10. MICROBIOLOGICAL ANALYSIS 10.1 Characteristics of indicator organisms To assure a safe water supply, it is critical to monitor for the presence of possibile pathogens. However, it would be expensive and time consuming to check the water supply for all of them, instead, an indicator organism is used to assay for fecal contamination. The detection of indicator bacteria is preferred over direct pathogen detection because the former are considered to be normal, non-pathogenic intestinal inhabitants that are present in feces and wastewater in much higher numbers than pathogenic microorganisms and because they are technically easier to detect and quantitate than pathogens. Present standards for the sanitary quality of water, foods and other materials, with respect to fecal contamination, are expressed in terms of concentrations of indicator bacteria. Indicator organisms must have four properties to be useful for water analysis: - the only natural environment of the microbe should be in association with feces and it should always be present. - it should not grow outside of its natural environment. - the bacterium should survive longer than the most viable pathogen, but not so long so that historical events are detected. - it should be easy to detect. Coliforms come closest to fulfilling all these criteria and are the standard indicator organisms used to test for the biological pollution of water. The word "coliform" has been used to describe various genera of the family Enterobacteriaceae that ferment lactose. Total coliforms are operationally defined as "all facultative anaerobic, gram-negative, nonspore-forming, rod-shaped bacteria that ferment lactose with gas formation within 48 hr. at 35oC." The fecal coliform group are considered to be a more specific indicator of fecal contamination because the total coliform group probably includes more bacteria of nonfecal origin. The basis for this separation is a higher incubation temperature of 44.5OC, at which presumably coliforms of only fecal origin will grow. Coliforms from non-fecal, environmental sources are generally incapable of growing at this elevated temperature. Thus, fecal coliforms can be defined as gram-negative, non-sporeforming, rod-shaped bacteria which ferment lactose with the production of gas at 44.5oC within 24 hours. Or, using the newer chromogenic substrate media, the fecal coliforms would hydrolyze ONPG (o-nitrophenyl-beta-D-galactoside) at 44.5oC within a specified time (24-28 hours). The fecal coliform test is applicable to investigations of surface and ground water pollution, sewage treatment systems and general monitoring of natural waters for sanitary quality, including recreational and shellfish waters. It is also used in addition to the coliform test in the examination of potable waters. In recent years a new approach to detecting total and fecal coliform bacteria has become widely used that is not based directly on lactose fermentation but instead is based on detecting the expression of beta-galactosidase activity. The expression of this enzymatic activity is detected by the ability of the bacteria to hydrolyze and utilize a chromogenic substrate rather than lactose. This substrate is o-nitrophenyl-beta-Dgalactoside (ONPG). When the coliform bacteria hydrolyze ONPG, o-nitrophenyl is released, which imparts a yellow color to the originally colorless medium, thereby demonstrating the presence of coliform bacteria. So, the definition of coliforms is now broadened to include any bacterium that hydrolyzes ONPG in a selective culture medium under defined growth conditions of incubation temperature (35 oC) and time (24-28 hours). Most recently, there is increased interest in detecting E. coli exclusively as the lactosefermenting "coliform" that invariably indicates fecal contamination. An early approach to this effort was the use of four biochemical tests (called the IMViC tests) to separate E. coli from other lactose-fermenting Enterobacteriaceae:. It was later shown that this approach is not very reliable, and alternative methods were developed: - Indole test - detects indole production from tryptophane. E. coli is positive (+); many other coliforms are negative. - Methyl Red test - detects acid production in the medium; intended to distinguish between type of fermentation (mixed acid versus butylene glycol). E. coli is (+) and some other coliforms are (-). - Voges-Proskauer test - detects acetoin, an intermediate in the butylene glycol pathway. Acetoin is oxidized to diacetyl under alkaline conditions in the presence of air, and when reacted with creatine, it forms a pink color. E. coli is (-) and some other coliforms are (+). - Citrate utilization as sole carbon source. E. coli is (-) and many other coliforms are (+). Standards for clean, safe water vary, depending upon the waters intended use. Drinking water