Specimen Transport Guidelines Quiz

Microbiology Lecture (L03)

• Principles and Methods of Diagnosis Clinical Sampling
  • Cradle-to-Grave Principles: covers the entire process of clinical sampling from ordering to reporting
  • Ordering: Initiates the process
  • Collection/Sampling: Collection of sample from the patient.
  • Transportation/Storage: Safe and appropriate transportation and storage of the collected sample.
  • Specimen Processing: Analyze the collected specimen in the lab.
  • Diagnosis: Determine the cause of disease using lab results.
  • Treatment: Treatment based on the diagnosis
  • Result Interpretation: Interpreting lab results
  • Reporting: Provide results to the relevant people/offices.
  • Disposal of Specimen: Proper disposal of the specimen.

Good Quality Clinical Specimen Collection/Sampling Principles (1)

• Compliance with Statutory Requirements, Standard Operating Procedures (SOPs), & Professional Standards
• American Society for Microbiology recommendations and guidelines
• Clinical & Laboratory Standards Institute recommendations and guidelines
• WHO (World Health Organization) guidelines
• Quality Assurance-critical to ensure the reliability of the collected samples.
  • Includes methods, requirements and procedures for sample collection, including line draws, blood cultures, and venipuncture in children.
• Guide to Requests for Laboratory Testing: Provides information for collecting correct samples based on testing required for the samples.

Good Quality Clinical Specimen Collection/Sampling Principles (5)

• Awareness of the Usage of RIGHT Clinical Specimen Containers
• Stool Collection Cup with Small Spoon: Use of collection cup for stool samples
• Midstream Urine (MS) container with boric acid: Using appropriate container for urine samples needing preservation
• Blood Sampling Holder + Winged Needle: For blood samples
• Vacuum Blood Collection Tubes: For various blood types
• Specimen containers should be used appropriately for their intended purposes
• Detailed procedures for collection of correct samples

Good Quality Clinical Specimen Collection/Sampling Principles (7) – Safe Transportation of Collected Specimen Principles

• Compliance to Requirements – Local Laboratory, international standards
• Emergency Spill Kit: Requirements for emergency spills
• Transport container with Biohazard Label: Ensuring secure transport
• Vertical placement of containers when carrying samples
• Temperature regulations for transport of clinical specimens

Specimen Transportation - Temperature Requirement

• Specimens should be transported to the laboratory as soon as possible • Ideally, within the same day after collection.
• If delay is unavoidable, specimens should be refrigerated at 4°C, except for certain types requiring room temperature
• Specific temperature requirements for different specimens (e.g., blood, CSF)

Microbiological Tests Used In The Diagnosis Of Tuberculosis (TB)

• Sputum for acid-fast bacilli (AFB) direct smear and culture examination
• Mycobacterial culture (6-8 weeks)
• Other possible clinical samples include gastric washings, bronchial aspirate, pleural fluid, biopsy specimens of the lung, or non-respiratory specimens, such as early morning urine (EMU), lymph node aspirate, pericardial fluid, cerebrospinal fluid, and joint fluid.

Specimen Collection - Catheter

• Catheter Specimen Urine (CSU): from Catheter Sampling Port.
• After Catheter Insertion
• Collect Urine from Urine Bag
• Use alcohol swabs to disinfect the sampling port and the urine bag outlet for sterilization.

Specimen Collection - Midstream Urine

• Midstream Urine (MSU): Urine For Culture & Sensitivity Tests
  • A test to identify the presence of bacterial and fungal (yeast) infections, which may lead to urinary tract infections(UTI) in adults
  • Before procedure, perform hand hygiene
  • Clean urethral opening and genital area.
  • Pass the first portion of the urine into the toilet and collect midstream urine into the MSU specimen container to one-half full.
  • Seal, label, and deliver to clinical lab immediately, store at 4-8°C if not delivered immediately.

First Catch/ Void Urine / Clean Catch Urine

• Clean urethral opening and genital area with a wet tissue.
• Collect first catch urine into the specimen container without preservatives.
• Seal, label, and send to the Clinical Laboratory immediately if possible, otherwise store in a cool place

Skin Disinfection For Sterile Sites

• Various Skin disinfectants are available to apply, with the duration of application varying depending on the chosen disinfectant

Identifying Microbes By Staining

• Gram Stain
• Ziehl-Neelsen Stain

Identifying Microbes By Microscopy

• Microscopes are used to examine microscopic appearance of microbes to assist in identifying specific samples

Microbiological Culture

• Used to identify microbes by growing/culturing microbes for visual inspection

Blood Culture Medium

• Blood culture: blood sample submitted for culture of microorganisms
• enables the recovery of potential pathogens from patients suspected of having bacteremia or fungemia
• Various types of tubes, including aerobic and anaerobic tubes

Blood Culture Videos

• Video links are provided

Genotypic Methods

• Examination of genetic material (DNA/RNA)
• Frequently used to identify microorganisms when culturing bacteria is unnecessary or impractical

DNA & RNA

• Deoxyribonucleic Acid (DNA)
• Ribonucleic acid (RNA)
• Nucleic acids- Two main types, Ribonucleic acid (RNA) and Deoxyribonucleic Acid (DNA)

DNA/RNA Components

• Nucleosides: A nitrogenous base and a five-carbon sugar (ribose or deoxyribose)
• Nucleotides: A nitrogenous base, a five-carbon sugar, and one or more phosphate groups

What is Deoxyribonucleic Acid (DNA)?

