Baldwin a Rainer Abart a.
Under a Creative Commons license. Abstract Focused ion beam FIB sample preparation technique in plan-view geometry allows direct correlations of the atomic structure study via transmission electron microscopy with micrometer-scale property measurements. Recommended articles Citing articles 0. Published by Elsevier B.
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There are special transport systems, such as bags, vials or tubes with an anaerobic atmosphere, micro-haematocrit capillary tubes Trypanosoma spp. Blood culture bottles, lysis-centrifugation bottles, tubes and bottles with screw closure, vacuum tubes with additives EDTA, citrate or separating gel for serum samples , sterile petri dishes and syringes for obtaining aspirates can also be used..
The consequences of a poorly taken, poorly preserved or poorly transported sample, can result in a failure in the isolation of the aetiological agent or the isolation of possible contaminating microorganisms that can generate unnecessary or inappropriate treatments. Since a large part of the determinations in Microbiology are based on the growth capacity of microorganisms, the conditions of collection and transport must ensure their viability at all times.
The Microbiology laboratory should prepare a clear and concise manual with the rules for collecting and transporting samples 2 which is available to all professionals who may request samples for microbiological study and, if there are doubts about the suitability of the samples or how to obtain them, the Microbiology laboratory must always be contacted before proceeding with the collection.. The collection of samples for microbiological studies can vary depending on whether they are going to be processed using conventional methods or if they will be processed using automated methods.
Automated systems can only perform the cultivation from liquid samples directly or in liquid transport media. The containers depend on the type of sample and sterile containers will be used for abscess samples, catheters, sterile fluids except blood , prostheses, valves and other devices, tissues and biopsies, faeces, urine, semen, skin scraping, hair and nails, and all respiratory samples. The swab will be used with gel or liquid transport medium automated seeding and PCR techniques in all genital exudates, conjunctival exudates, ENT ear, nose and throat exudates, wounds, burns and skin ulcers if aspiration is not possible.
Blood cultures and bone marrow will be sent in blood culture bottles sterile fluids are also possible, except for CSF. Blood smears for parasites in a tube with EDTA, for serological determinations in vacuum tubes with gel and, for nucleic acid detection tests, vacuum tubes with EDTA or specialised tubes. The syringes used for aspiration of the samples can be used as containers..
Sampling for the study of viruses can be done with any type of swab except those made from calcium alginate or wooden stick. The use of transport medium for viruses during the collection of samples depends to a large extent on the sample itself; liquid samples such as blood, CSF, urine and bronchoalveolar lavage fluid do not usually require it, so they must be transported and processed paying special attention to the optimal temperature and storage times.. Finally, there are some particular containers, such as the brush in special transport medium for the papilloma virus or a tube with heparin for the study of Leishmania spp.
Regarding the volume of the sample, it is always recommended to obtain the maximum that can be obtained and from the most purulent area. The minimum volume for inoculating a plate or an enrichment broth is one drop 0. As a general rule, in the liquid samples for each type of determination, a minimum of 1—2 ml and a maximum volume between 10 and 20 ml will be requested. The sampling procedure will be done as aseptically as possible and whenever feasible prior to taking antibiotics. There are samples for which peculiar methods are described that must be taken into account and in which the manual of sampling of the Microbiology Department should be consulted, such as the neutralisation of gastric juice with sodium carbonate for the study of mycobacteria..
The most commonly used rapid tests, excluding fresh examinations and staining are: immunofluorescence, agglutination, immunochromatography ICT , enzyme immunoassay EIA and molecular microbiology techniques real-time PCR and multiplex PCR. By means of the latter, an isolated or several infectious agents can be detected simultaneously bacteria, viruses, fungi, parasites , including antibiotic-resistant genes, in a short time, with little manipulation and preparation of the samples and with precise results.
These techniques can present specific requirements including the transport system and sample preservation that will depend on the technique available in each laboratory.
Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay
There are, for example, panels marketed for diagnosis of respiratory infections from samples of nasopharyngeal aspirate or exudate or urine, gastrointestinal infections from fresh faeces or in Cary-Blair medium, blood or bone marrow infections or from direct blood with EDTA, serum, special media or positive blood culture bottle, central nervous system infections from CSF or urine, sexually transmitted infections from urethral exudate, endocervical exudate or urine, and skin and mucous infections from skin lesions.
PCR techniques are also available for rapid diagnosis of carrier status, such as detection of Staphylococcus aureus , Streptococcus agalactiae or bacteria that produce carbapenemases in nasal, pharyngeal or rectal exudates.. Each molecular detection test can be performed on specific samples, presenting specific requirements that will differ depending on the technique used, so that the collection system and storage conditions may vary depending on the manufacturer's specifications..
In general, samples collected for microbiological studies should be sent as quickly as possible to the Microbiology laboratory.
They can be transported at room temperature if their shipment is not delayed after they are obtained, although some will require ice for transport. In the event that they cannot be transported immediately, the following general recommendations may be followed, although with exceptions 1,3,5 : a. There are bacteria that are especially sensitive to environmental conditions: Shigella spp.
The transport of samples of biological material 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 must be managed by the hospital itself, by the health service or by any transport organisation or agency that has been authorised.
Coded Private Information or Specimens Use in Research, Guidance (2008)
Spain has adopted the recommendations described by the United Nations regarding the transport of infectious substances. These recommendations are reflected in international legislation through the following international transport regulations. For road transport, the European Agreement concerning the International Carriage of Dangerous Goods by Road is applied in 48 countries.. 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..
Local and national regulations for the transport of infectious substances.. The principles on which safe transport is based at the national or local level are the same as those applied for international transport and the purpose is that the sample has no possibility of leaving the container under normal transport circumstances. When the laboratory is required to send samples to an external centre that is within the European Union EU , current regulations state that the shipment must only comply with the regulations reflected for collection, packaging, labelling and shipping procedures, and no document is necessary for the package to leave the country..
If the laboratory is outside the EU, the sponsor has two options: request voluntary registration in the register of importers and exporters of biological samples or apply for a one-off import and export licence for biological samples.. Dangerous goods are assigned UN numbers and, based on their classification of danger and their composition, they are assigned the corresponding official transport designations.
Infectious substances are classified in accordance with division 6. Thus, infectious substances are divided into the following categories.. 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 humans and animals will be assigned to UN 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 The requirements for packaging, labelling and documentation of infectious samples currently in force are determined by the UNCETDG and are included in packing instructions P and P These requirements are established according to whether the infectious sample belongs to category A UN or category B UN , respectively..
To transport all infectious substances, the basic triple packaging system must be used. This transport system comprises three layers: 1. 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 fluid in case of breakage or leakage..
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 fluid in case of breakage or leakage.. 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. Each package prepared for transport must be correctly marked and labelled and accompanied by the relevant shipping documents..
Category A infectious substances can only be transported in containers that meet the specifications corresponding to UN class 6. In the packages containing the material to be transported, marks are shown that provide information about their content, the nature of the danger they pose, as well as the packaging standards applied.. The marks of the containers shall be located in such a way that they are clearly visible and not covered by any other label or mark.
There are two types of labels: hazard labels and handling labels. Those commonly used in these packages include: hazard label for category A infectious substances and for microorganisms and genetically modified organisms that meet the definition of category A infectious substance; hazard label for certain microorganisms and non-infectious genetically modified organisms UN and for solid carbon dioxide dry ice UN ; hazard label for liquid nitrogen; handling label for cryogenic liquids liquefied gases at very low temperatures in air transport or orientation label to indicate the position of closures of primary containers, for the air transport of category A liquid infectious substances in quantities exceeding 50 ml per primary container.
