Sunday, December 9, 2007

Group Post: MMIC dPBL-1

Biochemical and Culture Testing


CASE 1

Possible Organisms Biochemical Tests & Results Culture agars
Escherichia coli
Gram Stain: -
Oxidase: -
Lactose: +
Lysine: +
TSI slant: +
Indole: +
Methyl red: +
VP: -
Citrate: -

5% Sheep Blood Agar
Eosin-Methylthionine Blue Agar
MacConkey Agar
Pseudomonas aeruginosa
Gram stain: -
Oxidase: +
Pyocyanin: +
Fluoreseein: +
Citrate: +
Nitrase: +
Lipase: +
Ureases: +/-
Indole: -
TSI: -

Pseudomonas Agar P
Pseudomonas Agar F
MacConkey agar plate
Eosin-Methylthionine Blue agar
Cetrimide agar
Staphylococcus aureus
Gram Stain: +
Catalase: +
Coagulase: +

5% Sheep Blood Agar
Mannitol Salt Agar
Staphylococcus saprophyicus
Gram Stain: +
Catalase: +
Coagulase: -
Oxidase: -
Phosphatase: -
Urease: +
Lipase: +
2-hour PYR broth hydrolysis: -
D-trehalose; +

5% Sheep Blood Agar
Mueller-Hinton Agar Lawn with Urine
Enterococcus faecalis
Gram Stain: +
Catalase: -

5% Sheep Blood Agar
Chocolate Agar
6.5% NaCl Concentration Agar (halotolerant)
Bile Esculin Agar (BEA) Slants
Proteus-Providencia-Morganella
e.g. Proteus mirabilis

Gram Stain: -
Lactose: -
Oxidase: -
Urease: +
Indole: -
Nitrogen Reductase: +
Methyl Red: +
Vogues-Proskauer: -
Catalase: +
Phenylalanine Deaminase: +

MacConkey Agar
CLED
Klebsiella-Enterobacter-Serratia
e.g. Klebsiella oxytoca

Gram Stain: -
Oxidase: -
Lactose: -
Urease: -
Nitrate: +
Indole: +
Sucrose: +
Dextrose: -
Methyl Red: -
Vogues-Proskauer: +
Gelatin: -
Amylase: +
Lipase: -
Catalase: +
Citrate: +
H2S: -

5% Sheep Blood Agar
MacConkey Agar
Trypticase Soy Agar
Klebsiella-Enterobacter-Serratia
e.g. Klesiella pneumoniae

Indole: -
Sucrose: +
Dextrose: -
Methyl Red: -
Vogues-Proskauer: +
H2S: -
Lysine Decarboxylase: +

5% Sheep Blood Agar
MacConkey Agar

Done by Lizzie


CASE 2

Campylobacter jejuni
Oxidase (+)
Sensitivity to nalidixic acid

Blood agar with antibiotics to other fecal microbes
Fail to grow at 25C, must grow at 42C
Microaerophilic (grow at 5% oxygen + 10% carbon dioxide)
Shigella species
TSI (alkaline slant and acidic butt, with no gas and no H2S)

MacConkey's or EMB agar (colourless colonies)
Anaerobe
Escherichia coli
TSI (acidic slant and acidic butt, with gas ,but no H2S)
Indole test (+)

MacConkey's (pink colonies) or EMB agar (green sheen colonies)
Anaerobe
Clostridium perfringens
ELISA to detect Clostridium perfringens Enterotoxin

TSC agar containing egg yolk
Neomycin blood agar
Strict anaerobe
Clostridium difficile
Cytotoxicity test on human cell-line
ELISA to detect Clostridium perfringens exotoxin

Cycloserine cefoxitin fructose egg yolk agar (CCFA)
Vibrio Cholerae
Oxidase (+)
TSI (acidic slant acidic deep; no gas)
Agglutination of bacteria by polyvalent O1 antibody

TCBS (yellow colonies), Blood agar
Vibro parahemolyticus
Oxidase-positive
Grow in 10% NaCl

TCBS (green colonies)
Bacillus cereus
Lecithinase (+)
Motile (swarming on agar)
Catalase (+)
Indole (-)
Nitrate (+)
Urease (-)
Citrate (+)
MR (-)
VP(+)
TSI (Alkaline slant, acidic deep)
Oxidase (-)
Lactose fermenting; sucrose non-fermenting

