Lecture 9 Safe handling of infectious microorganisms.docx

**Lecture 9 Safe handling of infectious microorganisms --** collection, transport, processing, analysis & reporting **Roles of Clinical Microbiologists** - May consult with health care professionals. - Devise laboratory testing for optimum management - Diagnosing infectious diseases - L...

**Lecture 9 Safe handling of infectious microorganisms --** collection, transport, processing, analysis & reporting **Roles of Clinical Microbiologists** - May consult with health care professionals. - Devise laboratory testing for optimum management - Diagnosing infectious diseases - Liaise with the treating physician. - Designing and developing new tools - Quality assurance (QA) & quality control (QC) **Responsibilities of clinical microbiologist** These are required by clinicians to address infectious diseases optimally - Guidelines for proper collection - Specimen transport - Identification of microorganisms - Susceptibility testing - Reporting of test results - Consultation with clinicians **Diagnostic cycle** - Pre-analysis phase collecting, transporting, labelling and getting everything set up before running the tests - Analysis phase identification of the microorganism and the susceptibility testing you needed. - Post-analysis phase reporting, consultation that happens after the analytical phase **Specimen collection** Proper collection of specimen is crucial to the confirmation of the pathogen What's infected, where is the infection, treatment. Some things might require multiple collections (samples) or samples from multiple locations - Infection site types of sample - Time incubation period, - Quantity the severity of infection -- more shedding of bacteria = much easier to identify - Collection device, container doing PCR -- should put into some solution, which will preserve the nucleic acid. Parasite in stool -- enriching media that's going to keep growing - Antibiotics collecting a sample in relation to starting treatment -- whether taking antibiotics or not, antibiotics that can be used onto the plate -- novobiocin, bacitracin, optochin -- for diagnosis - Smears **Sample information** - Minimum information on the sample collection container name, what it is, when it was collected, date of birth, sterile containers -- sealed **Sample transport** important -- From the time the samples get collected until the time the sample is being processed, we need a seamless chain where it's documented and handled properly. 1. Maintain the sample as near its original state as possible with minimum deterioration 2. Minimise hazards to specimen handlers by using tightly fitting collection devices worry is not only about protecting the samples but about the people around the sample. - **Stuart's, Amies, Cary-Blair transport media** depends on what you want to do with the sample downstream. - carbohydrates, peptones, other nutrients - Sodium thioglycolate (anaerobic microorganisms Clostridium) - Semisolid agar (prevent oxygenation) - Preferably within 2 hours should happen quickly -- tests on the clotting factors of blood should be processed immediately - The stool sample does not have to be immediate. **Receiving samples** Biosafety cabinet -- used when taking some respiratory things so that you don't inhale them. Certain types of stool will also go in there. Depends on how dangerous it is to the person and how likely it is the thing could get into. Receive samples =\> put the information onto the system =\> track them =\> allow the physician to see the information. **Specimen acceptability and rejection criteria** - No label - Prolonged transport time - Improper or leaking container wrong container - Unsuitable for request the wrong sample - Duplicated specimen on same day, just test 1 unless there is a request - Received in formalin fixative - Insufficient sample for multiple request - Overgrown or dried-out culture plates - Obvious contaminated specimen Post analytical phase **Reporting of results** when you have a definitive diagnosis or presumptive diagnosis. - Results should be issued as soon as useful information becomes available. - Gram staining - Growth from sterile body fluid/tissue - Presence of microorganisms that would require the patient to isolate *C.difficle*, TB - Growth of mycobacteria Not correct because mycobacteria very slow grower. Takes weeks or months to grow - Inclusion of interpretative statements - notification of improper specimen collection or handling. If you discard a sample, you need to tell them why -- document it and give a reason. - reporting of relevant susceptibility results only - clear, no ambiguous terminology - explanation of unusual organism names As much as a physician is trained and specialised in what they do, they are not a medical microbiologist. - inclusion of normal values with numerical data counting CFU - reporting negative results from special tests (e.g., "no Helicobacter spp. isolated") Not growth should also be included - reporting normal flora from contaminated sites (e.g., "normal skin flora") - reporting of results in a semiquantitative form robust growth, moderate growth, minimal growth - reporting of all isolates from normally sterile sites - naming source of reference for further information - reports must be distinctly presented **Case study:** Handling of Specimens During the COVID-19 Pandemic **Overview** During the COVID-19 pandemic, handling biological specimens requires stringent safety protocols to prevent transmission of SARS-CoV-2, the virus causing COVID-19. These protocols involve using appropriate personal protective equipment (PPE) and specific handling techniques to minimize the risk of exposure, especially during procedures that may generate aerosols or droplets. **High-Risk Specimens and Activities** High-risk specimens include those from the respiratory tract due to their potential to carry high concentrations of the virus. Activities that generate aerosols are particularly risky and require additional precautions. **High-risk Specimens:** 1\. Bronchoalveolar lavage 2\. Sputum 3\. Nasopharyngeal swabs 4\. Oropharyngeal swabs 5\. Nasal swabs 6\. Nasal tissue 7\. Oral tissue 8\. Lung tissue 9\. Tracheal aspirates 10\. Pleural fluids 11\. Saliva 12\. Spit 13\. Salivary glands 14\. Buccal swabs **High-risk Activities:** \- Any procedures that can generate aerosols, such as uncapping or aliquoting specimens. **Safety Measures** \- Universal PPE: Includes coats, gloves, eye protection, and face protection (face shields or bench shields) to protect against splashes. \- Biosafety Cabinets/Chemical Fume Hoods: High-risk specimens should be handled in these environments to contain aerosols and droplets. **Safe Handling of Specific Specimens** \- Low-risk Specimens: Blood, cerebrospinal fluid (CSF), urine, and fixed respiratory tissue generally do not require special handling. \- Stool Specimens: While SARS-CoV-2 RNA can be detected in stool, it is not considered infectious. **Point of Care Testing** \- COVID-19 Testing: Point of care testing for COVID-19 involves collecting and manipulating nasal or nasopharyngeal swabs. Ideally, this should be done in a biosafety cabinet, but practical alternatives include: \- Using viral inactivation buffers \- Direct dosing devices that avoid manipulation of the sample **Case Study: Phlebotomy Top Gun Presentation** At the Mayo Clinic Laboratories Phlebotomy Conference, the \"Phlebotomy Top Gun\" case-based presentation involves interactive audience participation to address real-world phlebotomy scenarios. **Example Case Question: Which specimens should be handled in a biosafety cabinet or chemical fume hood during the COVID-19 pandemic?** \- Options: 1\. Blood, CSF, and pleural fluid. 2\. Stool, urine, and blood. 3\. Pleural fluids, oropharyngeal swabs, and saliva. 4\. Buccal swabs, nasopharyngeal swabs, and tracheal aspirates. 5\. Answers 3 and 4 are both correct. 6\. All of the above answers are correct. **Correct Answer:** Based on available data and guidelines, **answers 3 and 4 are correct.** These include high-risk respiratory specimens that should be manipulated in a biosafety cabinet or chemical fume hood to mitigate the risk of SARS-CoV-2 transmission. **Conclusion** Proper handling and safety protocols are crucial when dealing with biological specimens during the COVID-19 pandemic to protect healthcare workers from potential exposure to SARS-CoV-2. By following these guidelines and using appropriate PPE and containment strategies, the risk of transmission can be significantly reduced.