and the water in swimming pools must be of the highest purity. There can be no more than one positive sample (>1 coliform/100 ml) in 40 samples tested in a month and the concentration of fecal coliforms must be zero. Another usefull measure is heterotrophic plate count. It includes all of the microorganisms that are capable of growing in or on a nutrient-rich solid agar medium. Two incubation temperatures and times are used: 37 °C for 24 hours to encourage the growth of bacteria of mammalian origin, and 22 °C for 72 hours to enumerate bacteria. The main purpose of colony counts is in comparing the results of repeated samples from the same source. If number of colonies increase substantially for the short time, there may be cause for concern. 10.2 Selecting a bacteriological analytical technique Two specific methods was developed and standardized for microbiological assesment of water. The first is Multiple Fermentation Tube Technique (also known as Most Probable Number Technique). In this method measured portions of a water sample are placed in test-tubes containing a culture medium, and then are incubated for a standard time at a standard temperature. The second technique is Membrane Filter Technique. A measured volume of sample is passed through a fine filter that retains bacteria. The filter is then placed on culture medium and incubated. 10.3 Multiple fermentation tube technique The multiple tube coliform test has been a standard method for determining coliform group bacteria since 1936. It involves adding the water sample to a set of tubes, each of which contains either lactose broth or lauryl tryptose broth and an inverted tube. The tubes are then incubated at 35 ± 0.5º C for 24 to 48 hours (fecal coliforms are incubated in a water bath at 44.5 ± 0.2º C). If gas production is observed in an inverted tube after incubation, the sample contains total coliforms. The multiple-tube fermentation technique is applicable to the analysis of fresh, salt, or brackish waters as well as muds, sediments, and sludges. When multiple tubes are used in the fermentation technique, results of the examination of replicate tubes and dilutions are reported in terms of the Most Probable Number (MPN) of organisms present. This number, based on certain probability formulas, is an estimate of the mean density of of coliforms in the sample. Coliform density provides the best assessment of water treatment effectiveness and the sanitary quality of untreated water. The precision of each test depends on the number of tubes used. The most satisfactory information will be obtained when the largest sample inoculum shows no gas in all or a majority of the tubes. Bacterial density can be estimated by the formula given or from the table using the number of positive tubes in multiple dilutions. The number of sample portions selected will be governed by the desired precision of the result. MPN tables are based on the assumption of a Poisson distribution (random dispersion). However, if the sample is not adequately shaken before the portions are removed or if clumping of bacterial cells occurs, the MPN value will be an underestimate of the actual bacterial density. Presumptive Phase: Use lauryl tryptose broth in the presumptive portion of the multiple-tube test. a. Reagents and culture medium: Add dehydrated products to water, mix thoroughly, and heat to dissolve. pH should be 6.8 +/- 0.2 after sterilization. Before sterilization, dispense sufficient medium, in fermentation tubes with an inverted vial, to cover inverted vial at least one-half to two-thirds after sterilization. Alternatively, omit inverted vial and add 0.01 g/L bromcresol purple to presumptive medium to determine acid production, the indicator of a positive result in this part of the coliform test. Close tubes with metal or heatresistant plastic caps. b. Procedure: 1.Arrange the fermentation tubes in rows of five tubes each in a test tube rack. The number of five-tube rows and the sample volumes selected depend upon the quality and character of the water to be examined. For potable water use five 20-mL portions, ten 10mL portions, or a single bottle of 100 mL portion; for nonpotable water use five tubes per dilution (of 10, 1, 0.1 mL, etc.). Shake sample and dilutions vigorously about 25 times. Inoculate each tube in a set of five with replicate sample volumes (in increasing decimal dilutions, if decimal quantities of the sample are used). Mix test portions in the medium by gentle agitation. 