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Which one

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Which one

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  1. Public health microbiology Disciplines and laboratory methods Prepared by: Satu Kurkela and Sabine Dittrich And Aftab Jasir

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

  9. 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. Veterinary data Environmental data 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... 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)

  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! http://ecdc.europa.eu/en/activities/microbiology/pages/ 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. 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 stepSpecies 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

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

  21. Sheep blood agar plate culture Bacillus anthracis Bacillus cereus. 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 IodineFix Alcoholde-stain Safranin stain

  25. 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)

  26. Step 3:Isolated bacteria are speciated • Generally using biophysiological tests Example Salmonella and E-coli

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

  28. 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).

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

  30. Minimum spanning tree of 240 strains Salmonella Enteritidis by MLVA 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

  31. PFGE MRSA typed with PFGE & MLST McDougal LK et al, 2003, J Clin Microbiol 41:5113-20

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

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

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

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

  36. Diagnostic methods time line Prof. Matthias Niedrig, RKI

  37. 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 ?

  38. Acknowledgment

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