Public health microbiology
Download
1 / 41

Which one - PowerPoint PPT Presentation


  • 201 Views
  • Uploaded on

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Which one' - Kelvin_Ajay


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
Slide1 l.jpg

Public health microbiology

Disciplines and laboratory methods

Prepared by: Satu Kurkela and Sabine Dittrich

And Aftab Jasir






Objectives of the lecture l.jpg
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 l.jpg
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 l.jpg

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 l.jpg
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 l.jpg

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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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


What disciplines do you need at a ph laboratory l.jpg
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…


Slide17 l.jpg
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


Part 2 from story to reality step by step species versus strains discriminating features l.jpg
Part 2: From story to reality Step by stepSpecies versus strains Discriminating features


Classification l.jpg
Classification

  • Strain: one single isolate or line

  • Species: related strains

  • Type: sub-set of species

  • Genus: related species

  • Family: related genera


Slide20 l.jpg

Steps in isolation and identification

  • Step 1: Streaking culture plates

    • colonies on incubation (e.g 24 hr)

    • size, texture, color, hemolysis

    • oxygen requirement


Slide21 l.jpg

Sheep blood agar plate culture

Bacillus anthracis

Bacillus cereus.

CDC/Dr. James Feeley



Isolation and identification l.jpg
Isolation and identification

  • Step 2: Colonies Gram stained

    • cells observed microscopically


Slide24 l.jpg

Gram Stain

Gram negative

Gram positive

Heat/Dry

Crystal violet stain

IodineFix

Alcoholde-stain

Safranin stain


Gram stain morphology l.jpg
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 l.jpg
Step 3: Isolated bacteria are speciated

  • Generally using biophysiological tests

Example Salmonella and E-coli


Slide29 l.jpg

Step 4:

Antibiotic susceptibility testing

Not susceptible

Susceptible

Bacterial

lawn

Growth

No growth

Antibiotic disk

29


Dna structure l.jpg
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).


Molecular differentiation l.jpg
Molecular differentiation

  • Genomics

  • Gene characterization

    • Sequencing

    • PCR (Polymerase chain reaction )

    • Specific part of a gene

    • 16SrRNA

    • Restriction digests

  • Hybridization


Genotypic typing methods l.jpg

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 l.jpg

PFGE

MRSA typed with PFGE & MLST

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


Slide35 l.jpg


Rapid diagnosis without culture l.jpg
Rapid diagnosis without culture proteins

  • WHEN AND WHY?

    • grow poorly

    • can not be cultured

    • Need speedy results


Bacterial dna sequences amplified directly from human body fluids l.jpg
Bacterial DNA sequences amplified directly from human body fluids

  • Polymerase chain reaction (PCR)

  • Great success in rapid diagnosis

  • of tuberculosis.


Serologic identification l.jpg
Serologic identification fluids

  • antibody response to the infecting agent

  • several weeks after an infection has

  • occurred


Diagnostic methods time line l.jpg
Diagnostic methods time line fluids

Prof. Matthias Niedrig, RKI


Conclusion part2 choice of typing method l.jpg
Conclusion part2: fluidsChoice of typing method

  • Pathogen

  • Reproducibility

  • Discriminatory power

  • Exchangeability of data!

  • Study question

    • Local/global and short/long term epidemiology

  • Availability and resources

?



ad