2. Incubate inoculated tubes or bottles at 35 +/- 0.5oC. After 24 +/- 2h swirl each tube or bottle gently and examine it for heavy growth, gas, and acidic reaction (shades of yellow color) and, if no gas or acidic growth has formed, reincubated and reexamine at the end of 48 +/- 3h. Record Presence or absence of heavy growth, gas, and acid production. If the inner vial is ommited, growth with acidity signifies a positive presuptive reaction. c. Interpretation: Production of gas or acidic growth in the tubes or bottles within 48 +/- 3h constitutes a positive presumptive reaction. Submit tubes with a positive presumptive reaction to the confirmed phase. The absence of acidic growth or gas formation at the end of 48 +/- 3h of incubation constitutes a negative test. An arbitrary 48-h limit for observation doubtless excludes occasional members of the coliform group that grow very slowly. Confirmed Phase a. Culture Medium: Use brilliant green lactose bile broth fermentation tubes for the confirmed phase. Add dehydrated ingredients to water, mix thoroughly, and heat to dissolve. pH should be 7.2 +/- 0.2 after sterilization. Before sterilization, dispense, in fermentation tubes with an inverted vial, sufficient medium to cover inverted vial at least one-half to two-thirds after sterilization. Close tubes with metal or heat-resistant plastic caps. b. Procedure: Submit all primary tubes or bottles showing heavy growth, any amount of gas, or acidic growth within 24h of incubation to the confirmed phase. If active fermentation or acidic growth appears in the primary tube earlier than 24h, transfer to the confirmatory medium, preferably without waiting for the full 24h period to elapse. If additional primary tubes or bottles show active fermentation or acidic growth at the end of a 48h incubation period, submit these to the confirmed phase. Gently shake or rotate primary tubes or bottles showing gas or acidic growth to resuspend the organisms. With a sterile metal loop 3 mm in diameter, transfer one loopful of culture to a fermentation tube containing brilliant green lactose bile broth. Remove and discard applicator. Repeat for all other positive presumptive tubes. Incubate the inoculated brilliant green lactose bile broth tube for 48 +/- 3 h at 35 +/- 0.5oC. Formation of gas in any amount in the inverted vial of the brilliant green lactose bile broth fermentation tube at any time within 48 +/- 3 h constitutes a positive confirmed phase. Calculate the MPN value from the number of positive brilliant green lactose bile tubes. c. Alternative procedure: Use this alternative only for polluted water or wastewater known to produce results consistently. If all presumptive tubes are positive in two or more consecutive dilutions within 24 h, submit to the confirmed phase only the tubes of the highest dilution (smallest sample inoculum) in which all tubes are positive and any positive tubes in still higher dilutions. Submit to the confirmed phase all tubes in which gas or acidic growth is produced only after 48 h Completed Phase To establish the presence of coliform bacteria and to provide quality control data, use the completed test on at least 10% of positive confirmed tubes. Double confirmation into brilliant green lactose bile broth for total coliforms and EC broth for fecal coliforms may be used. Consider positive EC broth elevated temperature (44.5oC) results as a positive completed test response. Parallel positive brilliant green lactose bile broth culture with negative EC broth cultures indicate the presence of nonfecal coliforms and must be submitted to the completed test procedures to validate the presence of coliforms. a. Culture media and reagents: Add ingredients to water, mix thoroughly, and heat to dissolve. pH should be 6.8 +/- 0.2 after sterilization. Before sterilization, dispense in screwcapped tubes. After sterilization, immediately place tubes in an inclined position so that the agar will solidify with a sloped surface. Tighten screw caps after cooling and store in a protected, cool storage area. b. Procedure: 1. Using aseptic technique, streak one LES Endo agar or MacConkey agar plate from each tube of brilliant green lactose bile broth showing gas, as soon as possible after the observation of gas. Streak plates in a manner to insure presence of some discrete colonies separated by at least 0.5 cm. Observe the following precautions when streaking plates to obtain a high proportion of successful isolations if coliform organisms are present: (a) Use a sterile 3-mm-diam loop or an inoculating needle slightly curved at the tip; (b) tap and incline the fermentation tube to avoid picking up any membrane or scum on the needle; (c) insert end of loop or needle into the liquid in the tube to a depth of approximately 0.5cm; and (d) streak plate for isolation with curved section of the needle in contact with the agar to avoid a scratched or torn surface. Flame the loop between second and third quadrants to improve colony isolation. Incubate plates (inverted) at 35 +/- 0.5oC for 24 +/- 2h. 2. The colonies developing on LES Endo agar are defined as typical ( pink to dark red with a green metallic surface sheen); atypical (pink, red, white, or colorless