Biochemical characterization of enteric bacteria

1.       Major intestinal disease: typhoid (salmonella typhi), Dysentery (shigella dysenteriae), cholera (vibrio chloerae), Travelers Diarrhea (E.coli)

2.       Enterobacteria: gram negative rods that are frequently found In the intestinal tract

3.       Facultative anaerobe: a bacterium that can grow in anaerobic intestinal tract but also in the presence of oxygen

4.       Selective medium: medium to prevent growth of some species but permitting others to survive

5.       Differential medium: medium that enables the investigator to distinguish one species from another. This is usually done through use of a chemical reaction which causes the color of the medium or the colonies to change.

 

Major type of Media

1.       MacConkey Agar: lactose fermenting organisms produce red colonies on this plate medium. Gram positive bacteria are inhibited. The ingredients include lactose, bile salts and neutral red (pH indicator).

2.       XLD: organisms that ferment the constituent carbohydrates produce yellow or red colonies on this plate medium. If lysine decarboxylase is produced colonies are red. Colonies may be black is H2S is produced. The medium contains xylose, lactose, sucrose, phenol red (pH indicator), bile salts, lysine and ferric ammonia citrate (H2S detection).

3.       TSI: triple sugar iron agar is used in the form of a slant tube. If an organism can use lactose or sucrose, the entire tube will turn yellow (acid). Gas may push the agar up the tube or form large bubbles. If only the glucose is used, the base (butt) of the agar slant will turn yellow but the slant itself will remain red. An organism that produces H2S will cause the formation of a black pigment in the tube. Besides the sugars, the medium contains phenol red (pH indicator) and iron salts (H2S detection).

4.       Simmons citrate: this medium will turn blue if an inoculated organism can uses citrate. The medium includes citrate and thymol blue (pH indicator) and is prepared as an agar slant.

5.       Urea agar: organism that can break down urea can be recognized by changing the color of this medium. Phenol red is the indicator

6.       Iron agar: this medium is used for the detection of H2S produced by some species

7.       Fermentation broth: test to determine if an organism can use a specific carbohydrate. The broth has phenol red to test for acid produced from the carbohydrate. A tiny inverted tube (Durham tube) is present to assay production of gas.

8.       Decarboxylase broth: medium can detect the ability to produce decarboxylase by a color change of the tube

9.       Motility medium: if growth spreads from a straight vertical stab line of inoculation, bacterium may be motile

10.   Entereotube II: multiple test medium made by Roche Diagnostics that can assay for several qualities at once

11.   Biology automated redox-based system: identify the genus and species the system assays the ability of an organism to oxidize a panel of 95 carbon sources in a 96-well microplate. If an organism being tested uses a specific carbon source, this is detected by the redox dye, tetrazolium violet. The GN microplate panel of carbon sources is used for gram negative aerobic bacteria (enteric, non-fermenter and fastidious species) while the GP microplate panel of carbon sources is used for gram positive aerobic bacteria. The data base software for the system contains 503 gram negative species/groups and over 200 gram positive species/groups.

-          A gram negative rod doesn’t stain purple because of peptidoglycan is thin. Gram positive does, because thick wall.

-          Peptidoglycan cannot absorb crystal violet.

-          The tube media must be inoculated by pure strain because we only want to get bacteria information for one bacteria and properly identify/asses a single species

-           E-coli can cause cholangitis, K. pneumonia causes pneumonia, P. vulgaris causes UTI and P. aeruginosa causes meningitis.

Phage titration

1.       Phage: this is a virus that infects bacteria

2.       Plaque: infective center (clear area) caused by a phage on a lawn of bacteria on a plate. It contains thousands of new phage. In this area the bacteria have been killed

3.       Plaque forming unit (PFU): a phage particle that is capable of forming a plaque on a lawn of bacteria

4.       Methods to measure virus concentration: phage titration or phage assay, routine test dilution (RTD), electron microscopy (EM), hemagglutination titration, dose to infect 50% of subjects (ID50) and dose to kill 50% of subjects (LD50)

5.       # of plaques x 10 x 1 / Tube dilution = titer in PFU/mL

6.       Dilution goes in 10-2, 10-4, 10-6 ect.

-          Every phage particle doesn’t make a plaque because plaque formation is dependent on the assay and conditions. Also not every virus finds bacteria to attack, virus may be defective or the bacteria is dead. Another instance could be multiple viruses attack one bacteria

-          Plaques stop growing because as the cell lawn become saturated the cell growth rate goes down since lysis requires rapid metabolism for growth. (run out of bacteria to infect)

-          Bacteria that survived/didn’t get infected by the phage on the zero dilution plate are mutants.

