QC Microbiology Training Theoritical Content Complete Part 1 - 3

Introduction to Quality Control
Microbiology
in Pharmaceutical and Food Industries
Mohamed Abo-Elgheit
BSc. Microbiology and Chemistry,
TQM Diploma AUC,
MBA AASTMT
mhmd.aboelgheit@gmail.com
Learning Objectives
1. To understand the role of Quality Control Microbiology Lab in the
pharmaceutical and the food industries.
2. To get an overview on The Management System of a Quality

Control Microbiology Lab.
3. To be familiar with microbiological tests and processes.
4. To get to know career path and qualifications of the QC

microbiologist.
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This Training Course Will help you…
1. Be ready for an interview as a fresh graduate for the QC
microbiologist job.
2. Easily understand and grasp further topics on the main subject of

the course.
3. Deepen your understanding of GMP, GLP and Quality in relation

to Microbiological Analysis.
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Course Content
• PART 1 QC Microbiology Lab in Food and Pharma
• PART 2 Activities in Microbiology Lab
• PART 3 To be a QC Microbiologist
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PART 1
Quality Control Microbiology Lab
I. What is Microbiology?
II. What is Microbiological QC? Role? Scope?
III. QC Microbiology Lab Design, Equipment and System
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What is Microbiology?
• Microbiology is the study of microscopic
organisms
• The term microbiology was coined by Louis

Pasteur.
• Microbiology emerged as a science since the

invention of powerful lenses and microscopes.
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Branches of Microbiology
• Microbiology is the study of microscopic

microorganisms:
• Bacteriology (the study of bacteria)
• Mycology (the study of fungi)
• Phycology (the study of algae)
• Virology (the study of viruses)
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Microbiology in the Tree of Life
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Bacteria
• Bacteria are prokaryotic

single cell organisms
• Prokaryote == lack
nucleus, no nuclear
membrane around the
chromosomal DNA.
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Gram Stain and Cell Wall
Bacteria are 2 groups:
• Gram +ve Bacteria:
• High peptidoglycan (polysachharide) in
cell wall
• Retain the stain
• Gram –ve Bacteria:
• Low peptidoglycan
• High lipopolysaccharide in cell wall
• Don’t retain the stain
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Bacteria: Gram Stain and Cell Wall
Staphylococcus auresus
E. coli
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Bacteria: Aerobic vs. Anaerobic
• Aerobic bacteria utilize oxygen to make energy.
• Anaerobic bacteria don’t require oxygen to make their

energy so they can survive without oxgen.
• Some anaerobic bacteria cannot survive in presence of

oxygen, also called “obligate anaerobic bacteria”
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Fungi
• Fungi are a group of eukaryotic living organisms that
include, but not limited to, yeasts and molds.
• Eukaryote == has a true nucleus
• Yeasts: single cell eukaryotic organisms
• Molds: multicellular filamentous eukaryotic organism.
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Fungi: yeast and molds
Candidia albicans
Rhizopus sp.
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Normal Flora (Human Microbiome)
Staphlyococcus aureus
• Skin
• Upper Respiratory Tract
Escherichia coli
• Intestine
Lactobacillus spp.
• Vaginal Tract
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PART 1
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What is Quality?
• Quality refers to the degree to which a set of
characteristics of a product (or service) fulfils requirement
(ISO 9000:2015)
• Quality is the totality of features and characteristics of a
product or a service that bear on its ability to satisfy stated
or implied needs (American Society of Quality)
• Quality is:
• Fitness for use
• Meeting (or exceeding) customer expectation
• Conformance to requirements / Standards/ Specifications
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What is Quality Control?
• With many products that a person uses or consumes a
Quality Standard/ Specs must be met for it to be
considered safe for the market.
• Quality Control is testing a sample of the product against
specifications, to ensure conformity:
• CONFORM = PASS = Meeting specification
• NONCONFORM = FAIL = Not meeting specification
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Microbiological Quality Control Scope
Allowing the microbiologists monitor and control microbial
content to ensure manufacturing of safe product:
1. Testing the product against microbiological
specifications
• Microbiological Analysis Tests
2. Studying the microorganisms associating with
manufacturing
• Environmental Monitoring and control
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Manufacturing flow chart and role of
Microbiological QC
Warehouse
RM Sampling RM Testing
Raw Material • EM QC Fail
(QC) (QC)
Manufacturing Dispensing
Finished Reject
• EM • EM QC PASS
Goods
FG Sampling FG Testing
QC PASS Release
(QC) (QC)
Reject QC Fail
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Microbiological QC scope
• Microbiological QC is concerned with:
• Sampling & Testing (RM, intermediate, FG)
• Release/ Reject (RM, FG)
• Environmental Monitoring (Dispensing, Manufacturing)
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PART 1
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Good Manufacturing Practices (GMP)
• Good Manufacturing Practices (GMP) are a set of practices
which ensures that the products are consistently produced
and controlled according to the quality standards (WHO).
• GMP should be integrated into all steps of production.
• Areas where GMP impacts: facilities, equipment,

