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 representingthe member states of the EU within the ECDC National Microbiology Focal Point Network
8 Why focus on this? Public health is multidisciplinary Epidemiologists Laboratory specialistsCliniciansVeterinariansEnvironmental specialistsNursesAnd more…Activities must be coordinated to reach common goals!
9 “The two sides of the same medal” The Lab – Epi challengeEpidemiologists and lab specialists are infectious disease experts with different:Perspective and approachSkills and knowledgeWorking 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 dataClinical microbiology– Evidence of the presence of pathogen, but not everyone can be sampled and the problems don’t stop there...Veterinary dataEnvironmental dataPublic health microbiology
11 Different laboratories... ...with different roles Primary health care laboratoriesHospital laboratoriesIndependent diagnostic laboratories (state, regional or private)Academic research laboratoriesVeterinary LaboratoriesEnvironmental LaboratoriesReference laboratoriesPublic 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 pathogensPopulation-dynamicsVirulence, persistence, resistanceImplications for control measures3. Microbiological safety of food and water4. Quality assurance of diagnostic results5. Information management, communication and coordination6. Biosafety7. Develop new tests/ Optimize existing tests8. 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 servicesMany public health laboratories conduct both public health and researchSome 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 labsRegional labsHospital labsReference labsInternational lab networksFIND OUT!microbiologicalcooperation_nationalmicrobiologicalfocalpoints.aspx
16 What disciplines do you need at a PH laboratory Bacteriologists / Virologists / ParasitologistMedical MicrobiologistsMolecular BiologistsImmunologistsPost doctoral researchers / PhD studentsTechnicians / technical assistance / AnalystPhylogenetic / molecular epidemiology specialistsEnvironmental specialistsZoonosis specialistsEpidemiologists/ StatisticiansPublic Health MicrobiologistsFIND 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 goalsUnderstand that one is not only supporting the other, you work together for the same goalsEstablish and keep up lines of communication from the beginning to the endCommunicate expectationsAgree on authorship issues before the start of the projectShare data and information efficiently and openly; do not hide data and informationUnderstand that there are different perspectivesRecognize different skillsRespect 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 strainsType: sub-set of speciesGenus: related speciesFamily: related generaIsolation 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 platescolonies on incubation (e.g 24 hr)size, texture, color, hemolysisoxygen requirementPicture
21 Sheep blood agar plate culture Bacillus cereus.Bacillus anthracisCDC/Dr. James Feeley
31 DNA structureDNA is usually a double-helix and has two strands running inopposite directions.(There are some examples of viral DNA which are single-stranded).Each chain is a polymer of subunits called nucleotides (hence the namepolynucleotide).
32 Molecular differentiation GenomicsGene characterizationSequencingPCR (Polymerase chain reaction )Specific part of a gene16SrRNARestriction digestsHybridization
33 Genotypic typing methods Minimum spanning tree of 240 strains Salmonella Enteritidis by MLVAFingerprint-based methodsPlasmid profile, RFLP(restriction fragment length polymorphism), PFGE, AFLPCharacter-based methodsMLVA (Multiple Loci VNTR Analysis), ribotyping (restriction fragments that contain all or part of the genes coding for the 16S and 23S rRNA ), microarray’sSequence-based methodsMLSTSNP=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 strainsNetherlandsJapanUnited StatesArgentinaFranceNew ZealandKyrgyzstanSpainItalyGreeceCanadaSouth AfricaAustria4915Cluster 113186/2215143711Cluster 2Cluster 3Borgen et al, BMC 2008