Pathogenic Microbiology: MCB313 Sample Collection & Transport - PDF

COURSE CODE: MCB313 COUSRE TITLE: PATHOGENIC MICROBIOLOGY Module 2: Handling of Hazardous Materials and Shipment Regulations Week Work: Collection of specimens from various body sites and methods of transportation and storage. Handling, packaging and shipment of cult...

COURSE CODE: MCB313 COUSRE TITLE: PATHOGENIC MICROBIOLOGY Module 2: Handling of Hazardous Materials and Shipment Regulations Week Work: Collection of specimens from various body sites and methods of transportation and storage. Handling, packaging and shipment of cultures and hazardous materials. What are Hazardous Materials? Every clinical laboratory specimen/samples from human, animals and plants and from any part(s) of the human, animal or plant is considered hazardous until proven otherwise. This is because clinical samples may contain infectious particle(s) (bacteria, viruses, fungi, parasites, genetic materials etc) for which diagnoses is required and other infectious materials not envisaged. Other laboratory hazardous materials Chemicals and reagents: Liquids Gases Dust Vapours mists or fumes  Other laboratory hazardous materials  radiations/radioactive  electrical equipment  clinical waste  soiled fabrics (clothing, bedding, etc)  medicines that contain hazardous biological agents. Specimens from various body sites Blood Bronchoalveolar lavage Tissue (biopsy, autopsy) Exudates from any part of the body. Aspirates DNA and Genetic Material Pus Urine swabs eg wound, vaginal, Stool/faeces rectal, eye, nasal Sputum Skin snip/scrapings Bone marrow Nail clips Saliva/gastric Semen Cerebrospinal Fluid (CSF) Egg cells, etc Collection of specimens from various body sites Several methods are used for specimen collection based on ethical approvals and standard/ specific protocols to ensure the safety and integrity of the collected specimens.  Some samples, can be obtained easily as the body naturally eliminates them.  Others are quick and easy to acquire because they reside in the body’s orifices.  For some, surgery will be essential to access the required sample. Common Methods of Sample Collection Samples that can be obtained easily as the body naturally eliminates them: Urine: clean the genital area and void a bit of urine before collecting the specimen into the container (early morning, mid-stream urine capture, clean catch). If a urinary catheter is required (catheter urine) Stool samples: Stool samples can be collected in a wide mouthed container, or small portion scooped into a vial, or a small amount smeared on special test paper Sputum Patients are instructed to cough up sputum from as far down in the lungs as possible. By taking several deep breaths before expectorating into the collection cup  Samples that are quick and easy to acquire because they reside in the body’s orifices. Secretions and tissues from the female reproductive system: Samples of vaginal secretions are obtained by running a cotton swab over the walls of the vagina; cervical cells for a Pap test are obtained using a cotton swab and spatula or a tiny brush. Speculum is used to dilate the vagina to  Secretions and fluids from the nose or throat The specimen is collected by running a swab over the area of interest and processed for testing, such as cultures. People typically respond to swabbing of their throat with a momentary “gag” reflex  Samples from open wounds and sores If a wound or sore is located in the outer layer of skin, the specimen is typically collected on a swab by brushing the swab over the area and gathering a sample of fluid or pus. If a wound or infection is deep, however, a needle and syringe may be used to aspirate a sample of fluid or pus from the site.  Samples that requires minor surgery to access (Samples from within) Blood Blood samples can be collected from blood vessels (capillaries, veins, and sometimes arteries) by trained phlebotomists or medical personnel. The sample is obtained by needle puncture (venipuncture) Collection of blood from an arm Tissue biopsy Samples of tissue may be obtained from a number of different body sites, such as breast, lung, lymph node, or skin. Tissue biopsies are usually performed in a hospital operating room. It can be collected using procedures, such as:  Needle biopsy — A needle is inserted into the site and cells and/or fluid are withdrawn using a syringe.  An excisional biopsy is a minor surgical procedure in which an incision is made and a portion or all of the tissue is cut from the site.  A closed biopsy is a procedure in which a small incision is made and an instrument is inserted to help guide the surgeon Cerebrospinal fluid (CSF) A sample of cerebrospinal fluid is obtained by lumbar puncture, often called a spinal tap. It is a special but relatively routine procedure. It is performed while the person is lying on their side in a curled up, fetal position or sometimes in a sitting position. The back is cleaned with an antiseptic and a local anesthetic is injected under the skin. A special needle is inserted through the skin, between two vertebrae, and into the spinal canal. Collection of cerebrospinal fluid (CSF) by lumbar puncture  Containers for sample collection There is a great variety of containers in which laboratory samples can be collected, with a common characteristic to all of them being that they are sterile and with a leak- proof seal.  