1. Public health microbiology
Disciplines and laboratory methods

2. Ones upon the time there was a microbiologist

3. Epidemiologist?????

4. Which one?????

5. And she found a way; PH microbiologist

6. 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

7. 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

8. Why focus on this? Public health is multidisciplinary Epidemiologists
Laboratory specialists
Clinicians
Veterinarians
Environmental specialists
Nurses
And more…
Activities must be coordinated to reach common goals!

9. “The two sides of the same medal”
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!

10. Epi and lab – room for synergy?
Infecious disease epidemiology
– Hypothesis -> risk factors -> methods to make conlusions from incomplete data
Clinical microbiology
– Evidence of the presence of pathogen, but not everyone can be sampled and the problems don’t stop there...
Veterinary data
Environmental data
Public health microbiology

11. 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

12. Some important PH Laboratory tasks
Confirm diagnosis for targeted interventions (detection, monitoring, outbreak response, and providing scientific evidence)
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)

13. 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)

14. 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) 14

15. 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!
microbiologicalcooperation_nationalmicrobiologicalfocalpoints.aspx

16. 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
Epidemiologists/ Statisticians
Public Health Microbiologists
FIND OUT!
…..what is the difference and who is the best contact for what…

17. Communicate expectations
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

18. Part 2: From story to reality Step by step Species versus strains Discriminating features

19. Classification Strain: one single isolate or line
Species: related strains
Type: sub-set of species
Genus: related species
Family: related genera
Isolation and identification of bacteria from patients aids treatment since infectious diseases caused by different bacteria have a variety of clinical courses and consequences.

20. Steps in isolation and identification
Step 1: Streaking culture plates
colonies on incubation (e.g 24 hr)
size, texture, color, hemolysis
oxygen requirement
Picture

21. Sheep blood agar plate culture
Bacillus cereus.
Bacillus anthracis
CDC/Dr. James Feeley

22. Mixed colonies

23. Isolation and identification
Step 2: Colonies Gram stained
cells observed microscopically

24. Gram Stain Gram negative Gram positive Heat/Dry Crystal violet stain
Iodine Fix
Alcohol de-stain
Safranin stain

25. Check gram staining principles

27. 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)

28. Step 3: Isolated bacteria are speciated
Generally using biophysiological tests
Example Salmonella and E-coli
Get a picture of both

29. Antibiotic susceptibility testing
Step 4:
Antibiotic susceptibility testing
Not susceptible
Susceptible
Bacterial
lawn
Growth
No growth
Antibiotic disk

31. 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).

32. Molecular differentiation
Genomics
Gene characterization
Sequencing
PCR (Polymerase chain reaction )
Specific part of a gene
16SrRNA
Restriction digests
Hybridization

33. Genotypic typing methods
Minimum spanning tree of 240 strains Salmonella Enteritidis by MLVA
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

34. MRSA typed with PFGE & MLST
McDougal LK et al, 2003, J Clin Microbiol 41:

35. sequence typed, by geographical origin
81 human strains
Netherlands
Japan
United States
Argentina
France
New Zealand
Kyrgyzstan
Spain
Italy
Greece
Canada
South Africa
Austria 4 9 15
Cluster 1 13 18
6/22 1 5 14 3 7 11
Cluster 2
Cluster 3
Borgen et al, BMC 2008

36. Noroviruses
Norwalk virus Hawaii virus Snow Mountain virus Mexico virus Desert Shield virus Southampton virus Lordsdale virus GI GI.1, GI.2 GII GIII

37. Protein profiling: defining a species by characteristic proteins
Proteomics: defining all proteins expressed by a species under specific growth conditions

38. Rapid diagnosis without culture
WHEN AND WHY?
grow poorly
can not be cultured
Need speedy results

39. Bacterial DNA sequences amplified directly from human body fluids
Polymerase chain reaction (PCR)
Great success in rapid diagnosis
of tuberculosis.

40. Serologic identification
antibody response to the infecting agent
several weeks after an infection has
occurred

41. Diagnostic methods time line
ELISA/HIA
Prof. Matthias Niedrig, RKI

42. 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 ?

43. Acknowledgment