Information Sheet RISK ASSESSMENT FORM FOR AN ACTIVITY INVOLVING GENETICALLY MODIFIED MICROORGANISMS
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1 Information Sheet RISK ASSESSMENT FORM FOR AN ACTIVITY INVOLVING GENETICALLY MODIFIED MICROORGANISMS The Risk Assessment Form must be completed and permission received from the GM Safety Committee prior to commencement of any project. A new Form should accompany any grant application which proposes work likely to be covered by the ACGM Regulations. The Form should be completed in typescript. A "Word" template is available from the Health and Safety Advisor (Biological Sciences) (HSA(BS) (David Nelson) who will be happy to answer any queries regarding this Form. You may wish also to consult the University Health and Safety Department Web Site for further information. This form consists of a number of questions which are intended to prompt the assessor to consider the potential human health and environmental hazards of their GM activity and what control measures are needed to reduce the associated risks as low as possible. Most routine cloning work with E.coli K12 derivatives will require only a brief. However, no matter how trivial a cloning procedure may appear a risk must be carried out. For activities where there is some uncertainty a more in depth is. The detail will vary, but if a hazard is identified then a more detailed risk must be carried out The main Risk Assessment Form is set out in three main sections: 1. risk to human health 2. consideration of the nature and scale of the actual activity 3. risk to the environment before deciding on the final classification Sources of Useful Information The following sources provide additional information which will assist you in the successful completion of your risk. Advisory Committee On Genetic Modification (ACGM) Compendium Of Guidance: Advisory Committee On Dangerous Pathogens (ACDP) Guidance On The Categorisation Of Biological Agents: Current HSE Newsletters giving guidance on the new regulations: Department of Environment, Food and Rural Affairs (DEFRA) home page: David Nelson 1 05/04/02
2 1. Section 1: Background and objectives of GMO project Brief, yet clear outline only please. If the project involves a number of related GM activities, outline how they are related and the objectives of each activity. 2. Section 2: Summary and conclusions of risk What are the main risks to human health and the environment? If none, briefly explain why. What containment level is to contain the GMO? 3. Section 3: Details of host cells / vector and target DNA / gene A Bacterial Systems Host The bacterial host should be named. If a commercially available strain the supplier s information should be attached (unless one of the common strains such as the JM, Series, DH5, XL-1 blue etc. are being used). Host ACDP If the host organism is a pathogen the ACDP Category should be listed. These categories are outlined in "Advisory Committee on Dangerous Pathogens: Categories of Pathogens according to Hazard and Categories of Containment. Third Edition 1998". If a veterinary pathogen is to be used then the "Specified Animal Pathogens Order 1998" should be consulted. These documents are on the web at (ACDP) or (Animal Pathogens). If the pathogen is a novel pathogen please contact the HSA(BS). K-12 derivatives of E. coli, which include commonly used strains such as C600, DH1, DH5, HB101, INV1, JM109, TB1, TG1, X-1Blue and the commercial derivatives of them are noncolonising and disabled (for BL-21 see below). They are equivalent to hazard group 1, as they are not pathogenic to humans or animals. They often have auxotrophic requirements (this may vary from strain to strain) which are unlikely to be satisfied outside laboratory cultures. They have very limited survivability in the environment. Recent research commissioned by the HSE (Chart et al An investigation into the pathogenic properties of Escherichia coli strains BLR, BL21, DH5a and EQ1. J Applied Microbiology, 89, p ) showed that BL21 is unlikely to be pathogenic, lacking any of the pathogenic mechanisms associated with E. coli strains involved in enteric infections. BL21 may be considered unlikely to colonise and establish a persistent infection in the gut of a healthy individual. This information implies that BL21 can be considered broadly equivalent to K12 strains in many circumstances, and that, in most cases, work which uses this host can be classified as a Class 1 activity. However, there are some instances where using a K12 strain would be preferable. For example, work that involves the cloning of a bacterial pathogenicity determinant into BL21 will need careful consideration and may in some cases warrant classification as Class 2. In all cases the classification of the work will be dependent on factors such as; the plasmids to be used, sequences to be inserted, and how the GMM is to be used as well as the nature of the host strain. Vector/Source The plasmid/bacteriophage vector should be described. If a commercially available vector, the supplier's information should be attached. The puc series of plasmids (and those like them, which includes many commercial vectors; this includes pat153, pbr, pbluescript, pbs, pgem, pcat, pex, pt7, pmsg, pxt, pembl) are nonmobilisable. The selectable marker gene (Amp R ) codes for resistance to an antibiotic not in clinical use. This may not be true for other antibiotic resistance genes such as Tet R. David Nelson 05/04/02 2