Antibiotics (Tube dilution Test)

1.       Antibiotic: a chemical synthesized by a microbe that will kill or inhibit other microbes

-          Producers of antibiotics

o   Streptomyces, Bacillus, Penicillium, Cephalosporium 

2.       Tube dilution antibiotic sensitivity assay: a known concentration of antibiotic is diluted in a two-fold tube dilution series and a drop of test organism is added to each tube to observe if good growth will occur. The antibiotic concentration in the highest dilution tube that shows no culture growth is called the minimum inhibitory concentration (MIC).

3.       Kirby-Bauer or disc method of determining antibiotic sensitivity: paper discs containing antibiotics are used to test for inhibition of bacterial growth in the vicinity of the disc on an agar plate. For standardization of the technique, a type of agar called Mueller-Hinton is used for the plates. To determine if an isolate is resistant or sensitive to an antibiotic, the growth inhibition zone diameter (including disc diameter) is compared with values produced by reference organisms of the same species on a standard table. Two antibiotics that produce the same inhibition zone diameter do not have equal efficacy because many factors, such as diffusion rates, effect results.

-          It is important to know the MIC of an antibiotic used to cure infection so you know what the levels are need to be bactericidal (prevent growth/kills) to microorganisms. MIC of penicillin or streptomycin would not be the same as tetracycline because they work differently so that part of the cell is likely to be different also. The tube dilution test was most quantitative because you are measuring effectiveness with the quantity of antibiotic.

Antibiotics (disc assay)

1.       The concentration of the disc is the number printed on the disc in units or microorganisms

2.       Zone size: could be powerful but doesn’t diffuse fast enough/ small in size

3.       Have to use the same type of hardening agent in agar

-          A bacteriostatic antibiotic suppressed the growth of bacteria.

-          Bactericidal antibiotic kills bacteria.

-          The function of penicillinase is to be used in medicine to treat allergic reaction to penicillin by hydrolyzing and inactivating penicillin.

-          The two organisms didn’t show the same sensitivity pattern is staph epidermis and e-coli because staph epidermis is gram positive and e-coli is gram negative

-          The peptidoglycan is the structural difference (thick or thin).

-          Plasmids are used to study genes encoded in bacteria and code for resistance against antibiotics. They decrease the efficiency of an antibiotic because help with antibiotic resistance

-          By understanding which bacteria are resistant to which antibiotics, newer and better antibiotics can be made

-          Volume of agar, size of antibody, and another thing affect

 

INHIBITION ZONE DIAMETER

Agent

Disc Potency

Resistant

Intermediate

Sensitive

Carbenicillin

CB-100

100 ug

< or = 19

20-22

>or = 23

Chloramphenicol

C-30

30

< or = 12

13-17

>or = 18

Kanamycin

K-30

30

< or = 13

14-17

>or = 18

Tetracycline

Te-30

30

< or = 14

15-18

>or = 19

 

 

 

TRANSPOSON MUTAGENESIS

1.       Bacteriophage or phage: virus that infects bacteria

2.       Transposon: a small piece of linear DNA that contains a few genes that has the ability to replicate and jump into a different region of DNA

3.       Mutation: change in DNA sequence

4.       Mutagen: an agent that causes mutation

5.       Mutant: organism that contains a mutation

6.       Cell population fraction mutagenized: 2 x tetRCells/mL /109 cells/mL

a.       Multiplication by 2 because cells were diluted with an equal volume of phage

-          Phage that we used had a copy of transposon (Tn10) in its genome that carries a gene for tetracycline resistance. The phage passes the transposon

-          - The insertion of transposon into Tetr cells DNA makes tetracycline resistant cells mutant, and the transposon inserted has genes for enzymes tetracycline resistant, so the non mutant cells don’t grow

-          Phage cannot replicate and kill the cell of a wild type host strain. Sometimes the transposon will jump out of the phage DNA and into the host cell chromosome, making the cell tetracycline resistant

