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HOW TO ID AN UNKNOWN ORGANISM: Note: we are not performing all of these tests; I will describe the whole process to you but we will only do some of these tests. This whole transcript will be on the Unit 2 exam. METHOD OVERVIEW Obtain your unknown stock, and check it for purity by performing a Gram stain. Then use it to inoculate a working stock and a reserve stock. Each week, you check your working stock for purity by performing another Gram stain before using it to inoculate the media to perform the tests for that day. Use aseptic technique. You will not use the reserve stock unless your working stock becomes contaminated. Then determine the morphological characteristics of your unknown organism by performing a Gram stain, motility stab, capsule stain. If you have a Gram positive rod, you will also need to do a spore stain, since only Gram positive rods make spores (only certain species). Next, determine the cultural characteristics of your organism by observing the growth patterns in broth and on agar slants and plates. Determine the optimal temperature and oxygen requirements, and determine what type of hemolysis your organism displays. Next, determine the physiological characteristics of your organism. This will require about 1820 individual tests to find out what enzymes your organism makes, its fermentation pathway, etc. GETTING STARTED Perform a Gram stain. Since the longest step is air drying, make 3-4 slides and allow them to air dry at the same time, but only use one to perform your Gram stain. That way, if your culture is not decolorized properly, you have several slides ready to go so you can perform another stain quickly. When you observe your organism under the microscope, check to make sure your culture is pure. Sometimes, the Gram stain becomes contaminated or your culture may be contaminated. If you see more than one organism, you need to go back to the original pure culture and start again. If you only see one organism, the next step is to do a Negative stain with India ink, which is the best way to see the arrangements of the organism. Record the shape (rods or cocci?) and arrangement (singles, clusters, or chains?). Then use your unknown broth to inoculate 3 broths, 2 slants, and 2 plates. CREATE A WORKING STOCK AND RESERVE STOCK Inoculate 2 TSA slants by using a needle. Obtain the inoculum and place the needle in the TSA slant toward the bottom, and pull a straight line upwards on the surface of the slant. One of these slants will be labeled “working stock”. The working stock tube is the one used to obtain inoculums for other lab tests unless the stock becomes contaminated. Each WEEK, a new working stock tube is made so the culture stays young. To make a new working stock, just use the old working stock to inoculate a new tube. After growth is seen in the new tube the following week, you need to check for purity by performing a Gram stain. Once you know your new working stock is not contaminated, you can discard the old working stock tube. That means you need to write dates on these tubes. The second TSA slant made on the first day will be the reserve stock in case the working stock becomes contaminated. 1 MORPHOLOGICAL CHARACTERISTICS: Gram stain, size determination, motility, capsule stain, spore stain SIZE DETERMINATION If you have a Gram + organism, mix a loopful of it with a loopful of a Gram neg organism whose size is known. If you have a large organism, pick a large organism to compare it with. If you have a small organism, pick a small organism. Estimate the size of yours compared to the known. MOTILITY TEST (positive is E. coli, negative is Klebsiella pneumoniae) Inoculate a motility stab. Use a needle to obtain the inoculum. Stab the needle into the motility medium, almost all the way to the bottom, then pull the needle back out in a straight line, backing the needle out of the same stab line you made going in. Remember, these need to be incubated at room temperature (25°C). If they are placed at room temperature, the flagella will detach, giving a false negative result for motile organisms. Also remember that motility media uses TTC as a terminal electron acceptor. If the organism can use it, the media will turn red, meaning the TTC has been reduced. If there is no red color at all, you will need to do a wet mount or hanging drop to observe the organism directly to determine if it is motile. CULTURAL CHARACTERISTICS: Growth patterns, temperature, hemolysis, and oxygen requirements GROWTH PATTERNS Use your working stock and reserve stock to observe the growth patterns of your organisms and record that information in your journal. The terminology to use is in