Laboratory Manual Mic341 (Latest)
Laboratory Manual Mic341 (Latest)
MEDICAL MICROBIOLOGY
MIC341
EXPERIMENT 1: ANTIMICROBIAL SUSCEPTIBILITY TESTING
(A) Test a clinically isolated for susceptibility to antimicrobial using the disk
diffusion assay and the MIC assay.
(B) Read and interpret antimicrobial test and report appropriately.
Introduction:
The final step in processing a clinical specimen is to determine what antibiotic can kill
the infecting organism. This information is necessary for the doctor to recommend the correct
drug to be given. Antimicrobial susceptibility testing (AST) must be conducted using pure
cultures only, or the results must be invalid. There are two ways to do an AST : the Bauer-
Kirby disk diffusion assay or the classical Minimum Inhibitory Concentration (MIC) assay.
The MIC test provides more information regarding the concentration of antibiotic required,
but is more difficult to perform. The disk diffusion test is easier to perform but is suitable only
for aerobic bacteria. It is routinely used in clinical labs.
In the disk diffusion assay, bacteria to be tested is spread evenly onto an agar plate. A
disk containing specific amounts of an antibiotic is then placed onto the lawn and incubated
overnight. The inability of the test bacteria to grow around a particular disk (forming an
inhibition zone) indicates susceptibility to that antibiotic. The diameter of the inhibition zone
is measured and compared to a standard chart. In the MIC test, a series of twofold dilutions of
antibiotic is prepared. The test organism is then inoculated into each concentration, and
growth is checked by observing for turbidity. The highest concentration which no growth is
observed is taken as the MIC.
Material :
Each group will test all the 4 bacteria for their antibiotic susceptibility. Each member of the
group will work with one bacteria.
This is a test which uses antibiotic-impregnated paper disk to test whether a particular
bacteria are susceptible to specific antibiotic. A known quantity of bacteria is grown on agar
plate in the presence of a thin filter paper disc containing relevant antibiotics.
1. Dip a sterile cotton swab into the inoculum. Squeeze the cotton swab against the inner
wall of the bottle to remove excess fluid.
2. Spread the cotton swab on the Meller Hinton agar plate and swab evenly.
3. Repeat twice, turning the plate 60 ̊ at each swab (see diagram).
4. Replace the lid of the petri dish and hold at room temperature for at least 3 minutes to
allow surface moisture to be absorbed.
5. In about 15 minutes, place the antibiotic discs onto the surface and press firmly using a
pair of forceps. Arrange the discs so that their centers are at least 24 mm apart from
each other and 10 mm away from the edge of the agar. Alternatively, an automatic
disc dispenser can be used.
6. Within 15 minutes, invert the plates and place in incubator 37 ̊ C. At least for 16 hours.
(D)Reading results
Observations:
Disk assay: Collect all data from your group and fill in the table below:
Introduction:
The skin supports a large number of microorganisms which normally grow without
harming the host. This is known as the normal flora. In fact, the presence of the normal flora
helps protects the skin from infection by competitions of space and nutrients. Some of these
organisms, however, can attack the human body in immunocompromised hosts.
An important pathogen that is always found on the skin Staphylococcus aureus. It will
cause an infection in the events when the immune system is weakened, when there is injury
and when a medical device is inserted. S. aureus and another staphylococci, s. epidermis, are
major causes of nosocomial or hospital-acquired infections (infections acquired during a stay
in the hospital). The emergence of Methicilin-resistance S.aureus, or MRSA, is a major
medical concern since this bacteria is resistant to almost all available antibiotics.
The major groups of organism found in skin and wound infection include gram
positive cocci, Pseudomonas and some enterobactericeae. Clostridium may infect deep
anaerobic wounds. Blood agar is usually employed as a general culture medium while
MacConkey Agar is used to recover Gram negative bacteria. If S.aureus is suspected, a
Mannitol Salt Agar plate is also inoculated.
In this practical, we will perform a skin swab and see the diversity of organisms that is
present. We will also culture a pus sample. We will perform some tests for the identification
of S.aureus. You will also learn to prepare blood agar.
Material:
Procedures
1. Remove the 100 ml molten blood agar base from the water bath and cool to touch.
2. Aseptically add 5 ml of the human blood
3. Swirl to mix well, but avoid bubbles
4. Pour into 6 agar plates and allow to solidify.
1. Streak one loopful of the pus sample onto a blood agar plate.
2. Streak one loopful onto an MSA plate.
3. Incubate at 37˚C for at least 18 hours.
A gram stain showing Gram positive cocci will indicate the presence of Staphylocci or
streptococci.
1. Streak half (1/2) of a blood agar with S.aureus. Streak the other half with streptococci
pyogenes. Incubate 37̊C for at 24 hours.