colonies without sheen) after 24 h incubation; or negative (all others). Typical lactose-fermenting colonies developing on MacConkey agar are red and may be surrounded by an opaque zone of precipitated bile. From each plate pick one or more typical, well-isolated coliform colonies or, if no typical colonies are present, pick two or more colonies considered most likely to consist of organisms of the coliform group, and transfer growth from each isolate to a single-strength lauryl tryptose broth fermentation tube and onto a nutrient agar slant. (The latter is unnecessary for drinking water samples.) Estimation of Bacterial Density a. Precision of Fermentation Tube Test: Unless a large number of sample portions is examined, the precision of the fermentation tube test is rather low. For example, even when the sample contains 1 coliform organism/mL, about 37% of 1-mL tubes may be expected to yield negative results because of random distribution of the bacteria in the sample. When five tubes, each with 1 mL sample, are used under these conditions, a completely negative result may be expected less than 1% of the time. Even when five fermentation tubes are used, the precision of the results obtained is not of a high order. Consequently, exercise great caution when interpreting the sanitary significance of coliform results obtained from the use of a few tubes with each sample dilution, especially when the number of samples from a given sampling point is limited. b. Computing and Recording of MPN: To calculate coliform density, compute in terms of the Most Probable Number. The MPN values are given in Table 1 (as an example). Included in this table is the 95% confidence limits for each MPN value determined. If the sample volumes used are those found in the tables, report the value corresponding to the number of positive and negative results in the series as the MPN/100 mL or report as total or fecal coliform presence or absence. When the series of decimal dilutions is different from that in the table, select the MPN value from the table for the combination of positive tubes and calculate according to the following formula: MPN value(from table) x (10/largest volume tested) = MPN/100mL 95% Confidence # of tubes giving positive reaction MPN Index/100mL Limits (approximate) out of 10 of 10mL each Lower Upper 0 less than 1.1 0 3.0 1 1.1 0.03 5.9 2 2.2 0.26 8.1 3 3.6 0.69 10.6 4 5.1 1.3 13.4 5 6.9 2.1 16.8 6 9.2 3.1 21.1 7 12.0 4.3 27.1 8 16.1 5.9 36.8 9 23.0 8.1 59.5 10 greater than 23.0 13.5 infinite When more than three dilutions are used in a decimal series of dilutions, use the results from only three of these in computing the MPN. To select the three dilutions to be used in determining the MPN index, choose the highest dilution that gives positive results in all five portions tested (no lower dilution giving any negative results) and the two next succeeding higher dilutions. Use the results at these three volumes in computing the MPN index. In the examples given below, the significant dilution results are shown in boldface. The number in the numerator represents positive tubes; that in the denominator, the total tubes planted; the combination of positives simply represents the total number of positive tubes per dilution: Example 1 mL 0.1 mL 0.01 mL 0.001 mL Combination positives of MPN mL a 5/5 5/5 2/5 0/5 5-2-0 5000 b 5/5 4/5 2/5 0/5 5-4-2 2200 c 0/5 1/5 0/5 0/5 0-1-0 20 index/100 In c, select the first three dilutions so as to include the positive result in the middle dilution. 10.4. Membrane filter technique The Membrane Filter (MF) Technique was introduced in the late 1950’s as an alternative to the Most Probable Number (MPN) procedure for microbiological analysis of water samples. The MF Technique offers the advantage of isolating discrete colonies of bacteria, whereas the MPN procedure only indicates the presence or absence of an approximate number or organisms (indicated by turbidity in test tubes). The MF Technique is also used for microbial monitoring in the pharmaceutical, cosmetics, electronics, and food and beverage industries. The MF Technique is used in these industrial labs to monitor the presence of microorganisms in process waters and final product. In the Membrane Filter (MF) Technique, a vacuum pulls 100 mL of water sample through a 47 mm membrane filter held in place by a filter-holding device. Total coliform and other bacteria are retained on the filter. The filter is then placed on a special medium which allows the growth of total coliform and incubated at 35 ± 0.5º C for 22 to 24 hours. If a total coliform-like colony is observed on the membrane, the lab should make sure that it is a total coliform by using another test. The MF Technique provides presence or absence information within 24 hours. Advantages of the MF Technique • • • • • • • Permits testing of large sample