3 Target DNA/Gene The gene of interest which is to be cloned should be named. If a shotgun approach is to be taken or if more than one gene is being targeted this should be stated. Special mention should be given to the use of any potential oncogenic sequences. The method of cloning i.e. genomic, cdna, PCR, RT-PCR or other should be stated. Source The organism from which the nucleic acid is to derived should be described. Source ACDP If the organism from which the nucleic acid is to be derived is a pathogen, the ACDP Category should be listed. See Host ACDP (above) for further information. Scale The scale of the experiments proposed should be indicated i.e. < 100ml; < 1L; < 10L; > 10L. B Eukaryotic Systems In all situations where a project involves an initial cloning step in a prokaryotic host/vector system then Section 1 A (Bacterial Systems) should also be completed. Cell Line The cell type to be used should be described. Include species, cell type and any special features e.g. SV40 T antigen positive, EBV transformed. Tissue culture cell lines are normally Category 1, however, uncharacterised cell lines, those which are virus +ve or primary cultures of human or simian nervous system, lymphoid organs, etc, should be categorised as Category 2. Target DNA/Gene See section above. The normal biological function of the gene to be expressed should be described. If a non-human gene is being expressed the homology to its human counterpart should be stated (if known). Source ACDP If the organism from which the nucleic acid is to be derived is a pathogen, the ACDP Category should be listed. See Host ACDP (above) for further information. Selection System The selection system to be used should be described. C Viral Vectors Target DNA/Gene See above. The normal biological function of the gene to be expressed should be described. If a non-human gene is being expressed the homology to its human counterpart should be stated (if known). Source ACDP If the organism from which the nucleic acid is to be derived is a pathogen, the ACDP Category should be listed. See Host ACDP (above) for further information. Cell The cell type to be used should be described. Virus The virus to be used should be fully described. If commercially available the supplier s information should be attached. If non-commercial, then all available information on genotype, etc, should be supplied. David Nelson 05/04/02 3
4 Virus ACDP If the virus is a pathogen, the ACDP Category should be listed. See Host ACDP (above) for further information. Selection System The selection system to be used should be described. 4. Section 4: Identification of potential harmful effects of the GMM to human health This section considers: the potential harm to human health from the pathogenicity, biological effects, and toxicity of the host organism / cell, foreign gene product and the mobility of the plasmid risk that, in the event of exposure, the GMM could actually cause harm to human health before assigning a provisional containment level. A Potential harm to human health Specifically the following must be considered: a) Hazards associated with host (e.g. Host ACDP, colonisation potential) b) Hazards associated with the vector (e.g. mobilisation state) c) Hazards associated with inserted gene d) Hazards arising from the alteration of existing pathogenic traits e) Considerations relating to whether an inserted sequence, that does not give rise to a harmful phenotype in the recipient GMM, could give rise to harm as a result of natural gene transfer to another, possibly related, organism. B Risk that, in the event of exposure, the GMM could actually cause harm to human health For each potential hazard you are to assess the associated level of risk. Identify the level of risk of causing harm to human health represents by combining: a) the consequence, in the event of exposure, of the hazard (i.e. the level of harm that could theoretically be realised) and, b) the likelihood that, in event of exposure, the GMM could actually cause harm to human health using the matrix below. Express risk as high, medium, low, or effectively zero. Estimation of Risk Consequence of Hazard Likelihood of Risk High Medium Low Negligible Severe High High Medium Effectively Zero Medium High Medium Medium/Low Effectively Zero Low Medium/Low Low Low Effectively Zero Negligible Effectively Zero Effectively Zero Effectively Zero Effectively Zero David Nelson 05/04/02 4