-          Tetracycline resistant cells are mutant because the wild type were more susceptible to being killed and the mutants become less immune and progressed/reproduced since they can thrive in the media, also transposon inserted itself in making that cell a mutant

-          Common mutagenic agents are: x-rays, gamma rays and various chemicals

ALCOHOL PRODUCTION AND BACTERIA

1.       Butanol: a four carbon alcohol that can be used in making of important products such as plasticizers, lacquers and resins. Butanol currently has value for potential use as fuel extender or fuel. Butanol is made by the anaerobic bacterium known as Clostridium acetobutylicum. Synthesis of product by the organism has two phases. In acidogenesis there is a vegetative growth where organic acids acetate and butyrate are produced. In solventogenesis, acid produced are transformed into acetone, butanol and ethanol.

2.       Ethanol: a two carbon alcohol that is used in gasohol to reduce automotive emissions and reduce dependence on petroleum oil. E.coli and Klebsiella species have become important in biofuel research because strains (containing foreign genes) have been constructed by genetic engineering that produce ethanol. Moreover, E. coli has recently been genetically engineered to produce butanol and biodiesel respectively

3.       Fluid thioglycolate medium (FTM): a medium used for the cultivation of some of the less strict anaerobic bacteria. Sodium thioglycolate decreases the oxidation reduction potential (Eh) to assist growth of anaerobic bacteria. Resazurin is a pink oxidation reduction (OR) indicator which shows the condition of aerobiosis (presence of oxygen).

4.       Oxyrase: a commercial enzyme system used to help create anaerobiosis. Superoxide dismutase is an enzyme to help protect anaerobic bacteria from oxygen toxicity.

5.       Medium: industrial microbiology uses agricultural products as raw materials (carbon sources). Identification of new and inexpensive carbon sources is needed to decrease cost. Biodiesel glycerol byproduct is an example of potential carbon source for industrial microbiology. One liter of biodiesel glycerol byproduct is made for every three liters of biodiesel. 

 

pH Scale

Color

Orange

Gold

Light Green

Dark Green

pH

5-6

7

8

9

 

-          Glucose test strips provide a rapid solid phase chemistry enzyme (glucose oxidase and peroxidase) based assay to detect glucose. If glucose present, the pad will turn green.

-          Alcohol test strips provide a rapid solid phase chemistry enzyme (alcohol oxidase and peroxidase) based assay to detect alcohol. This test can score for alcohols having up to 4 carbons and will not react with glycerol. If alcohol present, it will turn blue.

-          Some microbes can grow in aerobic environments like FTM and e-coli and some cannot grow in an aerobic environment like c. aceto.

-          The significance of low pH in C. aceto is because it uses acidogenesis and produces acid as a byproduct. The presence of bacteria makes things more acidic, which is why E. coli and C. aceto have lower pH (more acidic)

-          The scientific name of the microorganism that is usually associated with yeast is Saccharomyces cervisiae  

-          Glucose is a simple sugar that is an important energy source in living organisms and is a component of many organic molecules. Glucose can be found in plant energy stores.

-          C. aceto and E. coli positive for alcohol

-          FTM is positive for glucose

-          Low Eh = anaerobic environment

o   Colorless and No oxygen present

-          High Eh

o   Pink and Oxygen present

 

Sample

Aerobic growth(+/-)

pH

Glucose (+/-)

Alcohol (+/-)

C. aceto

-

5-6 (orange)

-

+(blue)

E. coli

+

5-6 (orange)

-

+(blue)

FTM uninoculated

N/A

7 (gold)

+ (green)

-

 

AGGULTINATION TITER OF SERUM

1.       Serum titer: the greatest dilution of serum which causes agglutination

2.       Acute serum: a sample taken from a patient at the onset of an illness

3.       Convalescent serum: a sample taken from a patient during recovery of an illness or several days after the onset

4.       Identification of etiological agent: of the microorganism being tested as an antigen results in the observation of an increase in convalescent titer at least 4 fold greater than the acute titer, it is likely to be an infectious agent

-          Antibodies bind à signals à complements (male need more, females need less) à Bind at the back end of antibodies

-          Prozone effect is where there is an excess of antibodies causing no agglutination and post zone effect is where there is an antigen excess and no agglutination.

