Diagnostic Microbiology Lecture Notes PDF

# Diagnostic Microbiology ## For Fourth Level Applied and Analytical Microbiology Students **Prepared By:** Dr. Shimaa Ahmed Gouda **Lecture 1** (2024) ## Diagnostic Microbiology Diagnostic microbiology has been developing to rapidly detect and accurately identify implicated microorganisms in...

# Diagnostic Microbiology ## For Fourth Level Applied and Analytical Microbiology Students **Prepared By:** Dr. Shimaa Ahmed Gouda **Lecture 1** (2024) ## Diagnostic Microbiology Diagnostic microbiology has been developing to rapidly detect and accurately identify implicated microorganisms in test specimens through a variety of techniques. The field of diagnostic microbiology determines whether suspected pathogenic microorganisms are present in test specimens collected from human beings, animals, and environment, and if they are present, identifies them. ### 1. Collection of specimens for microbiological investigations #### A-Clinical samples First and foremost is the diagnosis of disease process and treatment of it. Hence care should be taken during collection of the specimens at bed sides. The following general rules must be observed while collecting a clinical sample. * **The specimens should be from the suspected infective condition.** * **Sterile swabs and sterile containers should be used to avoid contamination.** * **The sample should be in sufficient quantity to permit a thorough study.** * **The specimens should be clearly labelled with patient's name, date of collection, time of collection and hospital number. This sample should be always accompanied by complete laboratory.** #### ❖Tools used in collecting different specimen * Swabs * Syringe and needle * Sterile tubes, jars, bottles and petridishes * Surgical blade * Sterile tweezers * Anaerobic transport tube or vial * Fecal transport systems ### Clinical specimen collection and transport #### ➤ Clinical specimen types: 1. **Blood for culture** The following apparatus are required, sterile syringe, gauge, antiseptic solution to clean the skin, spirit lamp and media for the culture of different organisms. * **General precautions while collecting blood.** The skin should be cleaned properly with antiseptics. The site is allowed to dry, and blood should be collected then the samples of blood should be sent to the laboratory immediately. 2. **Urine** Urine should be collected in sterile wide mouth containers. * **In females:** Midstream urine sample should be collected after cleaning the external genitalia with soap and water. In some occasions catheterization should be done, but always avoid catheterization since there is a chance of introducing microorganisms in to the bladder. * **In males:** The glans is cleaned with soap and water and midstream urine should be collected. * **Urine specimens should be brought to the laboratory immediately within one hour. If that is not possible, they should be kept in the refrigerator for not more than 24 hours' time.** 3. **Stool samples and rectal swabs** Stool samples should be collected in sterile containers and immediately sent to the laboratory. Rectal swab is performed by inserting a cotton swab in the rectum not anus. 4. **Throat swab** This is a sterile swab fitted to a wooden stick kept inside sterile test tube; outside fitted with a cotton plug. The swab stick should be removed from the tube. Swab the back of the throat: without touching the other parts of the mouth. Replace the swab in the tube. 5. **Swabs from mouth and vagina** The swabs are taken from the mucosal surfaces and placed in a sterile test tube and sent to the laboratory. 6. **Skin scrapings** The affected area is swabbed with sterile gauze soaked in 70% alcohol and allowed to dry. The lesion is scrapped with a sterile surgical blade at the edge of the lesion. These scraps should be kept inside a sterile petridish or a sterile paper packet. 7. **Hairs** The unhealthy hairs present at the site of lesion should be plucked with sterile tweezers and kept in a sterile petridish and sent to the laboratory. 8. **Nail** A piece of the affected nail and the scrapings from the under surface of nails are sent to the laboratory. 9. **Other samples** The samples of spinal fluid, sputum, exudate from the draining sinuses and abscesses, sternal marrow can be collected by sterile syringe and needed by aspiration, scrapings from the edges of ulcers and abscesses are placed in sterile vials, sterile screw capped bottles. 10. **Biopsy specimens collected and sent in sterile containers to the laboratory.** #### ➤ Transport of specimens * **Prompt transport of specimens to the laboratory is required to preserve the viability of fastidious microorganisms, prevent overgrowth of fastidious microorganisms by more rapidly growing ones, and prevent multiplication of clinically insignificant numbers of microorganisms that are erroneously interpreted as being clinically significant.** * **Specimens should be transported in sterile, leakproof containers to prevent loss of sample, prevent extrinsic contamination, and avoid exposure of others to potentially hazardous materials.** * **The specimens for virus isolation should be collected in a transport medium and should be sent immediately, preferably kept in chilled packet in ice to the laboratory. For serological tests of certain viruses, specimens should not be frozen but should reach the laboratory within 24 hours of collection.** * **Specimens for anaerobic culture (pus, blood, urine and prostatic fluid) should be collected, and sent to laboratory in commercially prepared vials contain an atmosphere of oxygen-free gas and a small volume of transport medium with an indicator that remains colorless under anaerobic conditions. A few vials from each lot should be vented to ensure coloration of the indicator upon exposure to air.** ### B. Plant and soil specimens Plant and soil sampling can either be done for diagnostic (problem/diseased) or predictive (routine) purposes. Proper sampling is critical as it will affect the results and therefore the decisions made. #### a. Plant The accurate diagnosis of specific plant diseases depends upon several factors. * The specimen must arrive at the laboratory in a fresh condition. * Samples place in appropriate bags: leaf tissue in plastic bags with a moist paper towel to keep cool, moist, and protected from crushing, freezing and heat. * The root system must be placed in a separate plastic bag to avoid contamination of the leaves with soil. * A leaf sample should be large enough to give a good indication of the problem: approximately 10 to 20 leaves. * Label the sample with the pertinent information required. 1. Name of grower 2. Date of collection 3. Variety 4. Statement of problem 5. The history of cultural or chemical practices #### b. Soil Whenever possible, collect soil from the root zone (10-15 cm depth) of growing plants, where disease spores will be concentrated, and include some root matter. The general sampling patterns are as shown below; x=sampling position. * **Left:** Star pattern for sampling from a damaged area. * **Center:** circle pattern for sampling a shrub in an orchard. * **Right:** Zig-zag pattern for sampling a fallow field or one with no obvious disease symptoms. The image shows three diagrams of soil sampling patterns. * Left: A star pattern with 5 "x" markings inside the star. * Center: A circle with "x" markings on the perimeter. * Right: A rectangle divided by 4 "x" markings in a checkered pattern. The caption at the bottom of the images read: "Sampling patterns".