Regarding the documentation, a declaration of dangerous goods, a packing list or shipping list or pro forma invoice are required by the sender indicating the address of the recipient, the number of packages and a description of the contents, indicating their weight and value, and an import or export permit or declaration or both ; and a document on knowledge of air shipment, for air transport, or equivalent documents, for shipments by road, train and sea. In addition to the documents indicated, a list of the contents between the secondary packaging and the outer packaging shall be included in the goods assigned to numbers UN and UN The basic triple packaging system is applied, including for local surface transport, which must fully comply with the requirements of Instruction P For this type of transport, no dangerous goods documents are required, only for international shipments, a packing or shipping list or pro forma invoice, an import or export permit or declaration and a document on knowledge of air transport, or equivalent documents for shipments by road, train and sea are required..
Biological specimen - Wikipedia
Each Microbiology laboratory must have standards for the receipt and acceptance of samples for microbiological diagnosis that the requesting doctors must know. Given that all clinical samples are unique, every effort will be made to avoid rejection, trying to resolve in the section of recording and receipt of samples the problems that could be a cause for rejection. Each sample must be accompanied by the corresponding request application form or electronic request..
In the process of receiving the clinical sample, the following is required: — A correct identification of the sample: this fact is essential to be able to establish an unequivocal correspondence between the container in which the received sample is found, the sample it contains and the patient to which it belongs.. That the type of sample received is appropriate for the studies requested..
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That the volume or quantity of sample is what is necessary in order to carry out the planned microbiological studies.. That the sample has been transported in the appropriate container and in the transport and preservation conditions necessary so that its viability is not affected..
In all cases, the requesting doctor will be contacted informing him or her of the incident in the receipt of the sample to see if it can be solved or, if this is not possible, a new sample will be requested. Depending on the importance of it, it is possible to opt to process it before the resolution of the incident, so that the sample does not deteriorate.. Some of the usual conventional equipment required in the processing of a sample for microbiological study are: biosafety cabinets several levels depending on type of laboratory , stoves different temperatures and atmospheres , freezers, refrigerators and centrifuges.
The reviews, as well as any type of incident, of the devices or material must be detailed in the equipment maintenance sheet within the laboratory's quality plan and must be strictly complied with.. Most automated systems process liquid samples including swabs in liquid transport medium, exudates, aspirates, sterile liquids and urine.
Overall, they prevent labelling errors, work accidents, save time and make it possible to reorganise the work of laboratory technicians. Some of the main differences are that the method of inoculation is automatic by reusable metal loop WASP or automatic and manual with magnetic ball InoqulA.. In general, most samples are inoculated on sheep blood agar medium. In addition, for normally sterile samples from the respiratory tract and the genital tract, ear, conjunctival exudate, superficial, deep wounds and abscesses, a chocolate agar plate is added. A MacConkey agar plate is added to samples from non-sterile sources.
Most of these selective media use organic compounds and dyes as selective chemical toxins on certain bacteria. Likewise, the use of antibiotics included in the medium, alone or in combinations, facilitates the suppression of the growth of a type of bacteria or several, for example: Thayer-Martin medium N. Some components allow the differentiation of pathogens in a specific way according to metabolic reactions that are expressed as pH changes and, in other cases, these reactions produce colour changes in the colonies grown in chromogenic media.
There is a wide variety of chromogenic media marketed for the isolation of different microorganisms Acinetobacter spp. Liquid enrichment media, such as thioglycollate broth or brain heart infusion broth, will be used in sterile samples, superficial wounds, deep wounds and abscesses.
Media for anaerobes such as blood agar for anaerobes Brucella agar , laked blood with kanamycin and vancomycin agar or Bacteroides bile esculin BBE agar will be used in abscesses, biopsies, wounds and sterile liquids except CSF.. Each laboratory should monitor the quality of the culture media it uses, both those prepared in the laboratory itself and those commercially purchased preferably using collection strains American type culture collection [ATCC], Spanish Type Culture Collection [CECT]..
The reagents used in the seeding phase of the samples include those that are necessary to perform the fresh examinations such as distilled water, saline solution or Indian ink; those used in the different stains performed on the samples such as Gram stain although there are currently automated staining machines available on the market , the systems generating different incubation atmospheres and the commercial reagents necessary for the realisation of the rapid techniques used in the laboratory..
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