MYCOLOGY

1.       Hypha: filament of fungal cells

2.       Mycelium: mass of fungal hyphae

3.       Yeast: single celled fungi

4.       Pseudohyphae: short hyphal filaments consisting of rapidly dividing yeast cells

5.       Conidia: spores that develop on a conidiophore

6.       Conidiophore: modified hypha for spore production in some fungi

7.       Fruiting body: large complex structure in some fungi to make spores

8.       Bud: offspring of yeast attached to parent cell

9.       Aspergillus: a saprobe that can cause opportunistic infection of the lungs

10.   Candida Albicans: commensal organism that can be found on the skin, mouth, and in the genitourinary tracts that causes opportunistic infections.

-          Coccidioidomycosis is caused by C immitis and C posadasii

o   Fever

o   Cough

o   Chest pain — varying from a mild feeling of constriction to intense pressure resembling a heart attack.

o   Chills

o   Night sweats

o   Headache

o   Fatigue

o   Joint aches

-          Tinea corporis

o   Etiological agent: Trichophyton, Microsporum, and Epidermophyton TEM

o   Causes a scaly rash on the body

o   Ringworm of the body

o   On the scalp

o   In a man's beard

o   In the groin

o   Between the toes

-          Histoplasmosis

o   Etilogical agent: Histoplasma capsulatum

o   Chest pain.

o   Chills.

o   Cough.

o   Fever.

o   Joint pain and stiffness.

o   Muscle aches and stiffness.

o   Rash (usually small sores on the lower legs)

o   Shortness of breath.

-          HE ASKS A QUESTION ABOUT WHICH VIRUS DOES A A SPECIFIC SYMPTOM REPRESENT, IDK THE SYMPTOM I FORGOT IT I THINK IT WAS ITCHING OR RASH

 

PARASITOLOGY

1.       Parasite: an organism that lives on another to its detriment

2.       Trophozoite: adult vegetative form of a protozoan

3.       Cyst: small inactive state of a protozoan

4.       Proglottid: a segment of a tapeworm

5.       Scolex: the anterior or holdfast end of a tapeworm

6.       Entamoebba histolytica: pathogenic amoeba that causes severe dysentery and hepatic infection

7.       Giardia lamblia: flagellate that is a cause of weakness, abdominal pain and diarrhea

8.       Balantidium coli: ciliate that causes diarrhea, nausea and vomiting

·         Largest intestinal protozoan and non lethal

9.       Teania saginata: beef tapeworm that inhabits the small intestine and is associated with weight loss and abdominal pain

10.   Enterobius vermicularis: pinworm (roundworm) that inhabits the colon and causes itching

11.   Fasciola hepatica: liver fluke that infects the bile duct

-Human diseases can be caused by parasites because it is an organism that lives on another to its determent. Plasmodium: malaria (it is transmitted by a mosquito biting humans). Toxoplamsa gondii: taxoplasmosis (caused by eating uncooked meat).

 

KNOW WHAT TYPE OF AGAR IS THE COMMON ONE USED FOR MICROBIOLIGY

 Antibiotics (Tube dilution Test)

  1. Antibiotic: a chemical synthesized by a microbe that will kill or inhibit other microbes

-          Producers of antibiotics

o   Streptomyces, Bacillus, Penicillium, Cephalosporium 

  1. Tube dilution antibiotic sensitivity assay: a known concentration of antibiotic is diluted in a two-fold tube dilution series and a drop of test organism is added to each tube to observe if good growth will occur. The antibiotic concentration in the highest dilution tube that shows no culture growth is called the minimum inhibitory concentration (MIC).

  2. Kirby-Bauer or disc method of determining antibiotic sensitivity: paper discs containing antibiotics are used to test for inhibition of bacterial growth in the vicinity of the disc on an agar plate. For standardization of the technique, a type of agar called Mueller-Hinton is used for the plates. To determine if an isolate is resistant or sensitive to an antibiotic, the growth inhibition zone diameter (including disc diameter) is compared with values produced by reference organisms of the same species on a standard table. Two antibiotics that produce the same inhibition zone diameter do not have equal efficacy because many factors, such as diffusion rates, effect results. x

-          It is important to know the MIC of an antibiotic used to cure infection so you know what the levels are need to be bactericidal to microorganisms. MIC of penicillin or streptomycin would not be the same as tetracycline because they work differently so that part of the cell is likely to be different also. The tube dilution test was most quantitative.