production process, etc.
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Good Laboratory Practices (GLP)
• Good Laboratory Practices (GLP) are a set of practices which
ensures reliability and reproducibility in the lab.
• Reliability  to how extent the results are trustworthy
• Reproducibility  the ability to get the same results when some

factors changes e.g. analyst change, equipment change, etc.
• Reliability + Reproducibility = = Quality of data / results
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Good Laboratory Practices (GLP) Pillars
(Not inclusive)
1. Lab Staff
2. Lab Design and Environment
3. Lab Equipment
4. Documentation System
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Lab Staff (Human Resources)
• The primary contributor to ensuring GLP.
• Qualifications: certificates and experiences
• Training:
• On-job
• Ongoing, regular.
• Microbiological skills:
• Colony counting
• Plate pouring
• Media Preparation
• Aseptic Technique
• Etc…
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Aseptic Technique
• Bacteria are everywhere. It is important to take measures to
avoid contaminating your work with undesired bacteria.
• Aseptic Technique is a technique used by microbiologists
when handling microbial cultures
Disinfecting of working areas, and hand sanitation
Use of flames to kill bacteria that may enter vessels
openings
Working Under Biosafety Cabinet
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Microbiology Lab Design and Environment
• Separation of Microbiology lab from the production area. WHY??
• Segregation of clean and dirty activities. WHY??
• Dedicated spaces for samples, media, reference
microorganisms.
• Disinfection and sterilization can be effectively done
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Microbiology Lab Design
Microbiology
lab
Clean Areas Live Culture Areas
Washing Media
Sterilization Testing Growth Promotion
Preparation
Areas
MLT area Strain maintenance
Sterility Area Microbial Identification
PCR Area Decontamination Area

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Microbiology lab Equipment
(Not Comprehensive)
Generic Equipment Specific Equipment
Glassware Autoclave
Weighing balance Laminar Air Flow
pH meter Safety Cabinet
Filtration System Incubator
Oven Sample Homogenizer
Water Bath Microbial Identification System
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Autoclave (steam sterilization)
Steam
Sterilization
• Media
• Glassware
• Gowns
Decontamination
• Incubated
Cultures
• Contaminated
items
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Autoclave: mechanism
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Laminar Air Flow (LAF)
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Laminar Air Flow: air direction
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Microbiological Incubators
Bench Incubator Walk-in Incubator
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Lab Equipment: Calibration
• Measuring equipment used in
analysis should be calibrated
before using and at intervals.
• Calibration:
• Adjusting or standardizing your
equipment so it can give precise
and accurate measurements.
• It involves comparing your
equipment reading with another
calibrated equipment
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Lab Equipment: Performance Verification
• Additionally, equipment performing specific activities (e.g.
incubator), should be verified for its performance before
start use and at intervals.
• Performance Verification:
• A set of tests, inspections and assessments ensuring that an
equipment performs at intended by the manufacturer when
operating at your lab.
• To verify the performance of an incubator, you should study its
thermal distribution to ensure acceptable performance.
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Documentation System
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Procedure and Work Instructions
• Procedures are standard documentations of the critical
processes in the lab e.g. operation of autoclave, Media
Preparation.
• Procedure describes:
• The purpose of the process
• Responsibilities of each personnel involved in the process
• Detailing of the process activities.
• Procedure should be approved by an authorized personnel
(e.g. Lab Manager) prior being effective.
• Work Instructions/ Practices are just a simpler type of procedure.
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Records
• Records are documents generated by
applying procedures/ work instruction of
the processes.
• Records provide objective evidence on all
tasks done in lab e.g.:
• Media Preparation records
• Test performance and result records
• Equipment monitoring, calibration and
verification records
• Lab staff training records
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PART 2
Micro Lab Main Activities and Tests
I. Microbial Identification
II. Media Preparation and Control
III. Microbiological Testing Techniques
IV. Environmental Monitoring

