Public health microbiology

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Public health microbiology
Disciplines and laboratory methods
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Ones upon the time there was a microbiologist
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Epidemiologist?????
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Which one?????
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And she found a way PH microbiologist
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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

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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
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Why focus on this?

• Public health is multidisciplinary
• Epidemiologists
• Laboratory specialists
• Clinicians
• Veterinarians
• Environmental specialists
• Nurses
• And more

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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!

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Epi and lab room for synergy?

• Infecious disease epidemiology
• Hypothesis -gt risk factors -gt methods to make
  conlusions from incomplete data
• Clinical microbiology
• Evidence of the presence of pathogen, but not
  everyone can be sampled and the problems dont
  stop there...

Public health microbiology
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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

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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)

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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)

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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)

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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/p
ages/ microbiologicalcooperation_nationalmicrobiol
ogicalfocalpoints.aspx
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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
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Conclusions part1Conditions 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

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Part 2 From story to reality Step by
stepSpecies versus strains Discriminating
features
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Classification

• Strain one single isolate or line
• Species related strains
• Type sub-set of species
• Genus related species
• Family related genera

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Steps in isolation and identification

• Step 1 Streaking culture plates
• colonies on incubation (e.g 24 hr)
• size, texture, color, hemolysis
• oxygen requirement

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Sheep blood agar plate culture
Bacillus anthracis
Bacillus cereus.
CDC/Dr. James Feeley
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Mixed colonies
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Isolation and identification

• Step 2 Colonies Gram stained
• cells observed microscopically

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

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Step 3 Isolated bacteria are speciated

• Generally using biophysiological tests

Example Salmonella and E-coli
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Step 4 Antibiotic susceptibility testing
Not susceptible
Susceptible
Bacterial lawn
Growth
No growth
Antibiotic disk
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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).
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Molecular differentiation

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

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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 ),
  microarrays
• Sequence-based methods
• MLST
• SNPsingle nucleotide polymorphism typing

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MRSA typed with PFGE MLST
McDougal LK et al, 2003, J Clin Microbiol
415113-20
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sequence typed, by geographical origin
81 human strains
Borgen et al, BMC 2008
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Noroviruses

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

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

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Rapid diagnosis without culture

• WHEN AND WHY?
• grow poorly
• can not be cultured
• Need speedy results

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Bacterial DNA sequences amplified directly from
human body fluids

• Polymerase chain reaction (PCR)
• Great success in rapid diagnosis
• of tuberculosis.

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Serologic identification

• antibody response to the infecting agent
• several weeks after an infection has
• occurred

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Diagnostic methods time line
Prof. Matthias Niedrig, RKI
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Conclusion part2Choice of typing method

• Pathogen
• Reproducibility
• Discriminatory power
• Exchangeability of data!
• Study question
• Local/global and short/long term epidemiology
• Availability and resources

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Acknowledgment
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