5 The likelihood of harm to human health considers the ability of a GMM to establish an in vivo infection and the efficiency of subsequent in vivo propagation. Also involves an of the FITNESS of the GMM. The initial stage identifies features of GMM which have potential to cause harm, BUT these scenarios can be theoretical and it may be possible to provide justifications which say that the likelihood of these scenarios being realised is vanishingly small. Probabilistic Considerations In some cases it may be possible to assign a frequency, precise or approx, to an event e.g. plasmid transfer or recombination. In other cases may be possible to only use semi-quantitative methods based on previous experience with other GMMs or the working practice to be utilised, e.g. if relying on a disabling mutation then reversion rates of that mutation should be considered and if the rate is high then should consider multiple mutations. Caution must be applied when seeking to discount on the basis of Likelihood hazardous assume the worst and act accordingly. Fitness relates to the ability of a GMM to spread in vivo or within the community. Modifications to an organism may make a GMM more hazardous but may also render the GMM less fit. It should not be assumed that a GMM is less fit than the parental organism unless there is scientific evidence to support the claim. Assignment of Provisional Class Should consider the pathogenicity of the host i.e. ACDP-1= Level 1 etc. This gives an indication of containment level. Then judgement can be made about whether modification will make GMM more, or less, hazardous and the requirement for a higher or lower level of containment. Only consider for hazard to human health at this stage. Allocation to a particular containment level is dependant on the measures to protect the operator and the environment. These are outlined in Tables 1 4 (see Appendix 1) 5. Section 5: Nature and scale of the activity / review of controls necessary to safeguard human health Section 5 assigned a provisional Class based on identified hazardous properties of the GMM and by comparison with other classification schemes (e.g. ACDP). This relates to the minimal containment level for the GMM and does not take into account the nature of the actual work or detailed consideration of the control measures. Section 5 involves refinement of the appropriate control measures to safeguard human health. Two aspects are considered: a) Whether the nature of the GMM, and especially any uncertainty about its properties, would require any measures in addition to the basic containment level indicated by the provisional class. This is really a check on what you have already done. David Nelson 05/04/02 5
6 b) The nature of the activity to be undertaken e.g. the use of sharps, animals, aerosols, large scale, in vivo versus in vitro for recombination rates etc. This is more important than a) as the nature of the work may have important consequences for the likelihood of exposure and so subsequent control measures. 6. Section 6: Identification of potential harmful effects of the GMM to the Environment and assignment of additional control measures Objective is to determine the probability of harm to the environment arising as a result of escape of organisms from containment, including all possible routes of escape such as waste disposal. This is done by estimating the likelihood of an escape from the containment facility and consequences of such a release, and possible refinement of appropriate control measures (identified earlier for human health) to safeguard the environment. Consideration of possible harm to the environment is considered by the HSE to be equally as important as to human health. Definition of Harm: harm would be caused if populations of microorganisms in one or more ecosystems were affected in terms of number or function of those organisms, or if small numbers of endangered species were under threat. The procedure to follow is similar to that in Section 4 for human health above i.e. Hazard identification Assessment of likelihood of an escape from the containment facility (e.g. laboratory), assuming control measures associated with the provisional containment level assigned for the protection of human health are in place Assessment of consequences of hazards being manifested if the environment is exposed Determination of risk (likelihood X consequence) Management (control) of risk Should consider capacity to survive, establish, disseminate and or displace other organisms. Survival: look at survival in animal gut, soil, water etc. (E.coli K12 can survive up to 7 days in environment). Potential for transfer to other organisms. Even if GMM has limited capacity to survive will this be enough to allow transfer of gene. Stress induced by starvation/adverse conditions may for example increase plasmid transfer rates. Should also consider: Pathogenicity to animals and plants Products of gene expression that could be toxic to other organisms Phenotypic and genetic stability Potential for exposure Characteristics of local environment (urban, etc) Number of organisms potentially released Should also consult the Specified Animal Pathogens Order to determine if your host organism is covered by this legislation (c.f. ACDP for Human Pathogens). The risk table shown above (Section 4) should be used as guide for working out the level of risk associated with a particular operation based on the consequence of the hazard and the likelihood of that hazard being manifest. If all risks are low or effectively zero, then no additional control measures are necessary. If any risk exceeds these levels then additional control measures should be implemented so as to reduce all risks to low or effectively zero David Nelson 05/04/02 6