your lab manual. When you have recorded the morphology on your reserve stock, it will be kept in the refrigerator. You will not use it except in emergency. Also use your TSB tubes from your optimum temperature experiment to determine the pattern of grown in broth. DETERMINE OPTIMUM TEMPERATURE FOR YOUR ORGANISM Inoculate one loop-full of your organism into 3 TSB tubes. Label one tube 25 °C, one tube 30 °C, and one tube 38°C. Make sure your name is on the tube. These tubes will be used to determine the optimal temperature for your organism. Use the spectrophotometer to calculate their optical density at the next lab period. The tube with the most growth (highest OD) is the temperature they prefer. Organisms that grow well in room temperature as well as body temperature might be opportunistic pathogens. These tubes can also be used to determine their pattern of growth in broth. 2 HEMOLYSIS TEST (Controls: Beta = Staph aureus; gamma = E. coli, alpha = Strep bovis) Inoculate a blood agar plate. Streak for isolation again. You will use this plate to observe colony morphology and hemolysis patterns. Beta hemolysis means the organism can completely lyse red blood cells and they digest the hemoglobin (pathogenic bacteria), so there will be clear areas around the colonies on your plate. Alpha hemolysis means the bacteria can oxidize the iron in the hemoglobin, which turns the colony green, with NO clear areas. Gamma hemolysis means the organism is non-hemolytic, so there will be NO clear areas, and the colony will not be green. Controls are also made (positive and negative results) for blood agar plates, motility stabs, and thio tubes. Now it is time to determine the oxygen requirements by inoculating a sodium thioglycolate tube. SODIUM THIOGLYCOLATE TUBES (OXYGEN REQUIREMENT) This medium has an oxygen gradient, which means that most of the oxygen is at the top of the tube, and the least amount of oxygen is at the bottom of the tube. To prepare this medium, a reducing agent called Sodium thioglycolate was added, which removes the free oxygen by chemically binding with it. Therefore, thioglycolate broth is called a REDUCING MEDIUM. It gets rid of the oxygen. There is also a pink indicator dye called rasazarin that shows you where the oxygen is. Notice that the pink color is only at the top of the tube. We have to be careful not to shake the tube, or we will aerate it (add more oxygen). We need the oxygen gradient to be maintained for a successful test. The results of this test determine what oxygen requirements your organism has. Procedure: 1. Hold the thioglycolate tube carefully, taking care to move it gently without shaking, jiggling, or stirring them (which introduces oxygen into the medium). 2. Label the tube with your name, the date, the organism, and “Thio” for Thioglycolate. 3. Put some of your unknown bacteria on a sterile loop and gently push the loop straight down to almost the bottom of your tube. Do not touch the bottom as this may ruin the loop, and do not introduce air by stirring or shaking the tube! 4. Gently pull the loop straight out of the tube and sterilize it. 1. STRICT AEROBES require oxygen to grow. There will only be growth on the surface of the thio broth tube (pseudomonas and Bacillus megatarium) 2. STRICT ANAEROBES require the absence of all oxygen. There will only be growth at the butt (bottom) of the tube (clostridium). 3. FACULTATIVE ANAEROBES grow best aerobically but do not require it. Growth is throughout the tube, but is best at the top and decreases as one descends. (E.coli, staph aureus) 3 PHYSIOLOGICAL TESTS STREAK FOR ISOLATION Inoculate a TSA plate, using the streak for isolation method (draw 4 quadrants on the bottom of the plate, zig-zag the upper left quadrant, flame the loop, then draw the loop from quadrant 1 (Q1) into Q2 and zig-zag that second quadrant. Flame the loop, then draw the loop from quadrant Q2 into Q3 and zig-zag that third quadrant. Flame the loop, then draw the loop from quadrant Q3 into Q4 and zig-zag that final quadrant. You will use this plate to observe colony morphology on a plate. At the next lab period, you will also use this plate to perform the catalase and oxidase tests. CATALASE TEST (Control: positive = Staph aureus) Some facultative aerobes have the enzyme called catalase, which breaks down hydrogen peroxide (H2O2) into harmless water plus oxygen. Having this enzyme protects organisms from being destroyed by the H2O2 in the lysosomes of a white blood cell. Your instructor will lift the lid on your agar plate next lab period, and put one drop of H2O2 onto the colony. A positive test will show the oxygen bubbles rising up from the plate. That means the organism has the enzyme, so