There are special transport systems, such as:  Bags  Vials  tubes with an anaerobic atmosphere  micro-haematocrit capillary tubes  brushes in liquid transport medium  transport medium for universal virus  sterile tubes with fixatives for parasites or with preservative Containers for sample collection  Transport of samples of biological material The transport of samples of biological material can be: within a hospital or centre from a health centre to a hospital from one laboratory to another from one hospital to another within the same city or to another city All movement must be managed by the hospital, by the health service or by any transport organisation or agency that has been authorised. All specimens must be transported in a sealed biohazard bag.   Regulations for the international transport of infectious substances: International standards for the transport of infectious substances through any means of transport are based on the Recommendations of the United Nations Committee of Experts on the Transport of Dangerous Goods (UNCETDG). These recommendations are implemented through international legislation through the following international For air transport, the legally binding international regulations are the Technical Instructions for the Safe Transport of Dangerous Goods by Air, published by the International Civil Aviation Organization (ICAO). The International Air Transport Association publishes dangerous goods regulations (DGR) that incorporate the ICAO provisions and may add additional restrictions. For rail transport in countries of Europe, the Middle East and North Africa the Regulation concerning the International Carriage of Dangerous Goods by Rail is applied. For road transport, the European Agreement concerning the International Carriage of Dangerous Goods by Road is applied in 48 countries. For maritime transport, the International Maritime Dangerous Goods Code published by the International Maritime Organization is mandatory for all contracting parties to the international convention for the Safety of Life at Sea (SOLAS) For postal transport, the letter post manual published by the Universal Postal Union reflects the recommendations of the United Nations using the ICAO provisions as a basis for shipments Classification of hazardous (infectious) substances for transport of Dangerous goods Category A: an infectious substance that is transported in a way that, when exposed to it, is capable of causing permanent disability, is life- threatening or constitutes a deadly disease for previously healthy humans or animals. Therefore, the pathogens belonging to risk group 4 fall under this category, including the agents identified as new or emerging pathogens or the substances on which there are doubts about whether or not they meet the criteria for inclusion in this category. All substances that belong to category A and may cause disease in  Category B: infectious substance that does not meet the criteria for inclusion in category A. Infectious substances in category B will be assigned to UN 3373 Samples that are not subject to regulations on transport of dangerous goods those that do not contain infectious substances or that are not likely to cause diseases in humans or animals, those that contain microorganisms that are not pathogenic in humans or animals, those in which the pathogens present have been neutralised or inactivated in such a way that they do not pose health risks, environmental samples (including food and water samples) that are considered not to present appreciable risks of infection, i. drops of dried blood or samples for the detection of blood in faecal matter, ii.blood collected for transfusions or for the preparation of blood products, iii.tissues and organs destined for transplantation and iv.samples from patients presenting a minimum risk of containing pathogens if they are transported in a packaging/container designed to avoid any leak and on which the indication “Exempt human specimen” Preparation of shipments for transport The requirements for packaging, labelling and documentation of infectious samples currently in force are determined by the UNCETDG. These requirements are established according to whether the infectious sample belongs to category A (UN 2814) or category B (UN 3373), respectively. To transport all infectious substances, the basic triple packaging system must be used. This transport system comprises three layers: i. Primary container. It is the primary leak-proof and watertight container that contains the sample. This container should be wrapped in absorbent material with the capacity to absorb all the liquid in case of breakage or leakage. ii. Secondary container. Resistant, watertight, leak-proof container that encloses and protects the primary container. Several wrapped primary containers can be placed in a secondary container, but sufficient absorbent material must be used to absorb all the liquid in case of breakage or leakage. iii. Outer container. The secondary containers are placed in outer transport packages provided with a suitable cushioning material. The outer containers protect the contents from the external elements, such as physical damage, while the package is in transit. None of the faces of the outer container shall have dimensions less than 10 cm × 10 cm. Each package prepared for transport must be correctly marked and labelled and accompanied by the relevant shipping documents. https://www.google.com/search? q=packaging+and+shipment+of+laboratory+samples+youtube&client=firefox-b- d&sca_esv=875cca400690ed1e&ei=7I8WZ_7cMs61hbIP_LGGsA0&ved=0ahUKEwj-  Class work  Aseptic techniques: disinfection  Aseptic techniques: sterilization  disposal of cultures and safety measures  Dos and Don’ts in the clinical Microbiology Laboratory  Practical class: ---- disposal of cultures and safety measures