7 Assignment of the Containment Level and Class (1, 2, 3, or 4) The provisional Class assigned after Section 4 indicates a base level of containment necessary to control risks to human health. It does not, however, take into account the full risk and in particular the nature of the activity and any risks to the environment. Further revision of the provisional Class is to take account of the complete set of containment and control measures identified by for both human health and environmental protection. To decide the correct final classification users should determine what containment and control measures are by to control of the activity. To do this you should compare the selected measures necessary to control to both humans and the environment with the appropriate table of containment measures (see Tables 1 4, Appendix 1) Where this corresponds to a single containment level this will read across directly to give you the activity class; i.e. Level 1 = Class 1; Level 2 = Class 2, etc. Where the measures identified correspond to measures from two different levels of containment the class corresponds to the HIGHER of the levels. The regulations allow for a reduction in control measures from the appropriate containment level where shows that a particular containment measure(s) is not necessary. The person undertaking the activity must provide full justification to not apply a measure(s), supported by, to the competent authority (HSE). However, the full containment level must be applied until written agreement has been received from the HSE. It is especially important to note that classification is dependent on ONLY those containment measures that are shown by the RISK ASSESSMENT to be necessary to protect human health or the environment. Measures that result from convention, convenience or are for product/process protection are NOT relevant to the classification. David Nelson 05/04/02 7
8 7. Section 7: Waste Control Measures Introduction Prior to final discharge / disposal of waste from contained use activities, any risks to humans and the environment associated with any GMO must be removed by use of inactivation methods. Inactivation refers to the complete or partial destruction of GMMs so as to ensure that any contact between the GMMs and humans or the environment is limited to provide a high level of protection to both humans and the environment. Clearly, the degree of kill is related to the level of risk identified by. In the case of GMMs, this refers to material and waste contaminated with GMMs from all containment level activities. The only exception to this is if the user has the explicit agreement of the competent authority (HSE) to dispose of waste without inactivation. The Authority requires evidence that GMMs will not survive to any appreciable extent in the environment and that there are no associated hazards. For more hazardous GMMs, methods giving 100% kill are such as incineration or autoclaving. However, for less hazardous GMMs, methods giving less than 100% kill may be acceptable, such as chemical disinfection which typically gives a 5 log reduction in viability, or % kill. The following guidance indicates the minimal sorts of information that should be included in the risk. Clearly, greater detail is for activities that present a greater level of risk. Class 1 activities GMMs used in Class 1 activities are by definition of no or negligible risk. Therefore the information supplied can be relatively minimal. However, it is important to state clearly the methods used for each category of waste (e.g. autoclaving, disinfection etc.) Degree of Kill : indications of the expected level of kill should be included, but need not be precise. For chemical disinfection this could be in terms of below detectable level, approximately 4 logs reduction in viability etc. The degree of kill for chemical disinfection methods may come from documented and published protocols in the literature. If all waste products are autoclaved then 100% effectiveness can be quoted, although this can only be done when the autoclave has been for the conditions used in the decontamination of GMMs. Validation: it is important to include statements about how methods have been. For example, it should be confirmed that autoclaves have annual validation tests and information about disinfectant use should include statements to the effect that the appropriate concentration and time etc. conditions will be used that coincides with manufacturer s validation. Class 2 activities Similar information should be given as for Class 1 activities (see above). However, if GMMs pose an environmental risk particular care must be taken e.g. if the GMM is a plant pathogen and there are susceptible plants in the local environment. In such cases on site validation of the inactivation methods is and reliance on manufacturer s data would be less acceptable. Where possible the degree of kill expected should be stated more precisely than for Class 1. The use of a and well maintained autoclave is likely to offer the best of inactivation. Testing of cultures after the inactivation process for the presence of viable organisms should be carried out periodically. David Nelson 05/04/02 8