it is catalase +. NOTE: do not get catalase mixed up with oxidase. Catalase breaks down into oxygen, but is it not the oxidase test! OXIDASE TEST (Control: positive = Pseudomonas aeruginosa) Some aerobes have the enzyme called cytochrome oxidase, which is a molecule that is a terminal electron acceptor in the electron transport chain. On a piece of paper, place one drop of the oxidase reagent Dimethyl-p-phenylene diaminic hydrochloride (this substance is carcinogenic). Then use a toothpick to obtain the organism from your TSA plate, and scrape the sample onto the drop of reagent on the paper. The test should be done in comparison to a positive control, because time is essential in the development of the test results. Count the number of seconds it takes to turn purple and record the time in your journal. If purple is observed at any time, it is positive for oxidase. If there is no color change, it is negative. NOTES: Even if you figured out what organism you have, you need to continue to perform the assigned experiments. Know which tests show what color on a positive test: Brown, Orange or Red, Blue, Yellow, Diffused black pigment, Pink ring on top, etc. Know what reagents are used, what substrates in the media are broken down, and what the products are. UREA BROTH (Control = Proteus vulgaris) This test checks for the enzyme called urease, which breaks urea down into ammonium and carbon dioxide (water is not a product of this reaction). The ammonium will increase the pH. The medium has a pH indicator called phenol red. When pH goes up, it will turn bright pink (positive). CASEIN TEST (skim milk) (Control = Bacillus) Some organisms produce an enzyme called caseinase (a protease), which breaks down the protein that makes milk white. It breaks the protein down into small peptides that can be absorbed into the cell. Do a heavy streak in the center. Positive is a clearing (halo) around the area of growth of the organism because the milk is broken down and the white color disappears. Casein is what makes milk look cheesy when it is left unrefrigerated. 4 CITRATE TEST (Control: positive = Enterobacter aerogenes) Citrate is the sole carbon source in this medium. If the organism can use citrate as its only carbon source, the medium will become basic. The medium starts out green and turns blue if it is a positive test. It may only be blue at the top, which is still positive. Acid = green (negative) and base = blue (positive). A negative tube will also show no growth. Ingredients in the medium include 1) Indicator dye is Bromthymol blue, which is green when acids are present 2) Nitrogen source is Ammonium salts instead of peptones in order to test the ability of an organism to use a single specific carbon source This is the reaction: Citrate + NH4 increase in pH, turns the slant blue LIPASE (control: positive = Staph aureus) The Spirit Blue media has lipids. If the organism has the enzyme lipase, fatty acids will be released, and pH will decrease (become acidic). This will precipitate the blue dye. A positive result is a dark blue streak in the center of the plate where you inoculated it. If lipase if produced, the concentration of the blue will increase where it was inoculated. Having clearing is NOT a positive test; it should be darker blue. NOTE: If you have a Gram positive organism, and if it is not a spore former, you need to do an acid-fast stain. If it is positive, you have a mycobacterium, which is not really a Gram negative organism. Negative stains are done if there is a question about the arrangement of your organism. You can see their arrangements best with a negative stain. STARCH (Control = Bacillus) This media has starch. Some molecules, such as starch, cannot be taken into a bacterial cell because the molecules are so large. The organism can only use starch if it has an enzyme, called amylase, which can hydrolyze (break down) the starch into simple sugars that can be absorbed into the cell. We will flood the plate with iodine, which reacts with starch and turns it black. If the organism has the enzyme, there will be no more starch left, so there is nothing for the iodine to react with. Therefore, the presence of amylase will show up as a halo (area of clearing) around the organism (positive test). If the organism could not use the starch, the starch forms a complex with iodine to give a black precipitate around the organism. That means the organism is negative for amylase. NOTE: the black color only lasts a few minutes, so you have to read the test right away before the color disappears. GELATIN (Control = Bacillus) Some organisms produce an enzyme called gelatinase, which breaks down gelatin. If the gelatin is broken down, it becomes liquefied, and can no longer solidify, even when cooled in the refrigerator. Gelatin is a protein, so gelatinase is a protease. Gelatin is the only thing making the media solid. If it remains liquid, even after refrigeration, it is positive. Solid is negative. 