2. Transfer some cells from the middle of S.aureus colony onto a glass slide.
3. Add 3 drops of 3% H2O2. Watch for instant and sustained release of bubbles.
4. Repeats with S. pyogenes.
c. To differentiate between the two most common Staphylococci. S.aureus and S.epdemidis.
Test for fermentation of mannitol-(S.aureus +ve ; S.epidermidis –ve)
5. Streak half (1/2) of MSA plate with S.aureus. Streak the other half with S.epidemidis.
6. Incubate at 37̊C for 24 hours.
Note: If a gram stain indicates Gram positive cocci, Staphylococcus sp. and streptococcus sp.
should be suspected. A catalase test should then be carried out. There are three common
species which are common in infections: S.aureus, S.epdemidis and S.saprophyticus can be
identified by its resistance to the antibiotic novobiocin.
1 Tube of coagulase
Observations:
(B) Skin swabs on BA. Count how many different types of colonies formed. Describe
the morphology of the predominant colonies.
S.aureus S. pyogenes
Hemolysis on BA
Catalase
S.aureus S. epidermidis
Slide coagulase test
Discussion:
Conclusion:
Question:
2. For catalase test, it is not recommended to use cultures from a blood agar plate. Why?
3. In the catalase test, a slow reaction with a few bubbles is not considered positive.
Why?
4. In this practical, what are the functions of the blood agar, MacConkey agar and MSA?
5. You received a pus sample and was asked to check if its contain S.aureus. How will
you do it to obtain results in the shortest time? Draw your flowchart on the blank page
opposites.
EXPERIMENT 3: URINARY TRACT INFECTION
Introduction:
Freshly produced urine is sterile, but as it travels down the urethra, it can pick up
contaminants. The presence of bacteria in urine, thus may or may not indicate an infection.
Urinary tract infection can is usually due to organisms coming in from outside and entering
the urethra, and is more common in female.
Material :
• 4 calibrated loops
• Triple Sugar Iron slants
• SIM medium
• Voges-Proskauer medium
• Simmon’s Citrate medium
• Urea test broth
• MacConkey agar plates
• Eosin Methylene Blue Agar
• 2 urine samples from student- A&B
• Glass slide
• Microscope
• Plastic Conical Tube
• Appendorf tube
Either
Or
1. Observe the urine sample for the transparency, noting its quantity, color, clarity or
cloudiness, odor and etc.
1. Place about 10mL in plastic conical tube labeled with patient's name and cover tube with
tight fitting cover.
2. Place tube in a centrifuge and place a second tube containing an equal amount of water
(with tight fitting cover on) directly opposite tube with urine, to act as counterweight.
4. After centrifuge has stopped, remove the tube and pour off the supernatant, leaving any
sediment in the bottom of the tube.
5. With a plastic pipette, mix the remaining liquid and sediment and remove a few drops of
the mixture. If there is no obvious sediment present, remove a few drops of urine from bottom
of tube.
6. Place one drop of the sediment solution on a glass slide and cover with a cover slip.
7. Using the microscope, examine the sediment using phase contrast or bright light under low
(10x) and high (40x) power, scanning several fields to obtain average numbers of formed
elements.
First streak a straight line down the middle of the agar. Without flaming the loop or taking
any more samples, streak across the line in a zig-zag pattern until the entire plate is
covered.
6. Count the colonies on each plate and multiply by 1000. Report as the number of
colonies/ml.
7. From the MacConkey agar plate inoculated with sample A, pick a representative lactose-
fermentor colony and streak onto half of Eosin Methylene Blue Agar plate.
10. From the MacConkey agar plate inoculated with sample B, pick a representative non-
lactose fermenter colony and repeat steps 7-9.
Various bacteria from the enterobactericeae family are frequently isolated from urinary tract
infection. Although in most cases complete identification is not necessary, it is important to be
able to identify major groups. Nowadays, this is most conveniently achieved by using rapid
kits such as the API system. Nevertheless, the ability to perform an identification scheme is
still required for a microbiologist worth his salt.
You will be provided with 4 cultures on MacConkey Agar. Work in groups of eight; four
pairs. Each pair will run six tests on each bacteria. At the end, compile your results and fill in
the identification table in the Observation section.
5. Add 15 drops of Kovac’s reagent to the SIM medium. The development of a red color
within a few seconds indicate a positive test.
6. Transfer 1 ml of the Voges-Proskaueur medium to a clean test tube. Add 0.6 ml α-
naphtol followed by 0.2 ml of 40% KOH. Shake the tube gently and stand for 15
minutes. The formation of red color indicates a positive test. Read the results within
one hour.
7. Observe the Simmon’s citrate medium. A blue color indicates a positive reaction. If no
blue color is present, check for the growth of the colonies. Presence of colonies also
indicates a positive reaction,. In this case, further incubate another 24 hours and check
again.