Antibiotics (disc assay)

  1. The concentration of the disc is the number printed on the disc in units or microorganisms

  2. Zone size: could be powerful but doesn’t diffuse fast enough/ small in size

  3. Have to use the same type of hardening agent in agar

-          A bacteriostatic antibiotic suppressed the growth of bacteria.

-          A bactericidal antibiotic kills bacteria.

-          The function of penicillinase is to be used in medicine to treat allergic reaction to penicillin by hydrolyzing and inactivating penicillin.

-          The two organisms didn’t show the same sensitivity pattern is staph epidermis and e-coli because staph epidermis is gram negative and e-coli is gram positive.

-          The peptidoglycan is the structural difference (thick or thin).

-          Plasmids are used to study genes encoded in bacteria and code for resistance against antibiotics

-          By understanding which bacteria are resistant to which antibiotics, newer and better antibiotics can be made

 

INHIBITION ZONE DIAMETER

Agent

Disc Potency

Resistant

Intermediate

Sensitive

Carbenicillin

CB-100

100 ug

< or = 19

20-22

>or = 23

Chloramphenicol

C-30

30

< or = 12

13-17

>or = 18

Kanamycin

K-30

30

< or = 13

14-17

>or = 18

Tetracycline

Te-30

30

< or = 14

15-18

>or = 19

 

ALCOHOL PRODUCTION AND BACTERIA

  1. Butanol: a four carbon alcohol that can be used in making of important products such as plasticizers, lacquers and resins. Butanol currently has value for potential use as fuel extender or fuel. Butanol is made by the anaerobic bacterium known as Clostridium acetobutylicum. Synthesis of product by the organism has two phases. In acidogenesis there is a vegetative growth where organic acids acetate and butyrate are produced. In solventogenesis, acid produced are transformed into acetone, butanol and ethanol.

  2. Ethanol: a two carbon alcohol that is used in gasohol to reduce automotive emissions and reduce dependence on petroleum oil. E.coli and Klebsiella species have become important in biofuel research because strains (containing foreign genes) have been constructed by genetic engineering that produce ethanol. Moreover, E. coli has recently been genetically engineered to produce butanol and biodiesel respectively

  3. Fluid thioglycolate medium (FTM): a medium used for the cultivation of some of the less strict anaerobic bacteria. Sodium thioglycolate decreases the oxidation reduction potential (Eh) to assist growth of anaerobic bacteria. Resazurin is a pink oxidation reduction (OR) indicator which shows the condition of aerobiosis (presence of oxygen).

  4. Oxyrase: a commercial enzyme system used to help create anaerobiosis. Superoxide dismutase is an enzyme to help protect anaerobic bacteria from oxygen toxicity.

  5. Medium: industrial microbiology uses agricultural products as raw materials (carbon sources). Identification of new and inexpensive carbon sources is needed to decrease cost. Biodiesel glycerol byproduct is an example of potential carbon source for industrial microbiology. One liter of biodiesel glycerol byproduct is made for every three liters of biodiesel. 

 

pH Scale

Color

Orange

Gold

Light Green

Dark Green

pH

5-6

7

8

9

 

-          Glucose test strips provide a rapid solid phase chemistry enzyme (glucose oxidase and peroxidase) based assay to detect glucose. If glucose present, the pad will turn green.

-          Alcohol test strips provide a rapid solid phase chemistry enzyme (alcohol oxidase and peroxidase) based assay to detect alcohol. This test can score for alcohols having up to 4 carbons and will not react with glycerol. If alcohol present, it will turn blue.

-          Some microbes can grow in aerobic environments like FTM and e-coli and some cannot grow in an aerobic environment like c. aceto.

-          The scientific name of the microorganism that is usually associated with yeast is alcohol.

-          Glucose is a simple sugar that is an important energy source in living organisms and is a component of many organic molecules. Glucose can be found in plant energy stores.