5 IMViC This stands for a series of tests: 1) Indole 2) Methyl Red 3) Voges-Proskauer 4) Citrate The small “i” does not stand for anything; it just makes pronunciation easier. The IMViC tests are used to identify an organism in the coliform group. A coliform is a gram negative, aerobic or facultative anaerobic rod which produces gas from lactose within 48 hours. The presence of some coliforms indicates fecal contamination. We will perform the indole test as part of the SIM media. We performed the citrate test in the Simmon’s Citrate media. Now we need to perform the MR-VP test to complete the IMViC series. MR-VP TEST (Methyl Red/Voges-Proskauer) We do two tests with this medium: The MR test and VP test. We will inoculate one MR-VP tube today, let the culture grow until the next lab period, and then add 5 drops of Methyl Red to perform the MR test. In the next lab period, we will inoculate a new MR-VP tube, let the culture grow, and then add alpha-naphthol and potassium hydroxide reagents to perform the VP test. We are looking for glucose fermentation. Bacteria convert glucose to pyruvate using different metabolic pathways. One pathway produces unstable acidic products which quickly convert to neutral compounds. Another pathway (the butylene glycol pathway) produces neutral end products, including acetoin and 2,3-butanediol. A third pathway is the mixed acid pathway, which produces stable acidic end products which remain acidic. If an organism produces a lot of acid from the fermentation of sugars, it can override the buffer in the test media. If this happens, the amber media will turn red. MR-VP broth differentiates organisms that are single acid fermenters from organisms that are mixed acid fermenters because it contains over-riding buffers that affect organisms that are single acid fermenters. An organism that produces only one type of acid after sugar fermentation will not produce much acid, so the buffer blocks the media from changing color. But if the organism produces many different kinds of acids, it overrides the buffer and causes the color to change. MR = METHYL RED TEST Methyl Red is a yellow colored pH indicator which turns red if the organism uses the mixed acid fermentation pathway, which is that pathway that produces stable acidic end-products. If positive, the enzyme present is formic hydrogenylase. The acids will overcome the buffers in the medium and produce an acidic pH. When methyl red is added, it will go from yellow to red, which is positive for an organism that uses the mixed acid fermentation pathway. (Control: E. coli = pos; Enterobacter aerogenes = neg) NOTE: Methyl red differs from Phenol red Methyl Red: starts off yellow, turns red when acids are present (indicating glucose fermentation) Used in MR-VP test (the first part of the test) for mixed acid fermentation Phenol Red: starts off red, turns yellow when acids are present (indicating glucose fermentation) Used in Urea broth and in the Fermentation broths 6 VP TEST The VP test is an indirect method of testing for non-acid end products of glucose fermentation. It detects organisms that utilize the butylene glycol pathway and produce acetoin. We cannot test for butylene glycol, but we can test for acetoin. The VP reagents are called Barritts’s A (alpha-naphthol; 18 drops) and Barrett’s B (potassium hydroxide; KOH, 8 drops). These are added to MR-VP broth that has been inoculated with an organism that uses the butylene glycol fermentation pathway, the acetoin end product causes a rust or red color (Gram negatives tend to do this). Therefore, red is a positive result, colorless is negative. Shake gently after adding the reagents, wait 15 minutes, then shake again. (Control: Enterobacter aerogenes = pos; E. coli = neg) NITRATE REDUCTION TEST (control is E. coli) If nitrate (NO3) has an oxygen molecule removed, it has been reduced. The new molecule is nitrite (NO2). Nitrite can also be reduced to nitrogen gas (N2) if it loses oxygen. The reactions look like this: NO3 (nitrate) NO2 (nitrite) N2 (nitrogen gas) If an organism has the enzyme called nitrate reductase, it can reduce nitrate like this: NO3 (nitrate) NO2 (nitrite) Is this enzyme clinically important? Not really. Some of you have brown eyes and some of you do not have brown eyes. It serves as a way of classifying organisms on a flow chart. The nitrate broth we started with contains nutrients plus NO3, and it is clear. If is reduced, the tube is still clear, so