8. Check the KCN medium. A turbid medium indicates positive growth.
9. Check the urea broth. Red color indicates a positive reaction.
10. Check the ONPG test. Yellow color indicates a positive reaction.
Checklist: Each pair should have at the end of the practical
6 Biochemical tests
Observations:
Sample A Sample B
TSI reaction
Oxidase Test
Colony on EMBA
E.coli
Citrobacter sp.
Serratia marcescens
Proteus vulgaris
Test Escherichia Citrobacter Salmonella Klebsiella, Yersinia Proteus,
coli Enterobacter, Morganella,
Serratia Providencia
Lysine
decarboxylase
Discussion:
Conclusion:
Question:
Introduction:
Blood is normally a sterile fluid. The presence of bacteria in the blood gives rise to
bacteremia, which may develop into highly fatal septicemia. Consequently, all bacteria that
are detected in the blood are considered pathogenic. Organisms commonly found in the blood
are again part of the normal flora: the Gram +ve cocci, Gram –ve rods, Pseudomonas etc. This
organism may be present at a low level and direct isolation may not give results. Normally, a
blood culture is set up, where a certain amount of blood is collected aseptically and added to a
bottle of medium. This is then incubated for up to one week and checked daily. Upon positive
growth, a subculture is made to an agar plate for isolation and identification.
Various media may be used: Trypticase soy broth, thioglycollate broth and columbin
broth for general isolation, brain, heart infusion broth for fungi and Brucella broth and
Dextrose phosphate broth for Brucella. Usually, an anaerobic broth is also set up. It is also
recommended that a hypertonic broth is set up at the same time to recover cell-wall deficient
strains. This is achieved by using a general purpose broth, e.g. Columbia broth or Brucella
broth with added 10% sucrose.
The appearance of the culture after incubation usually provide clues regarding the type of
organism that is present (see Appendix). Subculture should be done within two days to
recover the organism. General purpose isolation medium such as MacConkey, Blood and
Sabouraud Dextrose agar inoculated. If particular bacteria are suspected, a selective agar may
be employed.
Materials:
Procedure:
1. Aseptically add 5ml of blood to the Thioglycollate broth and Trypticase soy broth.
5. Choose the culture bottle with the best growth and streak on all the type of medium
provided.
Observations:
Sample number:
Blood cultures appearance (Take note of tell-tale sign like hemolysis, bubbles, changes in
color, etc. Refer to the Appendix)
Colony morphology
MacConkey Agar
Blood Agar
What other tests will you do to confirm and why? Show your flowchart on the opposite page.
Introduction:
The cerebro-spinal fluid (CSF), which completely surrounds the brain and spinal cord,
is normally sterile fluid. Infection by microorganism usually involves the meninges, a
membrane surrounding the brain and spinal cord (meningitis). The infection is acute and life-
threatening, and thus the examination of CSF is an emergency procedure. Among the
organisms that can cause meningitis is Streptococcus pneumonia, Streptococcus agalactiae,
Haemophilus influenza, Neisseria meningitides, Gram -ve bacilli, Listeria monocytogenes.
Staphylococci, Leptospira, Treponema pallidum, Mycobacterium tuberculosis, Cryptococcus
neoformans, Candida, toxoplasma gondii, Naegleria and Acanthamoeba.
CSF specimens are collected under strict aseptic conditions to avoid contaminations
and false-positive. The specimen must be processed as soon as possible to maximize recovery
of the organism. The specimen must not be refrigerated, since some of the organisms are very
sensitive to cold. A Gram stain is usually performed to look for characteristics organism. The
sample is then centrifuged at 1,500g to concentrate the organisms in isolation. Both the
sedimented cells and the supernatant should be cultured. General purpose media such as,
Blood, Chocolate and MacConkey Agar are inoculated while selective media are used for the
more exotic organisms. The CSF specimen will also be tested for viral and other antigens
using serological methods.
Other body fluids such as aspirates, pleural fluid specimen, etc. are similarly treated, although
not as medical emergencies.
Materials: (per group of 4)
Procedures:
Select a sample that forms the same group as your sample in experiment 5. That is, if you
tested sample in #3 in exp 5, use sample for this practical too.
Usually, a chocolate agar is also inoculated to check for H.influenzae and N.meningitidis.
Here we will omit it as these organisms will not be in the doctored sample. It is also
recommended that a thioglycollate broth be inoculated. Some labs will inoculate a
Lowenstein-jensen media to recover M.tuberculosis. The presence of protozoa, fungi or yeast
can usually be observed microscopically.
Observations:
Sample number:
Colony morphology
MacConkey Agar
Blood Agar
Presumptive identifications:
What other test will you do to confirm and why? Show your flow chart on the opposite page.
Confirmed identification: