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Public health microbiology

Disciplines and laboratory methods

Prepared by: Satu Kurkela and Sabine Dittrich

And Aftab Jasir

objectives of the lecture
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
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

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…
the lab epi challenge
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

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

different laboratories with different roles
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
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)
where to find a public health microbiology laboratory regime
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
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
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



what disciplines do you need at a ph laboratory
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


…..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
  • 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 anthracis

Bacillus cereus.

CDC/Dr. James Feeley

isolation and identification
Isolation and identification
  • Step 2: Colonies Gram stained
    • cells observed microscopically

Gram Stain

Gram negative

Gram positive


Crystal violet stain



Safranin stain

gram stain morphology
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
Step 3:Isolated bacteria are speciated
  • Generally using biophysiological tests

Example Salmonella and E-coli


Step 4:

Antibiotic susceptibility testing

Not susceptible





No growth

Antibiotic disk


dna structure
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


molecular differentiation
Molecular differentiation
  • Genomics
  • Gene characterization
    • Sequencing
    • PCR (Polymerase chain reaction )
    • Specific part of a gene
    • 16SrRNA
    • Restriction digests
  • Hybridization
genotypic typing methods

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
mrsa typed with pfge mlst


MRSA typed with PFGE & MLST

McDougal LK et al, 2003, J Clin Microbiol 41:5113-20

Protein profiling: defining a species by characteristic proteins
  • Proteomics: defining all proteins expressed by a species under specific growth conditions
rapid diagnosis without culture
Rapid diagnosis without culture
    • grow poorly
    • can not be cultured
    • Need speedy results
bacterial dna sequences amplified directly from human body fluids
Bacterial DNA sequences amplified directly from human body fluids
  • Polymerase chain reaction (PCR)
  • Great success in rapid diagnosis
  • of tuberculosis.
serologic identification
Serologic identification
  • antibody response to the infecting agent
  • several weeks after an infection has
  • occurred
diagnostic methods time line
Diagnostic methods time line

Prof. Matthias Niedrig, RKI

conclusion part2 choice of typing method
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