Overview Microbiology

7/30/2019 Overview Microbiology

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Overview of microbiology

Binish Arif

Resident Microbiology

Aga Khan University Hospital


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Game plan

Scope of Microbiology Extent of the microbial world

Microbial diversity

History of Microbiology Diagnosisofinfection

Techniques Microscopy and Staining

Pure culture methods Quantitative methods

Result reporting


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What is microbiology?

the study of microorganisms

organisms too small to be seen with the

naked eye

except in large groups


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The universal tree of life


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The universal tree of life


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Microbial world

Viruses

Bacteria (Eubacteria and Archaea) Fungi (Yeasts and Molds)

Protozoa


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Benefits

Maintain balance of environment

(microbial ecology)

Basis of food chain Nitrogen fixation

Photosynthesis

Digestion, synthesis of vitamins

Manufacture of food and drink


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Benefits

Genetic engineering

Synthesis of chemical products

Recycling sewage Bioremediation: use microbes to remove

toxins (oil spills)

Use of microbes to control crop pests Normal microbiota


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Harmful effects

Cause disease

Food spoilage


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History of microbiology


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Pioneers of microbiology

Robert Hooke, (1665) Proposed the Cell Theory

Observed cork with crude microscope

All living things are composed of cells

Antoni van Leeuwenhoek, (1673) First observed live microorganisms (animalcules)

Schleiden and Schwann, Formulated Cell Theory: cells are the fundamental

units of life and carry out all the basic functions ofliving things

Pasteur, FR and Tyndall, (1861) Finally disproved S.G.


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Louis Pasteur (1822-1895), Chemist Fermentation (1857)

Pasteurization: heat liquid enough to kill spoilage

bacteria (1864) Vaccine development rabies

Proposed the germ theory of disease

Proposed aseptic techniques (prevent contamination

by unwanted microbes)

Director of Pasteur Institute, Paris (1894)


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Joseph Lister, (1867)

Used phenol (carbolic acid) to disinfect wounds

First aseptic technique in surgery

Robert Koch, (1876) Postulates Germ theory (1876)

Identified microbes that caused anthrax (1876),

tuberculosis (1882) and cholera (1883)

Developed microbiological media & streak plates for

pure culture (1881)


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Branches of microbiology

Bacteriology: study of bacteria

Mycology: study of fungi

Immunology: study of immunity

Edward Jenner: developed vaccination (1798)

Metchnikoff: discovered phagocytes (1884)

Paul Ehrlich : theory of immunity (1890)

Virology: study of viruses Beijerinck : discovered intracellular reproduction of

TMV; coined the term virus (1899)


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Microbiology lab

pulling in all directions

Health care Providers

Routine Service

Keeping up with changing technology &innovation

Other Clinical Labs: Reference work

Administration (Budget, finance, QA &QQC, Accreditation, Licensing, HR,

Institutional committees, etc)

Support to other partners/clients:

Infection control

Health Units

Academic institutions, Pharmacy,, etc

Clinical MicrobiologyLab


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Clinical Microbiology Labs

Routine clinical microbiology testing Licensed test menu

Reference microbiology (discipline speciality centre for excellence)

Quality assurance including accreditation

Laboratory surveillance Infectious Diseases, Epidemiology

Support to Infection Control program

Emergency outbreak preparedness & management Teaching & training

Research and development


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Parasitology: study of protozoa and parasitic worms

Chemotherapy Treatment of disease by using chemicals

Antibiotics produced naturally

Synthetic drugs


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Chemotherapy Alexander Fleming, (1928) discovered penicillin

Selman Waksman, (1944) discovered streptomycin

Problems Toxicity of drugs => Selective toxicity

Resistance of bacteria to drugs


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Recombinant DNA Technology Recombinant DNA

Genetic engineering/biotechnology

Microbial genetics mechanism by which microbesinherit genes

Molecular biology structure and function

(expression) of genes

Molecular epidemiology/diagnostics


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Role of Molecular diagnostic in

Microbiology

the paradigm shift

Traditional method have limited capability of providing

timely information to physicians

Advantages of molecular infectious disease testing over

conventional culture methods

Rapid test results (15 hr),

Relatively small sample size

High clinical sensitivity and specificity in the presence

of antimicrobial therapy Rapid identification of fastidious organisms

Direct detection of resistant strains


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Biotechnology GMOs/GEMs for industrial, pharmaceutical and

agricultural applications

Improvements of agriculture (plants and animals)

Gene therapy: inserting a missing gene or replacing a

defective one in human cells


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Diagnosis of infection


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The triad of infectious disease

1. The affected host

2. Infectious agent

3. The environment


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The diagnostic cycle

Patient consults physician

with signs/symptoms

of infectious disease

Preliminary reports may or

may not be issued.

Final culture report is

prepared and sent to the

physicians office, clinic or

hospital

Subcultures are examined,

and results of identification

systems are examined.