• Deoxyribonucleic Acid (DNA) is a molecule that stores genetic information needed for an organism's development and function
• DNA consists of two linked strands that are arranged in a double helix
• Each strand has a backbone comprised of repeating sugar (deoxyribose) and phosphate groups

What is Ribonucleic acid (RNA)?

• Ribonucleic acid (RNA) is a nucleic acid that is present in all living cells and has similar structure to DNA
• RNA is predominately single-stranded.

DNA vs RNA

• Key differences between DNA & RNA molecules
• RNA differs from DNA both chemically (use of ribose instead of deoxyribose, and use of uracil instead of thymine) and structurally

Commonly Used Genotypic Tests

• Polymerase Chain Reaction (PCR)
• Real-Time PCR

Polymerase Chain Reaction (PCR)

• PCR is a method used to rapidly produce numerous and identical copies of DNA or RNA molecules
• The method can potentially amplify even minute quantities of nucleic acids within a sample to identify specific DNA sequences

What Real-Time PCR?

• Video link provided
• Uses fluorescent labeling

Real-Time PCR and Ct value (cycle threshold)

• Ct measures the number of cycles needed to replicate DNA/RNA until it can be detected
• Lower value of Ct suggests a higher concentration of DNA/RNA initially

Significance of Ct value

• Ct < 35: Confident positive results
• Ct > 35: Might be false positive results

Immunological Test: Antigen - Antibody Reaction

• Antibodies bind to antigens
• A method used to determine the amount of a particular antibody or antigen in a sample
• Antibodies are types of proteins in the immune system
• Antibodies also called immunoglobulins (Ig)

Immunological Tests

• Serological tests based on antibody specificity, fitting like a hand in a glove
• Used to determine the immunological status of patients, to confirm a suspected diagnosis, or screen individuals for disease.

Antigen & Antibiotic Tests

• Serologic tests are used to determine if a person has been exposed to a particular microbe
• Serologic tests use antibody binding to a specific site (epitope) on an antigen

Antigen-Antibody Reaction

• Antigen: Any foreign material to the body, like viruses or a bacteria.
• Antibody: A protein component of the immune system that recognize foreign materials, neutralize them and offer protection from them in the future.

Got Vaccinated = Got Antibody = Got Protection?

• Video link provided
• Discussion of if vaccination=antibody=protection

Neutralizing Antibodies, Antibody Titer

• Neutralizing antibodies are antibodies that can block viruses from infecting cells
• Antibody titer is a blood test to determine the presence and amount of antibodies to determine if a person has been infected by a pathogen before

What Do IgG, IgM?

• Antibodies(Ig) are important elements of the human immune system.
• Types of antibodies include Immunoglobulin M and Immunoglobulin G (IgM and IgG)
• IgM is short-lasting, first line defense against bacteria or viruses
• IgG offers long-lasting protection ("previously infected" status)

Understanding Hepatitis B Serological Tests Results

• Discusses various Hepatitis B tests, including HBsAg, anti-HBs, and anti-HBc tests and their roles in diagnosing and monitoring Hepatitis B infection.
• Explaining the significance, what it means and how it helps establish a diagnosis.

Enzyme-linked Immunosorbent Assay (ELISA)

• Enzyme-linked immunosorbent assay (ELISA) is a common method used to detect the presence of antibodies, antigens, proteins, and glycoproteins in biological samples.
• Explanation of the step-by-step ELISA procedure.

Sandwich ELISA Protocol

• Video link provided for the Sandwich ELISA procedure

False Positive Result

• False positive result discussion regarding an instance of testing for pregnancy where the test was wrongly interpreted as positive
• Details of the false positive in that case are presented, including relevant events.
• Possible contributing factors to false positives were mentioned.

Serological Tests - Sensitivity vs Specificity

• Explaining aspects of serological techniques

HIV Laboratory Diagnostic Algorithm

• Details provided about HIV diagnostic tests.
• HIV screening and confirmatory tests explained

Lab. Results - Right Interpretation

• Importance of correctly interpreting test results

Specific Site Algorithm for Pneumonia...

• A detailed, specific site-specific algorithm for pneumonia diagnosis is described
• Key signs, symptoms and laboratory tests, including imaging evidence are explained

Catheter associated Urinary Tract Infection (CAUTI)

• Criteria/features needed to make the diagnosis of a urinary tract infection (UTI) when a patient has a catheter

Determining Clinical Significance Of Cultures

• Importance of culture results and their interpretation in identifying infections correctly.
• Discussion of the implications of false positive and negative results due to factors like sample contamination or antibiotic administration.

Take Home Message

• Summary of the key points covered concerning principles and methods of clinical sampling

Principles & Methods of Diagnosis Clinical Sampling

• Summary of the key strategies to be applied for correct sample collection, transport, processing, reporting, and treatment.