Sheep’s blood Agar (beta hemolytic), large greenish colonies),
Mannitol (grey colonies)
Yersinia enterocolitica
Motile at 25 deg
MR (+)
VP (-)
Urease (-)
Indole (-)
Citrate (-)
Catalase (+)
TSI (acidic slant acidic deep; no gas)

MacConkey Agar (small lactose negative colonies)
EMB
Staphylococci aureus
Catalase (+)
Citrate (-)
Coagulase (+)
Indole (-)ME (+)
Oxidase (-)
Urease (-)
VP (-)
TSI (acidic slant acidic deep)

Sheep blood agar (beta hemolytic, yellow colonies)
Mannitol salt agar (yellow colonies)
7.5% NaCl media

Done by Kent and Ye Tun


CASE 3

E. coli Oxidase -
Catalase +
Indole +
Methyl red +
Voges-Prokauer -
Citrate Utilization -
Urease -
TSI; H2S production Acid slant/ acid butt & gas produced;
+
MacConkey agar Lactose fermenters; (red colonies)
Blood agar β-hemolytic
Klebsiella sp (Klebsiella pneumuniae, Klebsiella oxytoca) Oxidase -
Catalase +
Indole +
Methyl red -
Voges-Prokauer +
Citrate Utilization +
Urease -
TSI; H2S production Alkaline slant/ acid butt;
-
MacConkey agar Lactose fermenters; (pink colonies)
Blood agar Mucoid colonies formed
Enterobacter (Enterobacter aerogenes) Oxidase -
Catalase +
Indole -
Methyl red -
Voges-Prokauer +
Citrate Utilization +
Urease
TSI; H2S production
MacConkey agar
Blood agar
Serratia Oxidase -
Catalase +
Indole
Methyl red -
Voges-Prokauer +
Citrate Utilization +
Urease
TSI; H2S production
MacConkey agar
Blood agar
Proteus mirabilis Oxidase -
Catalase +
Indole +
Methyl red +
Voges-Prokauer -
Citrate Utilization
Urease +
TSI; H2S production Alkaline slant/ acid butt;
+
MacConkey agar Non-lactose fermenters; (white colonies)
Blood agar Swarming observed
Morganella morganii Oxidase -
Catalase +
Indole
Methyl red
Voges-Prokauer
Citrate Utilization
Urease +
TSI; H2S production
MacConkey agar Non-lactose fermenters; (white colonies)
Blood agar
Pseudomona aeruginosa Oxidase +
Catalase +
Indole -
Methyl red
Voges-Prokauer
Citrate Utilization +
Urease
Coagulase
TSI; H2S production
MacConkey agar Non-lactose fermenters; (white colonies)
Blood agar
Staphylococcus aureus
Catalase +
Methyl red
Voges-Prokauer
Citrate Utilization
Coagulase +
MacConkey agar -
Blood agar β-hemolytic
Staphylococcus saprophyticus
Catalase +
Methyl red
Voges-Prokauer
Citrate Utilization
Urease +
Coagulase -
MacConkey agar Non-lactose fermenters; (white colonies)
Blood agar -
Enterococcus sp
Catalase
Indole
Methyl red
Voges-Prokauer
Citrate Utilization
Urease
Coagulase
TSI; H2S production
MacConkey agar
Blood agar

Done by Joan


CASE 4

Possible Organisms Biochemical Tests & Results Culture agars
Streptococcus pneumoniae
Gram Staining +ve
Catalase -ve

2. 5% Sheep Blood agar with Optocin sensitivity Alpha-hemolysis with sensitivity to optocin
Klebsiella-Enterobacter-Serratia (Klebsiella sp.)
Gram Staining -ve
Oxidase -ve
Indole +ve/-ve
MR-VP +/- or -/+
Citrate +ve
H2S Production -ve
Lysine Decarbocylase +ve

Lactose Fermentation (MacConkey agar) +ve
Bordetella pertussis
Gram Staining -ve
Oxidase +ve
Urease -ve
Nitrase -ve
Citrate -ve