Physician interprets reports

and institutes appropriatetherapy

After incubation, cultures

are examined. Definitiveidentification are set up.

Specimens are processed.

Culture media are selected,

inoculated and incubated.

Presumptive reports may or

may not be issued.

Physician examines patient

& makes a tentative clinical

diagnosis

Appropriate specimen(s)

is/are collected for culture.

All containers must be

properly labelled.

Written orders are

transcribed to a laboratory

request form. Form and

specimen are transported

to the laboratory

Upon receipt by the

laboratory, data from the

request form is entered into

a computer file or log book.

Analytical

Pre-analytical

Post-analytical

Specimen is directly

examined. Microscopic

mounts, smears, and stains

may or may not be set up.


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Microscopy and staining

Wet mounts

Staining Grams staining (Hans Christian Gram)

Acid fast staining (Ziehl-Neelsen stain)

Fluorescent antigen/antibody stains

Fluorochrome stains for mycobacteria (auramine and

rhodamine)


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http://en.wikipedia.org/wiki/File:Pseudomonas_aeruginosa_Gram.jpg


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Processing specimens

Selection of primary culture media

Determine the temperature and

atmosphere of incubation

Determine which of the isolates recovered

on primary media require further

characterization

Determine whether antimicrobial

susceptibility testing is required


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Quantitative culture methods

Urine specimens, lower respiratory tract

specimens

For urine --- 0.01l or 0.001l caliberated

inoculating loop.

1 colony = 1000 CFU/ml

10 colonies = 104 CFU/ml

100 colonies = 105 CFU/ml

I t t ti f lt


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Interpretation of cultures Characteristics of colonies

I t t ti f lt
http://upload.wikimedia.org/wikipedia/commons/8/8d/Bacterial_colony_morphology.png


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Interpretation of cultures

Reactions in agar media

Haemolysis on blood agar: Pigment production:

Changes in differential media:


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Result reporting

ASAP the results are available, without

any error

Electronic

Telephone

Paper


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Environmental factors and the spread of

communicable diseases in Pakistan

Environmental factors that influence:

Waterborne diseases From traditional to new ...Giardia to

Naegleria

Food (Processed & Imported)

Poultry industry ...Newcastle diseases and avian influenza

viruses that has adversely affected the investment and

growth rate of poultry industry in Pakistan

Climate Flooding after heavy rains result in sewage overflow

and widespread water contamination


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Environmental testing

Challenges & opportunities

Govt labs limited scope

Water, Food & Environmental testing

Fewer labs do: Mould & spore testing

In door - Air quality monitoring

Monitoring sterilization & disinfection outcomes

Water testing for bottled water Food testing (for imported foods)


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Scope of Microbiology

Microbial diversity

History of Microbiology

Diagnosisofinfection Techniques

Microscopy and Staining

Pure culture methods

Quantitative methods

Result reporting


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Microbiology 2015 Moving beyond PCR

Matrix-assisted laser desorption ionizationtime

of flight (MALDI-TOF)

routinely identifying colonies of bacteria

isolated from culture media or organismsrecovered from blood culture.

could be used as parallel and complementary

devices rather than as independent systems

Assist in unmasking multiple resistance

factors and allowing targeted therapy


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Future Staffing

Staffing mix:

Tech group: Will need fewer speciality trained

and more generalist.

Lab supervisor/directors will be skilled more inmolecular methods and less in classical

microbiology.

There will be more specialty-trained pathologists

and fewer PhD microbiologists. Those who will be more financially savvy, basing

administrative decisions on cost-effectiveness and

evidence-based medicine Speculations on Microbiology Lab of the future: CID. Vol 35. Ellen Jo Baron


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Future skills in interpreting complexdiagnostic test results

Skills will be required as we transition from classical,

culture-based methods to automated molecular

assays

Knowledge of human microbiome and theinteractions of difficult-to-culture organisms and

microbial flora and disease real time antibiogram!

Knowledge in the fields of genomics and proteomics

Learning of multiplexed, specimen-specificmolecular microbiology assays available for point-of-

care testing


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Communication

Future : Digital world

Use of real-time digital graphics image

capture to send slide images to an

expert at a distant site for

interpretation.

Same image can be easily included inthe laboratory report, which can be

instantly accessible at any location by

use of a handheld device with wireless

internet connectivity. Advances in IT will allow immediate

and global access to laboratory results

for all physicians treating a patient.


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Opportunities at AKUH-K

Facilitating R&D: Wet lab rental

Clinical trails testing for physicians & industry

Diagnostic instrumenttesting for validation for industry

Reference Centre for Excellence for SE Asia

Supplier of proficiency material for S.E Asia Environmental testing for Industry using molecular diagnostics

Infection Prevention & Control antimicrobial stewardship)

Training centre for lab personnel:

Molecular diagnostics

Lab Administration & Management

Infection Prevention & Control (Distance ED)

Others


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Thank you

Overview Microbiology

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