volumes. Reduces preparation time as compared to many traditional methods. Allows isolation and enumeration of discrete colonies of bacteria. Provides presence or absence information within 24 hours. Effective and acceptable technique. Used to monitor drinking water in government laboratories. Useful for bacterial monitoring in the pharmaceutical, cosmetics, electronics, and food and beverage industries. Allows for removal of bacteriostatic or cidal agents that would not be removed in Pour Plate, Spread Plate, or MPN techniques. The technique is unsuitable for natural waters containing very high levels of suspended material, sludges and sediments, all of which could block the filter before an adequate volume of water has passed through. When small quantities of sample (for example, of sewage effluent or of grossly polluted surface water) are to be tested, it is necessary to dilute a portion of the sample in sterile diluent to ensure that there is sufficient volume to filter across the entire surface of the membrane. Procedure 1. Add absorbent pads to sterile Petri dishes for the number of samples to be processed. Sterile pads may be placed in the Petri dishes with sterile forceps or with an automatic dispenser. 2. Soak the pads with nutrient medium. Nutrient medium may be dispensed with a sterile pipette or by carefully pouring from an ampoule or bottle. In all cases, a slight excess of medium should be added (e.g. about 2.5 ml). Immediately before processing a sample, drain off most of the excess medium, but always ensure that a slight excess remains to prevent the pad drying during incubation. Note: Absorbent pads soaked in liquid medium may be replaced by medium solidified by agar. In this case, Petri dishes should be prepared in advance and stored in a refrigerator. 3. Sterilise the tips of the blunt-ended forceps in a flame and allow them to cool. 4. Carefully remove a sterile membrane filter from its package, holding it only by its edge. 5. Place the membrane filter in the filter apparatus, and clamp it in place. If the apparatus has been disinfected by boiling, ensure that it has cooled down before inserting the membrane filter. 6. Mix the sample by inverting its container several times. Pour or pipette the desired volume of sample into the filter funnel. This volume should normally be chosen in the light of previous experience. If the volume to be filtered is less than 10 ml, it should be made up to at least 10 ml with sterile diluent so that the sample will be distributed evenly across the filter during filtration. 7. Apply a vacuum to the suction flask and draw the sample through the filter; disconnect vacuum. 8. Dismantle the filtration apparatus and remove the membrane filter using the sterile forceps, taking care to touch only the edge of the filter. 9. Remove the lid of a previously prepared Petri dish and place the membrane, grid side uppermost, onto the pad (or agar). Lower the membrane, starting at one edge in order to avoid trapping air bubbles. 10. Replace the lid of the Petri dish and mark it with the sample number or other identification. The sample volume should also be recorded. Use a wax pencil or waterproof pen when writing on Petri dishes. 11. If membranes are going to be incubated at 44 or 44.5 °C, the bacteria on them may first require time to acclimatise to the nutrient medium. After processing samples from areas of temperate climate, leave each Petri dish at environmental temperature for 2 hours before placing it in the incubator. Samples from areas of tropical climate may be incubated immediately. 12. Maintain the Petri dish in a humid atmosphere (e.g. in a plastic bag or in a small container with a moist pad in the base) and incubate it either in an incubator or in a weighed canister in a water bath. This ensures that the pad does not dry out during the incubation period. 13. The incubation periods and temperatures required for each culture medium are listed in Table 1. Characteristics of total coliform and thermotolerant coliform colonies grown on the various culture media are described in Table 2. 14. After incubation, count the colonies. Express the results as number of colonies per 100 ml of sample. Where smaller volumes have been used, results are calculated from the following formula: No. of colonies per 100 ml = [(No. of colonies)/(volume filtered)] × 100. The colonies counted at this stage are presumed to be coliform bacteria (presumptive results). Table 1. Culture media for membrane filtration Medium Uses Lactose TTC agar with Tergitol 7 Total or thermotolera nt coliforms Lactose agar with Tergitol 7 Total or thermotolera nt coliforms Membrane enrichment with Teepol broth Total or thermotolera nt coliforms Membrane lauryl sulphate broth Total or thermotolera nt coliforms Endo medium Total coliforms only LES Endo medium Total coliforms only