Borde+ - Gengou agar
BCYE agar

Done by Charmaine


CASE 5

Staphylococcus aureus
Gram Staining +
Catalase +
Coagulase +

Mannitol Salt Agar with 7-9% NaCl Mannitol fermentation
Sheep Blood Agar Hemolysis of blood agar
Streptococcus pyogenes
Gram Staining +
Catalase -
PYR (Pyrrolidonearylamidase) Test +

Sheep Blood Agar Beta Hemolysis
Enterococci
Gram Staining +
Bile- esculin test -

Sheep Blood Agar Gamma Hemolysis
6.5% NaCl Agar Can grow with 6.5% Nacl
Escherichia coli
Gram Staining -
Indole +
Methyl Red +
Voges Prokauer -
Citrate -
TSI Acid slant and butt with gas production but no H2S in TSI

MacConkey Lactose fermentative (deep red colony)
Eosin Methylene Blue( EMB) Green metallic sheen on EMB
Pseudomonas aeruginosa
Gram Staining -
Oxidase +
Catalase +
Indole +
Citrate +
Urease -
TSI -
Pyocyanin -
Fluroscein -

MAC Non- lactose fermentative (colourless colony on MAC)
Pseudo F agar PositiveFluorescein pigment in Pseudo F agar

Done by Ai Tee


CASE 6
Gardnerella vaginalis
Catalase -
Oxidase -
Vaginal pH test pH of vaginal fluid >5.0
Whiff test Release of bad-smelling odor when discharge is mixed with KOH
DNA Probe (Affirm™ VP III) High concentrations of G. vaginalis in VP III test

Chocolate agar Small, circular, convex, gray colonies
HBT agar
Colistin-oxolinic acid blood agar Beta-hemolysis
E. coli
Triple Sugar Iron (TSI) test TSI test show acid slant, acid butt with gas.
Indole test +
Methyl red test +
Voges-Proskauer (VP) test -
Citrate test -

EMB agar Black colonies with greenish-black metallic sheen on EMB agar
MacConkey agar Deep red colonies on MacConkey agar (lactose fermentor)
TSI agar
Pseudomonas aeruginosa
Oxidase test +
Catalase test +
Nitrase tese +
Lipase test +
TSI test Metallic sheen growth on the surface of TSI agar

EMB agar
Mac Conkey’s agar (sterile specimen)
Cetrimide agar (non-sterile specimen) Colonies appear flat, large, and oval. Secretes blue-green pigment (pyocyanin) on Cetrimide agar
TSI agar No colour change on TSI medium (K/K/g-/H2S- profile)
Neisseria gonorrhoeae
Oxidase test +
Direct immunofluorescence

Thayer-Martin chocolate agar Growth of spherical shape colonies on TM chocolate agar
Chlamydia Trachomatis
Direct immunofluorescence Presence of monoclonal antibodies (mAbs) to epitopes in the VS4 region of MOMP
ELISA Presence of Chlamydia antigens in ELISA test
PCR
DNA-based tests.

Blood agar
Mac Conkey’s agar
Trichomonas vaginalis
Vaginal pH test pH of vaginal fluid >4.5
PCR
Enzyme immunoassay Presence of T. vaginalis antigen in enzyme immunoassay
Direct Immunofluorescence.

Blood agar
Mac Conkey’s agar
Mobiluncus
Catalase test -
Indole test -
Oxidase test -

Blood agar Clear, colourless colonies, around 2mm.
Mac Conkey’s agar
Enterobacter-Klebsiella-Serrtia
-

Blood agar
Mac Conkey’s agar Deep red colonies on MacConkey agar (lactose fermentor)
Proteus-Providencia-Morganella
Urease test +
Indole test +

Blood agar Appear as swarming on blood agar.
Mac Conkey agar Colourless colonies on MacConkey agar (Non-lactose fermentor)
Enterococcus faecalis
Catalase test -

Blood agar Alpha, beta, or non-hemolytic on blood agar.
Mac Conkey agar
Candida albicans
-

Blood agar
Sabouraud’s agar Presence of white, butyrous colonies.
Staphylococcus saprophyticus
Catalase test +
Coagulase test -
Urease test +
Lipase test +

Blood agar
Mac Conkey’s agar Spherical, irregular grape-like cluster in culture.