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Microbial Identification
• Microbial identification is determination to which group the
microorganism under study belongs.
• Practically, it is a microbial characterization of an organism
through a pre-chosen tests appropriate for the purpose of
identification:
• Macroscopic morphology
• Staining and microscopic morphology
• Biochemical tests
• Genotypic characterization
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Macroscopic Identification
(Colony Morphology)
• Nine obviously different colonies!
• Differentiation Factors:
• Whole shape (circle, oval,
irregular)
• Size (diameter)
• Edge (regular, irregular)
• Color and pigments
• Opacity
• Elevation
• Etc.
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(Colony Morphology)
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Bacterial Colonies Morphology
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Why Macroscopic Morphology
1. Preliminary identification of
number and nature of
species
2. Expert microbiologist can
sometimes predicts ( but not
ensures) the type of a
bacterium from its colony
morphology.
3. Raise the need to purification
(colonies 4 X 3)
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Pure Culture techniques
• Pure culture is a microbial culture belonging to a single species/
strain.
• It is unlikely to find pure cultures of microorganisms in nature,
they are always mixed.
• Obtaining a single species culture from a mixed culture is called
Purification or Pure Culture Technique.
• Purification is essential before Identification
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Streak Plate Method
• Streaking is the beginning of learning Alphabetical
Microbiology
• The most common method for isolation and purification of
bacteria.
• It involves progressive dilution of an inoculum of bacteria
over the surface of Agar Media and then Incubation.
• Result  Some of the grown colonies will appear separated
from each other so they are now isolated.
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Pure Culture Obtained
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Why Purification?
• Accurate colony morphology:
• Some bacteria show different
colony morphologies based on
nature of surrounding species.
• Accurate cell morphology:

• Avoid mixed staining
• Fresh Culture
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Microscopic Morphology
• This include the microscopic appearance of a stained
preparation of the bacterial cell (staining techniques)
• Gram Stain
• Bacterial Spore Stain
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Gram Stain
• The primary staining technique used to differentiate
bacteria.
• Staining Reaction
• Cell shape
• Cell Size
• Cell arrangement
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Gram Stain: cell shape and arrangement
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Gram Stain Procedure
1. Applying a primary stain (crystal violet).
2. Adding a mordant (Gram's iodine).
3. Rapid decolorization with ethanol, acetone or a mixture

of both.
4. Counterstaining with safranin.
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Spore Staining
• Formation of spores is a very important survival
characteristics of some Gram Positive Rods e.g. Bacillus
and Clostridium.
• Spores are very resistant to normal sopre techniques (e.g.
Gram Stain) so it won’t retain stains.
• Spore staining using Malachite Green Dye and Safranin
Dye Counterstain is very common and useful technique in
identifying the presence of absence of spores.
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Spore Stain Procedure
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Media Preparation Broth Media
Dehydrated,
powdered media
Agar Media
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Media Preparation
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Media Preparation Generic Procedure
Adding
Weighing Dissolving
water
Storage Dispensing Sterilization
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Types of Media based on purpose:
1) General Purpose Media/ Growth Media:
Physical State Media Name Uses
Nutrient Broth NB
Enrichment, Sterility
Broth Tryptone Soy Broth TSB
Test
Enrichment, Transport
Nutrient Agar NA
Agar (purification),
Tryptone Soy Agar TSA
Enumeration
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2) Selective Media:
• Are used for the growth of only selected group of
microorganisms.
• For example:
• an antibiotic can be added to a medium components to make it
selective only to types resistant to this antibiotic.
• YM (Yeast an mold) medium has a low pH (acidic, inhibiting the
growth of bacteria.
• EMB contain methylene Blue that are toxic to gram positive
bacteria.
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3) Differential Media:
• Are used to visually distinguish
the growth of a specific
microorganism from another
growing types on the same
plate.
• MacConkey media is differential
for lactose fermenting bacteria
from non-lactose fermenting
bacteria
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Growth Promotion Test
(Culture Media QC Test)
• Growth promotion test is a QC test of prepared media to
ensure the media are able to enhance the microbial
growth as intended.
Inoculation Growth 50-
Incubation Inspection
(> 100 CFU) 200%
PASS
Growth
<50% or
>200%
FAIL
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McFarland Standard Values
Approximate Cell
McFarland Standard 1% BaCl2(ml) Count Density (x10^8
cells)
0.5 0.05 1.5 x 10^8
1.0 0.1 3.0 x 10^8
2.0 0.2 6.0 x 10^8
3.0 0.3 9.0 x 10^8
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Reference microorganism in GPT for TSA
Incubation period and

Reference Microorganism
conditions
Staphylococcus aureus ATCC 6538 30°–35° ≤3 days
Pseudomonas aeruginosa such
30°–35° ≤3 days
ATCC 9027
Bacillus subtilis ATCC 6633 30°–35° ≤3 days
Candida albicans ATCC 10231 30°–35° ≤5 days
Aspergillus brasiliensis ATCC 16404 30°–35° ≤5 days

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Microbiological Tests
• Microbial Limit Test

• Enumeration tests: TAMC, TYMC
• Detection Tests
• Sterility Test
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Microbial Limit Test
MLT
Microbial Enumeration Test Detection Test
Membrane Filtration
Determination for
presence of
absence of
objectionable
Plate Count Method microorganism
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Microbial Enumeration Test (bioburden)
• In this test, a general solid (agar) media is used to enhance

the growth of all microorganisms in a sample and hence
these microorganisms can be enumerated.
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Microbial Enumeration Test:
Membrane Filtration
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Microbial Enumeration Test:
Plate Count Methods
Sample
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Calculations
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Membrane Filtration VS Pour plate: think
microbiologically!
Membrane Filtration Pour Plate
Sample size Whole sample 0.1 – 1.0 mL
Accuracy Higher Lower
Sample form Soluble samples Soluble or insoluble

Samples with low Samples with high
bioburden bioburden
Tools Membrane filtration MFS is not required
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Microbial Enumeration Test: Media
Purpose Media
Total Aerobic Microbial TSA (tryptic soy Agar)

Count (TAMC)
PCA (Plate Count Agar)
Total Yeast and Mold SDA (Sabouraud Dextrose Agar)

Count (TYMC)
DG18 (Dichloran Gylcerol Agar)
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Tests for Detection of pathogen
• In such test, a solid media is used to enhance the growth of
a specified microorganism
• Test for E. coli
• Test for Salmonella spp.
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Detection simple procedure
1. Sample preparation
2. Enrichment in broth media
3. Selection in selective broth media
4. Streaking on Agar Media
5. Identification of grown colonies
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Example: Tests for E. coli
1 10 ml 2 3 4 5
(= 1 g Incubatio Incubatio
Streak
sampl n 1 ml n
e)
6
30 – 42 –
35ᴼC 44ᴼC
18- 24 24- 48 Incubatio 30 – 35ᴼC
hrs. hrs. n 18- 24 hrs.
90 ml
diluent + 10 (Mac.Brot
TSB 7
gram h)
sample
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Media for tests for detection
Test Media used
Escherichia coli MacConkey Agar (MCA) 42-44 ⁰C
MacConkey Broth (MCB) 30-35⁰C
Salmonella spp. Rappaport (RVB) 30-35⁰C

XLD Agar
Clostridia spp. Reinforced Medium for Clostridia 30-35⁰C

Columbia Agar 30-35⁰C
Candida ablicans Sabouraud Dextrose Broth (SDB) 30-35⁰C

Sabouraud Dextrose Agar (SDA) 30-35⁰C
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MLT Acceptance Criteria (USP, ch. 1111)
Dosage form TAMC TYMC Specified microorganism
Nonaqueous oral
103 102 Absence of E. coli
use
Aqueous oral use 102 101 Absence of E. coli
Rectal Use 103 102 NA
Absence of S. aureus
Cutaneous use 102 101
Absence of P. aeruginosa
Absence of S. aureus
Vaginal use 102 101 Absence of P. aeruginosa
Absence of C. albicans
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(3.2) Sterility Test
• Sterility test: is a qualitative test for presence or absence

of microorganisms. (sterile == no microbial presence
detected)
• In this test: a broth (liquid) media is used to enhance the
growth of any microorganism in the sample and hence
these microorganisms can be detected as a turbidity in
the culture media.
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Sterility Test
• Aseptic technique is very critical
to this test, as a single bacterial
cell growth fails the test.
• The Test is done in Class A with
background Class B.
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Sterility Test: media
Incubation
Media Used Targeted microorganisms
Conditions
Tryptic Soy Broth Aerobic bacteria and

20 – 25 ⁰C
(TSB) fungi
Fluid Thiglycolate Anaerobic bacteria

30 -35 ⁰C
Medium (mainly)
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Sterility Test
Filter the Incubate

sample for 14 Inspect
solution days
Clear Turbidity
PASS FAIL
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Sterility Test: closed system
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Viable Environmental Monitoring
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• Pharmaceutical and food manufacturing must be operated in controlled
areas.
• Controlled Areas  there are measures that control the quality of air and
environment in terms of:
1. Temperature and humidity (environmental conditions)
2. Air Particles
• Nonviable particles e.g. dust and fine particles (0.5 – 5 µm)
• Viable particles e.g. bacteria and fungi.
3. Cleanliness of the facilities (machines, buildings, etc)

4. Hygiene of operators
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• Viable EM role is:
• Monitoring the number of microorganisms in the facilities
• Monitoring the types of microorganisms in the facilities
• This typically means monitoring microorganisms:
• In the air
• On the surfaces of the machines and facilities
• Within the personnel hands and gowns
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Air
samples
EM Program
Personn
Surface
el
samples
samples
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Purpose of Viable EM:
• The goal of EM Program is:
• To ensure the cleanliness of the manufacturing facilities and area. All
manufacturing facilities should undergo regular cleaning and / or
sanitation program. EM ensure cleanliness effectiveness.
• To determine whether any pathogens (e.g. listeria, salmonella) are
living in the facilities and to respond accordingly if any positive results is
found
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EM vs. Testing products
• It is important to recognize that an acceptable EM results does
NOT mean that your product (e.g. food or medicine) is safe,
rather it verifies that your cleaning process is effective.
• On the other hand, unacceptable EM results does mean that

your product may be NOT safe, even it pass specifications
testing.
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Air samples
• The goal of air samples is to determine the microbiological
quality of air where food or medicine is produced through:
• Counting the numbers of microorganisms to ensure they are in
acceptable level that doesn’t indicate contamination.
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Air Sampling
Techniques
1. Settle Plate Samples:

• Settle Agar plates left
open for a specific
period in specific
locations.
• Also referred as PASSIVE
AIR SAMPLING
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Air Sampling
Techniques
2. Active Air Samples:

• Using a pump to
collect a specific
amount of air.
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Air Samples Culture
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Surface Samples
• The goal of surface sample is to challenge the cleanliness
of machines and facilities before and during manufacturing
processes.
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Surface Samples
• Examples of sampled surfaces:
1. Machine Internal Surfaces (sampling points, pipelines, cutting

blades, conveyers. (High Risk)
2. Machine External surfaces (external walls, buttons and control

boards that operators contact with) (Moderate Risk)
3. Walls and floors (Low Risk)
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Surface Sampling Technique
Surface Swab:
• Using a cotton swab to collect the microbes from a surface.
• To get a swab representative sample:

