Capacity Development | Training | Advocacy 

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Capacity Development

General resources

Laboratory set up resources

Below are a list of the policy documents, standard operating procedures (SOPs), forms, competency assessment forms (CAFs) and risk assessments that are in operation at the Centre for Clinical Microbiology (CCM). The specific documents you will need to cover your laboratories/departments will vary depending on the research you are conducting, what level of laboratories you have and whether you are part of a clinical trial.

These documents will need to be reassessed every six months/a year/two years etc. to ensure they are still relevant and up to date. You may find it useful to have a spreadsheet with all of these documents, how often they need to be reassessed, who is responsible for reassessing, who is responsible for signing off, and the date they will next need reassessing, to ensure you are able to keep track of them all.

There are different types of documentation, each of which is described briefly below:

Policy documents

Policy documents provide general overviews of the rules and procedures of your laboratory. The information within them covers all aspects of that item (e.g. ‘waste storage and removal’ covers the waste generated in all areas of the department, including the BSL2 and 3 laboratories, office waste, such as recycling of paper and old equipment, as well as specialised waste routes, such as chemicals). Policy documents will refer to a number of other related documents, such as SOPs and forms.

Standard operating procedures (SOPs)

SOPs detail the specific steps for a certain procedure. They should be used as a guide to follow, to ensure laboratory workers are all undertaking tasks in the same way. This ensures both the safety of the workers, as well as the standardisation of the procedure. As SOPs are specific to the processes you undertake in your laboratory, you will find that the templates we have uploaded are really more examples. You will have to research and complete each procedure you do in your laboratory to ensure the SOPs fit with your research.

Forms

Forms are documents on which laboratory workers record data from the laboratory. These are likely to include things such as weekly maintenance checklists, temperature logs for equipment such as freezers and incubators, as well as auditing procedures. Once printed, filled in and signed, these documents should be kept in hard and/or digital form as a record.

Competency assessment forms (CAFs)

CAFs record the items for a specific procedure/training which laboratory workers need to have been approved on. For example, a CAF for autoclave training will have multiple items that a laboratory worker will need to have been signed off on, such as ‘reading and understanding the different autoclave cycle settings’, ‘how to replace the printing paper’ and ‘what to do in the event of autoclave failure’. CAFs are a record of a laboratory worker’s training and as such, should be kept with the rest of the staff member’s training records. The CAFs should note how often staff members should be retrained on any particular procedure.

Risk assessments

UCL risk assessments are completed online using a website called RiskNet, then downloaded, printed and stored in a folder so that all members can read and sign the risk assessment, and refer to it when necessary. Risk assessments should cover all activities undertaken in the department and an individual assessment should be completed for individual procedures (e.g. ‘use of the autoclave’), or to cover different hazard group organisms (e.g. ‘working with HG3 organisms and materials that contain them) etc.

It is important that risk assessments cover the hazards and risks involved in the procedure (e.g. using a water bath (the hazard) could result in burns/scalds (the risk)) and the mitigations you have put in place to replace the hazard with a safer version (hazard elimination), or reduce these risks (risk control) (e.g. laboratory workers must wear heat-proof gloves when using the water bath, to prevent skin coming into contact with hot water/metal). It is useful to provide a risk matrix table (which shows the relationship between probability and severity of the risk), to ensure that any procedure covered by the risk assessment is not deemed too dangerous.

Risk assessments must be approved by an appointed health and safety officer, head of department or other relevant member of staff.

Note: The uploading of templates for these documents to the hub resource centre is ongoing, so please check back again soon, or contact us at pandora.id.net@gmail.com if you wish to request specific templates.

Note: We have added helpful notes in the margin of many of our templates and guides. Please ensure you can see all comments when you open the documents to get the full information provided.

Links to BSL3 laboratory resources

Quality control and documentation

Our partner site UCL has created template policy and SOP documents that can be used as a basis for documentation in any laboratory. As UCL is predominantly a TB clinical trials department, the examples in the templates are related to TB, but you will need to rewrite these documents to reflect the organism(s) you work on, the research you are doing and also the health and safety requirements of your organisation and country.[LE1] 

Training

How to run a workshop

Nanopore MinION training workshop

Click this link to see the workshop page.

TB molecular diagnostics workshop

Click this link to see the workshop page.

Oxford Nanopore sequencing for tuberculosis (NIMR, Dar es Salaam, Tanzania - August 2022)

Click this link to see the workshop page.

The workshop was broken down into six sessions that covered the whole pipeline (click on the links to view the presentations):

  1. Introduction to ONT sequencing (Dr Linzy Elton) (link to presentation here)
  2. Introduction to the TB sequencing pipeline (Dr Linzy Elton) (link to presentation here)
  3. CTAB extraction method (Dr Linzy Elton) (link to presentation here)
  4. DNA quantification methods (Dr Sylvia Rofael) (link to presentation here)
  5. Library preparation using Rapid Barcoding Kit (SQK-RBK004) (Dr Linzy Elton) (link to presentation here)
  6. Introduction to ONT bioinformatics (Dr Sylvia Rofael) (link to presentation here)
  7. Introduction to TB-Profiler (Dr Sylvia Rofael) (link to presentation here)

Download the workshop handbook here (coming soon).

Oxford Nanopore sequencing for tuberculosis (HerpeZ, Zambia - February 2023)

Click this link to see the workshop page.

The workshop was broken down into eight sessions that covered the whole pipeline and is an update of the presentations from Tanzania in August 2022, including the newer 96 sample version of the rapid barcoding kit (click on the links to view the presentations):

  1. Use of genomics in tuberculosis research and diagnostics in Zambia (Dr Kabengele Keith Siame, TDRC) (link to presentation here)
  2. Introduction to ONT sequencing (Dr John Tembo) (link to presentation here)
  3. Introduction to the TB sequencing pipeline (Dr Linzy Elton) (link to presentation here)
  4. CTAB extraction method (Caren Kabanda) (link to presentation here)
  5. DNA quantification methods (Dr John Tembo) (link to presentation here)
  6. Library preparation using Rapid Barcoding Kit (SQK-RBK110.96) (Dr Linzy Elton) (link to presentation here)
  7. Introduction to ONT bioinformatics (Dr John Tembo) (link to presentation here)
  8. Introduction to TB-Profiler (Dr Linzy Elton) (link to presentation here)

Download the workshop handbook here (coming soon).

Links to the video presentations can be found here.

Advocacy

Link to Chatham House's Sustainable laboratories initiative: https://www.chathamhouse.org/about/structure/global-health-security/sustainable-laboratories-initiative# 

Link to Chatham House's Sustainable laboratories prior assessment tool: https://www.chathamhouse.org/sites/default/files/publications/research/2019-06-18-Sustainable-Laboratories-Initiative.pdf

 

The resources on this page were (unless otherwise stated) developed by Dr Linzy Elton (UCL)