9 Class 3 activities For Class 3 activities most inactivation should be by of an autoclave. You will need to state how this is and monitored. In addition to annual validation using independent, monthly monitoring by of Browns tubes or independent thermologues is. Where there is a particular environmental risk, monitoring of each run must be done. 8. Section 8: Health Surveillance The GMO 2000 Regulations do not include a specific requirement for health surveillance for GM work, but other more general regulations, such as MHSWR and COSHH will be applicable in some cases. The requirements for health surveillance depend whether the genetic modification aspects of the work involve a significant risk to health, as determined by. Health surveillance is appropriate when: an identifiable health effect may be related to exposure there is a reasonable likelihood that the disease or effect may occur under conditions of the work there are valid techniques for detecting indications of the disease or health effect The General COSHH Approved Codes of Practice (ACoP) contains further interpretation on the need for health surveillance, whilst the ACGM Part 1 details different health surveillance mechanisms to be considered. 9. Section 9: Supporting References List all references that have been used to support comments made in. David Nelson 05/04/02 9
10 Appendix 1 For assessors information only There is NO requirement to submit tables with the completed GMM Risk Assessment Table 1: Containment Measures for Activities Involving Genetic Modification of Microorganisms in LABORATORIES Containment Levels 1 Laboratory suite isolation (note1) 2 Laboratory: sealable for fumigation Equipment 3 Surfaces impervious to water, resistant to acids, alkalis solvents, disinfectants and decontamination agents and easy to clean 4 Entry to lab via airlock (Note 2) 5 Negative pressure relative to the pressure of the immediate surroundings 6 Extract and input air from the laboratory shall be HEPA filtered 7 Microbiological safety cabinet/enclosure Containment Measures not not not not for bench for bench for bench and floor not not where not where not not HEPA filters for extract air not where 8 Autoclave on site in the building, and all procedures with infective materials to be contained within a cabinet/ enclosure in the laboratory suite (Note 4) for bench, floor, ceiling and walls HEPA filters for extract and input air (Note 3) Class III cabinet double ended autoclave in the laboratory David Nelson 05/04/02 10
11 System of Work 9 Access restricted to authorised personnel only 10 Specific measures to control aerosol dissemination not (via airlock key procedure) not to minimise to prevent 11 Shower not not where 12 Protective clothing suitable protective clothing suitable protective clothing 13 Gloves not where 14 Efficient control of disease vectors (E.g. rodents and insects) which could disseminate GMM's 15 Inactivation of GMM's in contaminated waste material Waste 16 Inactivation of GMM's in effluent from hand washing sinks, showers and similar effluents 17 Inactivation of GMM's in contaminated material and waste where where suitable protective clothing ; footwear where to prevent complete change of clothing and footwear before entry and exit not not where by by by by David Nelson 05/04/02 11
12 Other Measures 18 Laboratory to contain its own equipment 19 An observation window or alternative is to be present so that occupants can be seen not not, so far as it is reasonable practicable where 20 Safe storage of GMM's where 21 Written records of staff training not where secure storage where NOTES 1. In the Table above, "isolation", in relation to a laboratory, separation of the laboratory from other areas in the same building, or being in a separate building. 2. Entry must be through an airlock which is a chamber isolated from the laboratory. The clean side of the airlock must be separated from the restricted side by changing or showering facilities and preferably by interlocking doors. 3. Where viruses are not retained by the HEPA filters, extra requirements will be necessary for extract air. 4. Where the autoclave is outside the laboratory in which the activity involving genetic modification of micro-organisms is being undertaken, but within the laboratory suite, there shall be procedures for the safe transfer of material into that autoclave, which provide a level of protection equivalent to that which would be achieved by having an autoclave in that laboratory. David Nelson 05/04/02 12
13 Table 2: Containment Measures for Activities Involving Genetic Modification of Microorganisms in PLANT GROWTH FACILITIES Containment Levels Containment Measures Building Permanent structure (Note 1) Modification Equipment 2 Entry via a separate room with two interlocking doors 3 Control of contaminated run-off water System of Work 4 Efficient control of disease vectors such as insects, rodents and arthropods which could disseminate GMM's 5 Effective control of pollen, seeds and other plant material which could disseminate GMM's 6 Procedures for transfer of living material between the plant growth facilities, protective structure and laboratory shall control dissemination of GMM's where and to extent shows it is not where and to extent shows it is where so as to prevent runoff where so as to prevent runoff (via airlock key procedure) so as to prevent runoff where and to extent shows it is to prevent dissemination to minimise dissemination to prevent dissemination to prevent dissemination to prevent dissemination to prevent dissemination to prevent dissemination David Nelson 05/04/02 13