• 10 * 10 cm2, perpendicular directions
• Choose a hard-to-clean Area
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Swab Representative Sample
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Surface Sampling Technique
• The swab is then:
1. Streaked directly over an agar
plate (if the expected count is
relatively low)
2. Immersed in test tube containing
10 ml sterile solution to dispense
the microbes in order to make
serial dilution and plating (if the
expected count is relatively high)
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Personnel EM Sampling
1. Finger Plates:
• Agar plates contacting the
glove fingers of the personnel
hand.
2. Gown Swab
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PART 3: To be a QC Microbiologist
I. To Be a QC Microbiologist
II. QC Microbiologist Career Path
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QC Microbiologist
• QC Microbiologist is responsible for:
1. Microbiological Sampling
• raw material, water, intermediate and finished product samples.
2. Microbiological Testing
3. Environmental Monitoring
4. Reporting all the above
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To be a QC Microbiologist
• Qualifications:
• BSc. in Microbiology or Biology or any Biology relevant field.
• Some companies prefer specific specialities
• Pharma companies may prefer Pharma and science graduates
rather than others
• Biotechnology-based may prefer Biotechnology graduates rather
than others.
• Food companies may prefer agriculture graduates rather than
others.
• This is a case-by-case issue. Just search hard for your suitable
opportunity
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• Training and Certifications:
1. QC Microbiology Courses
• FOOD: ISO Food Microbiology Standards
• PHARMA: Pharmacopias and WHO guidelines
2. Quality Management Systems
• Quality Documentation System
• ISO 9001 and Internal Audit
• Quality Tools
• Etc.
3. Statistical Quality Control
• Control Charts
• Six Sigma
• Etc.
Mohamed Aboelgheit
10/21/2023 113
• Knowledge, skills, and abilities:
• Love to work with microbes. Some people
have microphobia!
• Detail-oriented:
• Aseptic technique, contamination sources,
frequent sanitation of hands.
• Do NOT worry about handling skills. It will get
sharpened over time
• Logical thinking:
• Problem solving
• Root cause investigation of contamination
• Time Management
Mohamed Aboelgheit
10/21/2023 114
QC Microbiologist Career Path
• Microbiologist
Entry Level • Biotechnologist
• Senior Microbiologist
Mid-Level • Team Leader
• Lab Supervisor
Experienced
Level • Lab Section Head
• Lab Manager
Managerial
Level • Quality Manager
Mohamed Aboelgheit
10/21/2023 115
Mohamed Aboelgheit
10/21/2023 116

QC Microbiology Training Theoritical Content Complete Part 1 - 3

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QC Microbiology Training Theoritical Content Complete Part 1 - 3

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Introduction to Quality Control

2. To get an overview on The Management System of a Quality

3. To be familiar with microbiological tests and processes.

4. To get to know career path and qualifications of the QC

2. Easily understand and grasp further topics on the main subject of

3. Deepen your understanding of GMP, GLP and Quality in relation

• PART 2 Activities in Microbiology Lab

II. What is Microbiological QC? Role? Scope?

III. QC Microbiology Lab Design, Equipment and System

• The term microbiology was coined by Louis

• Microbiology emerged as a science since the

• Microbiology is the study of microscopic

• Bacteria are prokaryotic

• Anaerobic bacteria don’t require oxygen to make their

• Some anaerobic bacteria cannot survive in presence of

• Eukaryote == has a true nucleus

• Yeasts: single cell eukaryotic organisms

• Molds: multicellular filamentous eukaryotic organism.

II. What is Microbiological QC? Role? Scope?

III. QC Microbiology Lab Design, Equipment and System

• Microbiological QC is concerned with:

• Sampling & Testing (RM, intermediate, FG)

• Release/ Reject (RM, FG)

• Environmental Monitoring (Dispensing, Manufacturing)

II. What is Microbiological QC? Role? Scope?

III. QC Microbiology Lab Design, Equipment and System

• GMP should be integrated into all steps of production.

• Areas where GMP impacts: facilities, equipment,

• Reliability  to how extent the results are trustworthy

• Reproducibility  the ability to get the same results when some

• Reliability + Reproducibility = = Quality of data / results

• Separation of Microbiology lab from the production area. WHY??

• Segregation of clean and dirty activities. WHY??

• Dedicated spaces for samples, media, reference

• Disinfection and sterilization can be effectively done

Clean Areas Live Culture Areas

MLT area Strain maintenance

Sterility Area Microbial Identification

PCR Area Decontamination Area

Weighing balance Laminar Air Flow

pH meter Safety Cabinet

Filtration System Incubator

Oven Sample Homogenizer

Water Bath Microbial Identification System

Bench Incubator Walk-in Incubator

II. Media Preparation and Control

III. Microbiological Testing Techniques

IV. Environmental Monitoring

• Accurate cell morphology:

2. Adding a mordant (Gram's iodine).

3. Rapid decolorization with ethanol, acetone or a mixture

4. Counterstaining with safranin.

Storage Dispensing Sterilization

Physical State Media Name Uses

0.5 0.05 1.5 x 10^8

1.0 0.1 3.0 x 10^8

2.0 0.2 6.0 x 10^8

3.0 0.3 9.0 x 10^8

Incubation period and

Candida albicans ATCC 10231 30°–35° ≤5 days

Aspergillus brasiliensis ATCC 16404 30°–35° ≤5 days

• Microbial Limit Test

Microbial Enumeration Test Detection Test

• In this test, a general solid (agar) media is used to enhance