-          C. aceto and E. coli positive for alcohol

-          FTM, C. aceto and E.coli positive for glucose

-          Low Eh = anaerobic environment

o   Colorless

o   No oxygen present

-          High Eh

o   Pink

o   Oxygen present

Phage titration

  1. Phage: this is a virus that infects bacteria

  2. Plaque: infective center (clear area) caused by a phage on a lawn of bacteria on a plate. It contains thousands of new phage. In this area the bacteria have been killed

  3. Plaque forming unit (PFU): a phage particle that is capable of forming a plaque on a lawn of bacteria

  4. Methods to measure virus concentration: phage titration or phage assay, routine test dilution (RTD), electron microscopy (EM), hemagglutination titration, dose to infect 50% of subjects (ID50) and dose to kill 50% of subjects (LD50)

  5. # of plaques x 10 x 1 / Tube dilution = titer in PFU/mL

  6. Dilution goes in 10-2, 10-4, 10-6 ect.

-          Every phage particle doesn’t make a plaque because plaque formation is dependent on the assay and conditions. Also not every virus finds bacteria to attack, virus may be defective or the bacteria is dead. Another instance could be multiple viruses attack one bacteria

-          Plaques stop growing because as the cell lawn become saturated the cell growth rate goes down since lysis requires rapid metabolism for growth.

-          Bacteria that survived/didn’t get infected by the phage on the zero dilution plate are mutants.

 

TRANSPOSON MUTAGENESIS

  1. Bacteriophage or phage: virus that infects bacteria

  2. Transposon: a small piece of linear DNA that contains a few genes that has the ability to replicate and jump into a different region of DNA

  3. Mutation: change in DNA sequence

  4. Mutagen: an agent that causes mutation

  5. Mutant: organism that contains a mutation

  6. Cell population fraction mutagenized: 2 x tetRCells/mL /109 cells/mL

    1. Multiplication by 2 because cells were diluted with an equal volume of phage

-          Phage that we used had a copy of transposon (Tn10) in its genome that carries a gene for tetracycline resistance

-          Phage cannot replicate and kill the cell of a wild type host strain. Sometimes the transposon will jump out of the phage DNA and into the host cell chromosome, making the cell tetracycline resistant

-          Tetracycline resistant cells are mutant because the wild type were more susceptible to being killed and the mutants become less immune and progressed/reproduced since they can thrive in the media, also transposon inserted itself in making that cell a mutant

-          Common mutagenic agents are: x-rays, gamma rays and various chemicals

 

Biochemical characterization of enteric bacteria

  1. Major intestinal disease: typhoid (salmonella typhi), Dysentery (shigella dysenteriae), cholera (vibrio chloerae), Travelers Diarrhea (E.coli)

  2. Enterobacteria: gram negative rods that are frequently found In the intestinal tract

  3. Facultative anaerobe: a bacterium that can grow in anaerobic intestinal tract but also in the presence of oxygen

  4. Selective medium: medium to prevent growth of some species but permitting others to survive

  5. Differential medium: medium that enables the investigator to distinguish one species from another. This is usually done through use of a chemical reaction which causes the color of the medium or the colonies to change.

 

Major type of Media

1.       MacConkey Agar: lactose fermenting organisms produce red colonies on this plate medium. Gram positive bacteria are inhibited. The ingredients include lactose, bile salts and neutral red (pH indicator).

2.       XLD: organisms that ferment the constituent carbohydrates produce yellow or red colonies on this plate medium. If lysine decarboxylase is produced colonies are red. Colonies may be black is H2S is produced. The medium contains xylose, lactose, sucrose, phenol red (pH indicator), bile salts, lysine and ferric ammonia citrate (H2S detection).

3.       TSI: triple sugar iron agar is used in the form of a slant tube. If an organism can use lactose or sucrose, the entire tube will turn yellow (acid). Gas may push the agar up the tube or form large bubbles. If only the glucose is used, the base (butt) of the agar slant will turn yellow but the slant itself will remain red. An organism that produces H2S will cause the formation of a black pigment in the tube. Besides the sugars, the medium contains phenol red (pH indicator) and iron salts (H2S detection).

4.       Simmons citrate: this medium will turn blue if an inoculated organism can uses citrate. The medium includes citrate and thymol blue (pH indicator) and is prepared as an agar slant.

5.       Urea agar: organism that can break down urea can be recognized by changing the color of this medium. Phenol red is the indicator

6.       Iron agar: this medium is used for the detection of H2S produced by some species

7.       Fermentation broth: test to determine if an organism can use a specific carbohydrate. The broth has phenol red to test for acid produced from the carbohydrate. A tiny inverted tube (Durham tube) is present to assay production of gas.