14 NOTES 1. A permanent structure refers to a fixed structure with walls, a roof and a floor. Where the permanent structure is a greenhouse, that structure shall also have a continuous waterproof covering and self-closing lockable outer doors, and be located on a site designed to prevent the entry of surface run-off water. 2. The terms Modification/ (column 1) refer to whether a particular feature should be considered in addition to or as a modification of the containments considered in Table 1. David Nelson 05/04/02 14
15 Table 3: Containment Measures for Activities Involving Genetic Modification of Microorganisms in ANIMAL UNITS Containment Levels Containment Measures Facilities Isolation of Animal Unit (Note 1) Modification where and to extent shows 2 Animal facilities separated by lockable doors (Note2) 3 Animal facilities (cages etc) designed to facilitate decontamination (waterproof and easily washable material) 4 Floors, walls and ceilings easily washable Modification 5 Appropriate filters on isolators or isolated rooms (Note 3) 6 Incinerator for disposal of animal carcasses 7 Appropriate barriers at room exit and at drains or ventilation duct work. 8 Animals kept in appropriate containment facilities, such as cages, pens, tanks or isolators it is where and to extent shows they are where and to extent shows they are where and to extent shows it is not to be accessible where shows they are for floor where to be accessible for floor and walls to be accessible for floor, walls and ceiling where and to extent shows it is where where NOTES 1. In the Table above, "animal unit" a building, or separate area within a building, containing an animal facility and other areas including changing rooms, showers, autoclaves and food storage areas. 2. In the Table above and in Note 1 above, "animal facility" a facility normally used to house stock, breeding or experimental animals or one which is used for the performance of minor surgical procedures on animals. to be on site where the risk 3. In the Table above, "isolators" transparent boxes where small animals are contained within or outside a cage; for large animals, isolated rooms may be more appropriate. David Nelson 05/04/02 15
16 Table 4: Containment Measures for Activities Involving Genetic Modification of Microorganisms in PREMISES OTHER THAN THOSE REFERRED TO IN TABLES 1, 2 AND 3 Containment Levels 1 Viable microorganisms shall be contained in a system which separates the process from the workplace and wider environment (closed system) Containment Measures General where 2 Closed systems located within a controlled area 3 Control of exhaust gases from the closed system 4 Control of aerosols during sample collection, addition of material to a closed system or transfer of material to another closed system 5 Inactivation of bulk culture fluids before removal from closed system 6 Seals shall be designed to minimise or prevent release 7 The controlled area designed to contain spillage of the entire contents of the closed system 8 The controlled area sealable to permit fumigation not not where where not where not 9 Biohazard signs posted where where to minimise release to minimise release by to minimise release where where to prevent release to prevent release by to prevent release where and to be purpose built to prevent release to prevent release by to prevent release David Nelson 05/04/02 16
17 Equipment 10 Entry via airlock not not where 11 Surfaces impervious to water, resistant to acids, alkalis solvents, disinfectants and decontamination agents and easy to clean 12 Specific measures to adequately ventilate the controlled areas in order to minimise air contamination 13 The controlled area maintained at negative pressure relative to the immediate surroundings 14 Extract and input air from the controlled area shall be HEPA filtered System of Work 15 Access restricted to authorised personnel only 16 Decontamination and washing facilities provided for personnel 17 Personnel shall shower before leaving the controlled area 18 Personnel shall wear protective clothing 19 Written procedures and records of staff training for any bench where for any bench where for floor and any bench where not not where not not for extract air, optional for input air for bench, floor, ceiling and walls for input and extract air not not not where work clothing work clothing complete change before exit and entry not not David Nelson 05/04/02 17
18 Waste 20 Inactivation of GMM's in effluent from hand washing sinks and showers or similar effluents 21 Inactivation of GMM's in contaminated material and waste including those in process effluent before final discharge not not where by by by by David Nelson 05/04/02 18
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