Incubation temperature 18-24 hours at 35 ± 0.5°C or 37 ± 0.5°C for total coliforms and 1824hours at 44 ± 0.25°C or 44.5 ± 0.25°C for thermotolerant coliforms Remarks Adjust pH before sterilisation. Filter TTC supplement to sterilise. Tergitol supplement sterilised by autoclaving. Supplements of Tergitol and TTC to be added aseptically. Prepared plates have max. shelf-life of 10 days. Store in dark. 18-24 hours at 35 ± Prepared plates have max. 0.5°C or 37 ± 0.5°C for shelf-life of 10 days. Store prepared plates at 4°C. total coliforms and 1824hours at 44 ± 0.25°C or 44.5 ± 0.25°C for thermotolerant coliforms pH before 18-24 hours at 35 ± Check 0.5°C or 37 ± 0.5°C for sterilisation total coliforms and 1824hours at 44 ± 0.25°C or 44.5 ± 0.25°C for thermotolerant coliforms pH before 18-24 hours at 35 ± Check 0.5°C or 37 ± 0.5°C for sterilisation total coliforms and 1824hours at 44 ± 0.25°C or 44.5 ± 0.25°C for thermotolerant coliforms 35-37 °C Basic fuchsin may be a carcinogen. Also requires ethanol. Do not autoclave. Prepared medium has a shelf-life of 4 days. Store prepared medium at 4 °C in the dark. 35-37 °C Basic fuchsin may be a carcinogen. Also requires ethanol. Do not autoclave. Prepared medium has a shelf-life of 2 days. Store prepared medium at 4 °C in the dark. MFC Thermotoler ant coliforms 44 °C Do not autoclave. Discard unused medium after 96 hours. Rosalic acid stock solution has a maximum shelflife of 2 weeks. Check pH before sterilisation. Store prepared medium at 2-10 °C. Table 2. Colony characteristics following analysis by the membrane filtration method Medium Lactose TTC agar with Tergitol 7 Lactose agar with Tergitol 7 Membrane enriched Teepol broth Membrane lauryl sulphate broth Endo agar or broth LES Endo agar MFC medium Total coliforms at 35 or 37 °C Thermotolerant coliforms at 44 or 44.5 °C Yellow, orange or brick red Same as total coliforms coloration with yellow central at halo in the medium under the 35 or 37 °C membrane Yellow central halo in the Same as total coliforms medium under the Membrane at 35 or 37 °C Yellow colour extending on to Same as total coliforms the membrane at 35 or 37 °C Yellow colour extending on to Same as total coliforms the membrane at 35 or 37 °C Dark red colour with golden- (not applicable) green metallic sheen Dark red colour with golden- (not applicable) green metallic sheen (not applicable) Blue colonies Confirmatory tests For the examination of raw or partly treated waters, presumptive results may be adequate but, in certain other circumstances, it is important to carry out confirmatory tests on pure subcultures. To confirm the membrane results for total coliforms, each colony (or a representative number of colonies) is subcultured to tubes of lactose peptone water and incubated at 35 or 37 °C for 48 hours. Gas production within this period confirms the presence of total coliforms. To confirm thermotolerant coliforms and E. coli on membranes, whether incubated at 35, 37 or 44 °C, each colony (or a representative number of colonies) is subcultured to a tube of lactose peptone water and a tube of tryptone water. Tubes are incubated at 44 °C for 24 hours. Growth with the production of gas in the lactose peptone water confirms the presence of thermotolerant coliforms. Confirmation of E. coli requires the addition of 0.20.3 ml of Kovac’s reagent to each tryptone water culture. Production of a red colour indicates the synthesis of indole from tryptophan and confirms the presence of E. coli. 10.5 Quality assurance Quality assurance encompass a number of principles and cautions which ensure continuous quality and reproducibility of results. Analytical quality control that apply to microbiological laboratories comprises the preparation and control of laboratory consumables (media and dilution solutions, membrane filters and pads, plasticand glassware), and also a proper laboratory techniques and manuveurs. Special concern is given to monitoring of laboratory equipment. Incubators, refrigerators and freezers should be cleaned at least once a month. The manufacturers’ instructions should include advice on cleaning and may recommend suitable detergents and disinfectants. Water-baths may need more frequent cleaning to control bacterial growth. One should allways keep in his mind that some detergents and other agents used for the cleaning of laboratory glassware may influenced the growth of bacteria and interfere final results of analyses. Samples of glassware should be microbiologicaly examined regularly, for example once a month, if washing procedures and products are always the same. If procedures change, however, or new products are introduced, additional checks should be made. Laboratory plastics may also contain inhibitory residues and each new batch of plasticware should be checked.
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