8.       Decarboxylase broth: medium can detect the ability to produce decarboxylase by a color change of the tube

9.       Motility medium: if growth spreads from a straight vertical stab line of inoculation, bacterium may be motile

10.   Entereotube II: multiple test medium made by Roche Diagnostics that can assay for several qualities at once

11.   Biology automated redox-based system: identify the genus and species the system assays the ability of an organism to oxidize a panel of 95 carbon sources in a 96-well microplate. If an organism being tested uses a specific carbon source, this is detected by the redox dye, tetrazolium violet. The GN microplate panel of carbon sources is used for gram negative aerobic bacteria (enteric, non-fermenter and fastidious species) while the GP microplate panel of carbon sources is used for gram positive aerobic bacteria. The data base software for the system contains 503 gram negative species/groups and over 200 gram positive species/groups.

-          A gram negative rod doesn’t stain purple because it has a thick layer of peptidoglycan. Gram positive has a thin layer of lipid.

-          Peptidoglycan cannot absorb crystal violet.

-          The tube media must be inoculated by pure strain because we only want to get bacteria information for one bacteria.

-           E-coli can cause cholangitis, K. pneumonia causes pneumonia, P. vulgarus causes UTI and P. aeruginosa causes meningitis.

 

AGGULTINATION TITER OF SERUM

1.       Serum titer: the greatest dilution of serum which causes agglutination

2.       Acute serum: a sample taken from a patient at the onset of an illness

3.       Convalescent serum: a sample taken from a patient during recovery of an illness or several days after the onset

4.       Identification of etiological agent: of the microorganism being tested as an antigen results in the observation of an increase in convalescent titer at least 4 fold greater than the acute titer, it is likely to be an infectious agent

-          Antibodies bind → signals → complements (male need more, females need less) → Bind at the back end of antibodies

-          Prozone effect is where there is an excess of antibodies causing no agglutination and post zone effect is where there is an antigen excess and no agglutination.

 

MYCOLOGY

  1. Hypha: filament of fungal cells

  2. Mycelium: mass of fungal hyphae

  3. Yeast: single celled fungi

  4. Pseudohyphae: short hyphal filaments consisting of rapidly dividing yeast cells

  5. Conidia: spores that develop on a conidiophore

  6. Conidiophore: modified hypha for spore production in some fungi

  7. Fruiting body: large complex structure in some fungi to make spores

  8. Bud: offspring of yeast attached to parent cell

  9. Aspergillus: a saprobe that can cause opportunistic infection of the lungs

  10. Candida Albicans: commensal organism that can be found on the skin, mouth, and in the genitourinary tracts that causes opportunistic infections.

-          Coccidioidomycosis is caused by C immitis and C posadasii

o   Fever

o   Cough

o   Chest pain — varying from a mild feeling of constriction to intense pressure resembling a heart attack.

o   Chills

o   Night sweats

o   Headache

o   Fatigue

o   Joint aches

-          Tinea corporis

o   Etiological agent: Trichophyton, Microsporum, and Epidermophyton

o   Causes a scaly rash on the body

o   Ringworm of the body

o   On the scalp

o   In a man's beard

o   In the groin

o   Between the toes

-          Histoplasmosis

o   Etilogical agent: Histoplasma capsulatum

o   Chest pain.

o   Chills.

o   Cough.

o   Fever.

o   Joint pain and stiffness.

o   Muscle aches and stiffness.

o   Rash (usually small sores on the lower legs)

o   Shortness of breath.

 

PARASITOLOGY

1.       Parasite: an organism that lives on another to its detriment

2.       Trophozoite: adult vegetative form of a protozoan

3.       Cyst: small inactive state of a protozoan

4.       Proglottid: a segment of a tapeworm

5.       Scolex: the anterior or holdfast end of a tapeworm

6.       Entamoebba histolytica: pathogenic amoeba that causes severe dysentery and hepatic infection

7.       Giardia lamblia: flagellate that is a cause of weakness, abdominal pain and diarrhea

8.       Balantidium coli: ciliate that causes diarrhea, nausea and vomiting

●        Largest intestinal protozoan and non lethal

9.       Teania saginata: beef tapeworm that inhabits the small intestine and is associated with weight loss and abdominal pain

10.   Enterobius vermicularis: pinworm (roundworm) that inhabits the colon and causes itching

11.   Fasciola hepatica: liver fluke that infects the bile duct

-          Plasmodium: meningitis and Toxoplamsa gondii: taxoplasmosis