Institute Pasteur)
•At the national PH institute and in regional laboratories,
depending on infrastructure and size of country (eg. Germany,
UK, Sweden)
Keep in mind
Essential functions of a PHL are not exclusive
Many public health laboratories conduct both public health
and clinical diagnostic services
Many public health laboratories conduct both public health
and research
Some public health laboratories produce and sell
vaccines or biologicals (ex: Cantacuzino Institute,
Roumania: diagnostic antisera; Pasteur Institute, Senegal:
yellow fever vaccine)
Do you know your country's laboratory
system?
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
FIND OUT!
http://ecdc.europa.eu/en/activities/microbiology/pages/
microbiologicalcooperation_nationalmicrobiologicalfocalpoints.aspx
What disciplines do you need at a PH
laboratory
Bacteriologists / Virologists / Parasitologist
Medical Microbiologists
Molecular Biologists
Immunologists
Post doctoral researchers / PhD students
Technicians / technical assistance / Analyst
Phylogenetic / molecular epidemiology specialists
Environmental specialists
Zoonosis specialists
FIND
Epidemiologists/ Statisticians
Public Health Microbiologists
OUT!
…..what is the difference and who is the best contact for what…
Conclusions part1:
Conditions for successful collaboration between Lab and
Epi ( Satu and Sabine share experience with you)
Identify common goals
Understand that one is not only supporting the
other, you work together for the same goals
Establish and keep up lines of communication from
the beginning to the end
Communicate expectations
Agree on authorship issues before the start of the
project
Share data and information efficiently and openly;
do not hide data and information
Understand that there are different perspectives
Recognize different skills
Respect different working cultures
Part 2: From story to reality Step by step
Species versus strains
Discriminating features
Classification
Strain: one single isolate or line
Species: related strains
Type: sub-set of species
Genus: related species
Family: related genera
Steps in isolation and identification
• Step 1: Streaking culture plates
– colonies on incubation (e.g 24 hr)
– size, texture, color, hemolysis
– oxygen requirement
Sheep blood agar plate culture
Bacillus cereus.
Bacillus anthracis
CDC/Dr. James Feeley
21
Mixed colonies
Isolation and identification
Step 2: Colonies Gram stained
• cells observed microscopically
Gram negative
Gram positive
Heat/Dry
Crystal violet stain
Iodine Fix
Alcohol de-stain
Safranin stain
25
26
Gram stain morphology
Gram positive or negative
Shape
• cocci (round)
• bacilli (rods)
• spiral or curved (e.g. spirochetes)
Single or multiple cells
• clusters (e.g. staphylococci)
• chains (e.g. streptococci)
Step 3: Isolated bacteria are speciated
Generally using biophysiological tests
Example Salmonella and E-coli
Step 4:
Antibiotic susceptibility testing
Susceptible
Not susceptible
Bacterial
lawn
No
growth
Growth
Antibiotic disk
DNA structure
DNA is usually a double-helix and has two strands running in
opposite directions.
(There are some examples of viral DNA which are single-stranded).
Each chain is a polymer of subunits called nucleotides (hence the name
polynucleotide).
Molecular differentiation
Genomics
• Gene characterization
– Sequencing
– PCR (Polymerase chain reaction )
•
•
Specific part of a gene
16SrRNA
– Restriction digests
• Hybridization
Genotypic typing methods
Fingerprint-based methods
– Plasmid profile, RFLP(restriction
fragment length
polymorphism), PFGE, AFLP
Character-based methods
– MLVA (Multiple Loci VNTR Analysis),
ribotyping (restriction fragments that
contain all or part of the genes
coding for the 16S and 23S rRNA ),
microarray’s
Sequence-based methods
– MLST
– SNP=single nucleotide
polymorphism typing
Minimum spanning tree of 240 strains
Salmonella Enteritidis by MLVA
MRSA typed with PFGE & MLST
PFGE
McDougal LK et al, 2003, J Clin Microbiol 41:5113-20
Noroviruses
Norwalk virus
Hawaii virus
Snow Mountain virus
Mexico virus
Desert Shield virus
Southampton virus
Lordsdale virus
GI GI.1, GI.2
GII
GIII
Protein profiling: defining a species by
characteristic proteins
Proteomics: defining all proteins
expressed by a species under specific
growth conditions
Rapid diagnosis without culture
• WHEN AND WHY?
• grow poorly
• can not be cultured
• Need speedy results
Bacterial DNA sequences amplified directly from
human body fluids
• Polymerase chain reaction (PCR)
• Great success in rapid diagnosis
of tuberculosis.
Serologic
identification
• antibody response to the infecting agent
• several weeks after an infection has
occurred
Diagnostic methods time line
time of diagnosis
sensitivity
- virus isolation
1 – 7 days
high*
high**
- hybridisation
3 – 4 hours
high1
good
- PCR
3 – 4 hours
high2
good
30 min
low3
high
3 – 5 hours
good4
high
- ELISA
3 – 4 hours
high
low
- Immunofluorescence
(IFA)
- Immunoblot
2 – 4 hours
good
good
2 – 4 hours
good
good
- Neutralisation/
compliment fixation
- HIA
4 – 7 days
good
high
2 – 4 hours
low
good
Virus detection
- Electronmicroscopy
- capture ELISA
specificity
Serology
1
3
ca. 104 particle/ml,
 106 particle/ml,
2
4
ca. 200 genome equivalent/ml,
ca. 0.01 µg antigen/ml
* depending on
cultivation system
** depending on
detection System
Prof. Matthias Niedrig, RKI
Conclusion part2:
Choice of typing method
Pathogen
Reproducibility
Discriminatory power
Exchangeability of data!
Study question
• Local/global and short/long term epidemiology
Availability and resources
?
Acknowledgment