Done by Adrian

Sunday, December 2, 2007

Group Post: MMIC dPBL 1

List of possible organisms for each case
Diagnosis Possible bacteria species Morphology & Microscopy
Case 1 Urinary Tract Infection (UTI)
Staphylococcus aureus

Staphylococcus saprophyticus

Enterococcus faecalis

Gram Positive, Spherical-shaped, immobile and form grape-like clusters

Gram Positive, Cocci-shaped occur singly and in pairs, short chains, and grape-like clusters

Gram Positive, Cocci-shaped in pairs and chains
Case 2 Enterocolitis
Campylobacter jejuni

Shigella species

Salmonella species

Escherichia coli (entero-pathogenic; EPEC)

Clostridium perfringens

Clostridium difficile

Vibrio Cholerae

Vibro parahemolyticus

Bacillus cereus

Yersinia enterocolitica

Staphylococci aureus

Gram-negative rods

Gram-negative rods

Gram-negative rods

Gram-negative rods

Gram-positive rods

Gram-positive rods

Gram-negative rods

Gram-negative rods

Gram-positive rods

Gram-negative rods

Gram-positive cocci
Case 3 Urinary Tract Infection (UTI)
E. coli

Klebsiella sp (Klebsiella pneumuniae, Klebsiella oxytoca)

Enterobacter (Enterobacter aerogenes)

Serratia

Proteus mirabilis

Morganella morganii

Pseudomona aeruginosa

Staphylococcus aureus

Staphylococcus saprophyticus

Enterococcus sp.

Gram negative bacilli

Gram negative bacilli

Gram negative bacilli

Gram negative bacilli

Gram negative bacilli

Gram negative bacilli

Gram negative bacilli

Gram positive cocci

Gram positive cocci

Gram positive cocci
Case 4 Bronchitis
Strep. Pneumoniae

Klebsiella-Enterobacter-Serratia (Klebsiella sp.)

Bordetella pertussis

Gram positive, diplococci, lancet-shaped

Gram negative rods

Gram negative, coccibacilli
Case 5 Wound Infection
Beta Haemolytic Streptococci (Streptococcus pyogenes)

Enterococci (Enterococcus faecalis)

Staphylococci (Staphylococcus aureus/MRSA)

Clostridium

Pseudomonas aeruginosa

Enterobacter species

Escherichia coli

Klebsiella species

Proteus species

Bacteroides

Gram-positive facultative anaerobes cocci

Gram-positive facultative anaerobes cocci

Gram-positive facultative anaerobes cocci

Gram-positive anaerobe rod

Gram-negative aerobic rods

Gram-negative facultative rods

Gram-negative facultative rods

Gram-negative facultative rods

Gram-negative facultative rods

Gram negative Anaerobes rods
Case 6 Urinary Tract Infection (UTI)
Gardnerella vaginalis

Chlamydia trachomatis

Neisseria gonorrhoeae

Ureaplasma urealyticum

Staphylococcus saprophyticus

Enterobacteriaceae (E. coli, serratia, klebsiella, enterobacter, citrobacter)

Enterococci

Gram-negative rod with a gram-positive cell wall

Gram-negative bacteria, coccoid or rod-shaped

Gram negative cocci

Gram-negative bacteria

Gram positive, globular shaped, colonies resemble grape-like clusters

Gram-negative, rod-shaped

Gram-positive cocci which often occur in pairs (diplococci)
Authors: Lizzie, Kent & Ye Tun, Joan, Charmiane, Ai Tee and Adrian (according to case no.)


Brief description of diagnosis:


1. Urinary Tract Infection (UTI)


A urinary tract infection (UTI) is a bacterial infection that affects any part of the urinary tract. The urinary tract is made up of the kidneys, ureters, bladder, and urethra, and each plays a role in removing liquid waste from the body. Although urine contains a variety of fluids, salts, and waste products, it usually does not have bacteria in it. When bacteria get into the bladder or kidney and multiply in the urine, they cause a UTI.

Cystitis: bladder infection.

Pyelonephritis: kidney infection is much more serious.

Urethritis: urethra infection.