how can we tell if NO3 was reduced to NO2? If the organism has nitrate reductase, it will reduce NO3 to NO2 so there will be no more NO3 present , just NO2. First, we add reagent A to the tube. Reagent A will bind to NO2 , forming a complex. However, this complex is clear also, so it does not tell us anything. Then we add Reagent B, which turns the complex a red color. If you add reagents A + B and the tube turns red, the organism has nitrate reductase. However, some organisms with that enzyme reduce NO3 all the way to N2. They take all of the nitrate and reduce it all the way to nitrogen gas, as seen in this equation: NO3 (nitrate) NO2 (nitrite) N2 (nitrogen gas) In this case, there will be no NO3 or NO2 in the tube, so there is nothing for reagent A to react with, and reagent B will not turn the tube red, even though the organism has the nitrate reductase enzyme. Therefore, if you add Reagent A + B, the tube will be clear, yet the organism has the nitrate reductase enzyme. So, although a red color is a positive test, a colorless tube is NOT a negative test. When the tube is colorless, there are two possibilities: 1) The organism does not have nitrate reductase, and there is still NO3 in the tube 2) The organism has nitrate reductase, and there is no NO3 or NO2 in the tube. If a tube is colorless after adding Reagents A + B, we need to test the tube to see if there is NO3 in the tube. We do this by adding a little zinc powder by scooping some on the flat end of a toothpick and adding it to the tube. Zinc will react with NO3 if it is present (reduces any residual nitrate to nitrite) and it will turn red. Zinc is used to confirm a negative test. 7 Reagent A is sulfanilic acid Reagent B is alpha naphthalamine Reagent C is zinc powder A +B Red is positive A +B +C Red is negative DECARBOXYLASE BROTHS (Controls for ornithine: Enterobacter aerogenes = pos; Klebsiella pneumoniae = neg) This tests for the presence of the enzyme decarboxylase. This test is useful for differentiating the Enterobacteriaceae. This enzyme removes and digests the acidic carboxyl group (COOH) from amino acids, plus cleaves off NH3, which will raise the pH. The pH indicator is bromcresal purple. The media is made to start out slightly acidic (pH 6). Bromcresal purple is yellow when acids are present and purple when bases are present. Three tubes are inoculated. Each tube contains glucose plus one amino acid; either lysine, arginine, or ornithine. The carboxylase reaction requires an anaerobic environment, so each tube needs to be covered will a layer of sterile mineral oil to prevent air from reaching the culture. NOTE: PICK THESE TUBES UP FROM THE RACKS ONE AT A TIME AND LABEL THE TUBE BEFORE YOU PICK UP THE NEXT TUBE. THEY ARE ALL THE SAME COLOR AND YOU MIGHT GET THEM MIXED UP! Each decarboxylase enzyme produced by an organism is specific to the amino acid on which it acts. Therefore, we test the ability of organisms to produce arginine decarboxylase, lysine decarboxylase, and ornithine decarboxylase using three different but very similar media. If an organism is able to decarboxylate the amino acid present in the medium, alkaline byproducts are then produced. Ornithine decarboxylation yields putrescine (named after its putrid smell). Lysine decarboxylation results in cadaverine (smells like a cadaver). These byproducts are sufficient to raise the pH of the media so that the broth turns purple (in 48 hours). If you check it in 24 hours, you might see that it is yellow because it fermented the glucose in the medium, but that does not mean it is a negative test. You have to check it in 48 hours to allow the decarboxylase activity to occur. If the pH becomes alkaline because the organism has the decarboxylase enzyme, the media will turn purple in 48 hours (pos). DNASE TEST (Control = Serratus marcescens or Staph aureus) This tests for the presence of the enzyme, DNAse. It contains the indicator dye, Methyl green complexed with DNA. Digestion of DNA releases the dye, so in otherwise green agar, a clear halo formed around the growth indicates a positive test. 8 PHENYLALANINE AGAR SLANT (Control = Proteus vulgaris) We are looking for the enzyme, phenylalanine deaminase, which removes an NH2 group from cysteine to produce pyruvic acid, ammonia, and hydrogen sulfide. When 5 drops of ferric chloride is added to this, it will turn green, indicating a positive test. A negative test stays yellow. Don’t get this mixed up with the SIM media, where ferrous sulfate turns the media black. SIM MEDIA Get one SIM tube and use a needle to stab the media with your organism. Next lab period, we will add 10 drops of Kovac’s reagent to the tube and check for three things on this one tube. 1) H2S (sulfur) PRODUCTION: Certain bacteria produce H2S from the enzyme cysteine desulfurase. When the H2S reacts with ferrous sulfate in the medium, a dark precipitate of iron sulfide is produced and the media will turn black (positive for H2S production). (Control = Proteus vulgaris). Don’t get this mixed up with the phenylalanine test, where the addition of ferric chloride turns the media green. 2) INDOLE PRODUCTION: Tryptophanase breaks tryptophan (an amino acid) down into indole, pyruvic acid, and ammonia. If tryptophnase is present, the indole end product reacts with the reagent we will add next time (10 drops of Kovac’s reagent). If a red ring forms at the top of the tube, it is positive for indole, so the organism makes tryptophanase. (Control = E. coli). 3) Motility: You have already done a motility test, but this media will show you again if your organism is motile. The red dye is not in this media, so visualization is harder. FERMENTATION BROTHS (Control = E. coli is AG) We are looking for fermentation with acid (A) or acid + gas (AG). If there is fermentation, it will be yellow. If there is gas, the inverted miniature tube inside the media will fill with a gas bubble. If there is no fermentation, it is red, so record it as no change (NC) or Alk (protein digestion). The medium has a Durham tube (a miniature tube that is inverted on the inside of the test tube). If gas is produced, it will form a bubble inside the inverted tube. It also has phenol red as an indicator. Phenol red turns yellow if acid is present, and red if bases are present. Inoculate one each of the following tubes: glucose, lactose, mannitol, sucrose, and trehalose. After 24 hours, if the inoculated medium is yellow, it fermented the sugar in that tube. It may or may not have produced gas. Gas is produced during sugar fermentation, so when gas is present, fermentation is present as well, but not all organisms ferment with gas. If it is yellow, record it as (A). If it has gas in the Durham tube (a bubble that take up 10% of the tube, not a little bubble), record it as (AG). If it did not turn yellow (stays red), you have to look at it again in another 24 hours. After 48 hours, if the media is still red, the organism is negative for fermentation of that sugar. These tubes must be read in 24 hours, because in 48 hours, any change in color will revert to the original color. This is what happens: Some organisms that ferment sugars can also digest proteins. When these organisms begin to ferment a sugar, the media becomes acidic (yellow in 24 hours), which enables them to begin digestion of the proteins which are in the media. When proteins are digested, the media becomes 9 alkaline, and the media will turn back to red. If you want to know if it fermented the sugar, you need to read the tube in 24 hours. Suppose a student did not observe their tube right away, and then they see that it is red but it has gas. Since the gas is present, that indicates that it probably fermented the glucose (turned yellow at 24 hours, but he missed it), and then the organism proceeded to digest the protein, turning the media alkaline (back to red again). That would explain why it was red, but has gas (gas is produced during the fermentation process). OXIDATION-FERMENTATION (O-F) TEST FOR GLUCOSE We are looking for the ability to ferment or oxidize glucose. The pH indicator is Bromthymol blue, which is yellow when acid is present. You will STAB two O-F tubes of glucose. One tube will need a layer of sterile oil to create an anaerobic environment so we can check for fermentation. The other tube will not have oil, so we can have an aerobic environment to check for oxidation. Next time, you will see if it turns yellow. If it is yellow, record it as “A “ (acid present). If there is gas in the tube, also record “G”. If there was no change (stayed green), write “NC”. With oil AG NC NC Without oil AG A NC Results Ferments glucose Oxidative neither Control E. coli Pseudomonas aeruginosa Alcaligenes faecalis NOTE: After a person has identified if their organism is Gram positive, the next test is to do a spore stain. If it has no spores, then you need to do an Acid Fast stain to see if it is Mycobacteria. After a person has identified if their organism is Gram negative, the next test to do is to use a thioglycollate broth to determine oxygen requirements. NOTE: Be able to match enzymes to their tests, substrates, reagents, and controls. You should make a table to study from. In one column, put the name of the test. In the other columns, put the substrates, products, enzymes, reagents, etc., and what a positive and negative result would look like. END OF MATERIAL FOR IDENTIFICATION OF UNKNOWN BACTERIUM 10