Each type of UTI may result in more specific signs and symptoms, depending on which part of your urinary tract is infected. The symptoms shown in acute pylonephritis are closest to what is given in the case study, whereby it is an infection of your kidneys may occur after spreading from an infection in your bladder. Kidney infection can cause upper back and flank pain, high fever, shaking chills, and nausea or vomiting.

Pyelonephritis is an inflammation of the kidney and upper urinary tract that usually results from noncontagious bacterial infection of the bladder (cystitis). In acute pylonephritis, bacteria begin colonising the tubules and connective tissue of the kidney itself. Small abscesses and streaks of pus begin to appear in the renal cortex and medulla respectively. Pyelonephritis most often occurs as a result of urinary tract infection, particularly in the presence of occasional or persistent backflow of urine from the bladder into the ureters or kidney pelvis (vesicoureteric reflux).

Urinary catheterization is the insertion of a catheter into a patient's bladder through the urethra, to drain urine from the bladder into an attached bag or container. Indwelling catheters should be restricted to patients whose incontinence is caused by urinary tract obstruction that can not be treated, and for which alternative therapy is not feasible. However, the catheter may introduce bacteria into the urethra and bladder, resulting in urinary tract
infection. The risk for developing a UTI increases when long-term catheterization is required.

Bacteria causing UTI may be isolated from the vaginal discharge. UTI can also result from sexual intercourse where bacteria from the vaginal area is transferred to the urethra and bladder.

Authors: Lizzie, Joan and Adrian


2. Enterocolitis


Enterocollitis is the inflammation of the small intestine and colon. Disease-causing bacteria usually invade the small intestines and colon and cause inflammation (blood or pus in the stool, fever) and abdominal pain and diarrhea. Campylobacter jejuni is the most common bacterium that causes acute enterocolitis in the U.S. Other bacteria that cause enterocolitis include Shigella, Salmonella and EPEC (E. Coli Enteropathogenic). These bacteria usually are acquired by drinking contaminated water or eating contaminated foods such as vegetables, poultry, and dairy products.

Enterocolitis caused by the bacterium Clostridium difficile is unusual because it often is caused by antibiotic treatment. It is also the most common nosocomial infection (infection acquired while in the hospital) to cause diarrhea.

E. coli O157:H7 produces a toxin that causes hemorrhagic enterocolitis (enterocolitis with bleeding). There was a famous outbreak of hemorrhagic enterocolitis in the U. S. traced to contaminated ground beef in hamburgers (hence it is also called hamburger colitis).

Bacterial overgrowth of the small intestine.

Because of small intestinal problems, normal colonic bacteria may spread from the colon and into the small intestine. When they do, they are in a position to digest food that the small intestine has not had time to digest and absorb. The mechanism that leads to the development of diarrhea in bacterial overgrowth is not known.

Authors: Kent and Ye Tun

3. Bronchitis


Bronchitis is an inflammation of the bronchi of the lungs. There are two main types of bronchitis: acute and chronic bronchitis.

Acute bronchitis can be caused by viruses such as influenza A and B, parainfluenza virus, respiratory syncytical virus, coronavirus, adenovirus, and rhinovirus. Bacterias are also able to cause acute bronchitis. Air pollutants such as cigarette smoke, dusts, or fumes of chemicals are also able to cause acute bronchitis.

The symptoms of acute bronchitis include:

* Sore throat

* Chest congestion

* Sinus fullness

* Breathlessness

* Wheezing

* Slight fever and chills

* Overall malaise

* Cough

Chronic bronchitis is where by the signs and symptoms become prolonged, and is defined clinically as a
persistent cough that produces sputum (phlegm) and mucus, for at least three months in two consecutive years. Chronic bronchitis is part of chronic obstructive pulmonary disease (COPD).

Author: Charmaine

4. Surgical Site Infection (SSI)


There are different levels of SSI:

• Superficial incisional, affecting the skin and subcutaneous tissue.

• Deep incisional, affecting the facial and muscle layers.

• Organ or space infection affecting any part of the anatomy opened or manipulated during the operation.

Symptoms: Pain, fever, inflammation, swelling and pus formation



Causes of infection:

-Microbes contamination (most commonly by S. aureus, S. pyogenes or P. aeruginosa

-Migration of patients’ own bacterial normal flora

-The materials or equipment used in the operational procedures (for e.g.: poor surgical techniques)

Author: Ai Tee