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❗️ESSENTIAL UPDATE: Please declare your intention to participate as soon as possible, with all pictures/data to be submitted by the end of June.

Join our Slack group to be in direct contact with us by clicking HERE 

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 📌 On May 5, microbiologist and scientific lead for Antibiogo Nada Malou held an information session and Q&A on this challenge with JOGL's CEO Thomas Landrain. A must watch for likely participants with questions and seeking further details.

Catch the whole event here: https://youtu.be/GIkyP5zaU6Y

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🚨 THE CALL TO ACTION 🚨

Firstly, thank you for being here! 

This page will detail all of the specific information necessary to participate in our call to action and contribute to the Antibiogo app's efficacy. This will include who is able to participate, the program's main needs and objectives, and the process of participation. All of the information here is absolutely essential to participation, so be sure to read carefully.

Who can participate?

We are looking primarily for participants who have already performed antibiotic susceptibility tests (AST) in the past, or for autonomous microbiologists with access to at least a Biosafety Level 1 laboratory. All selected participants will be reimbursed for the lab consumables they will be using (see the FAQ’s for more details).  

The Objective

Thus far the Antibiogo mobile app detects the names of LiofilchemⓇ antibiotic disks very well because it has been trained on them. However, the antibiotic names of Bio-RadⓇ or OxoidⓇ pellets are still poorly detected.

We need participants to perform AST using these brands of antibiotic disks. By taking pictures and completing a sheet (details below), you will help us train the model and improve the name recognition of the antibiotic pellets of these two brands.  

Overview of the main steps:

Step 1 Apply to be a participant by creating a Project on JOGL and submitting it to this Challenge.

Step 2 Choose Your Antibiotic Brand & Select 6 different Antibiotics.

Step 3 Perform AST using these antibiotics.

Step 4  Take High Quality Picture of the results of your AST.

Step 5  Upload your pictures to our Shared Drive.

Step 6 Fill in the sheet with your data.

Step 7 Get reimbursed.

Continue below for greater, and necessary, detail.

SPECIAL REQUIREMENTS  

To make sure that your contributions can be used for Antibiogo’s database, we need to make sure that they meet certain criteria. Read through the following requirements carefully: 

• AST growth medium and culture concentration: The ASTs need to be made with a Mueller Hinton (MH) growth medium. Plates are to be inoculated using 0.5 McFarland (0.08 to 0.13 absorbance at 625nm for E. coli) of a pure culture of the chosen organism.

• Antibiotic brands: Antibiotic discs must be from Bio-RadⓇ or OxoidⓇ.

• Bacteria type: All used bacteria must be from the environment, from food and agriculture or from animals. No pathogenic bacteria or bacteria from human samples will be accepted. All bacteria must be identified at least with the genus. (Ex: Escherichia coli).

• Petri dish size: Use 90 mm Petri dishes for 6 antibiotics discs, and 120 to 130 mm for 12 antibiotic discs. You can either use round or squared ones.

• Antibiotics list: We need 20 photos of each antibiotic listed in the data sheet, for each of the two brands. There are 120 antibiotics in total for the 2 brands.

• Minimum contribution: 20 AST pictures of a set of 6 antibiotics constituted of at least 4/6 priority ones. 

STEPS IN DETAIL

STEP 1 - Apply to become a participant by creating a project on JOGL and submitting it to this challenge 

In order to be selected as a participant by the MSF Foundation, we need to make sure that you have the experience and equipment to perform ASTs. To assess these two points, we need you to create a project on JOGL, and submit it to this challenge (template to follow here). 

We will evaluate the applicants based on their JOGL profile information and if need be through a very short interview process.

STEP 2 - Choose Your Antibiotic Brand & Select (at least) 6 different Antibiotics

Before starting to perform ASTs, we invite you to select a set of antibiotics using this list (❗️note the are two tabs in the sheet, one for each brand). This will prevent several volunteers from working on the same set. First, choose one brand of antibiotic, then choose at least 6 different antibiotics, among which 4 are from the “priority” group. 

To book a set of antibiotics of one of the 2 brands for yourself, go to the data collection sheet and enter your email in the Volunteer's email column, on the same line as the antibiotic you wish to choose.

STEP 3 - Perform ASTs using the selected antibiotic disks

You can use standard protocols of AST, while following the special requirements for this experiment (See above).

See here an example video of AST: 

Please follow normal biosafety and biosecurity practices. Neither MSF Foundation or JOGL can be responsible for any accident occurring during manipulation.

STEP 4 - Take High Quality Picture of those ASTs

The data that the MSF Foundation will be using is pictures of your ASTs. Picture quality must then be a primary focus as it will influence all subsequent work. To ensure good picture quality, please follow all these recommendations:

• Use a device with at least a 12 MPX digital camera,
• If possible, put a black cardboard as a background to improve contrast. 
• Adjust frame to include the entire Petri dish,
• To avoid blur, adjust focus,
• Deactivate flash if necessary, to avoid glare
• Avoid direct light on the setup to have a diffuse lighting
• Avoid reflections on the Petri dish. When possible, remove the lid beforehand.

STEP 5 -  Upload your pictures to our Shared Drive 

Once you have taken your set of pictures, you will need to upload them into the MSF Foundation shared drive (a google account is required to upload pictures)

• A sub-folder will be created for every selected participants
• Access it using the following link: Collected pictures 
• (Optional) if you plan on contributing with several sets of 200 pictures, create subfolders (you can name with chronological numbers)
• Upload your set of 20 pictures into this folder. We recommend doing it as things progress as uploading pictures can take time, depending on your network connectivity.

If you need further guidance, this video shows you how to do it from your phone. The recorded screen is in French.

STEP 6 - Fill in the sheet with your data 

Once you have taken 20 pictures of a set, we need you to fill out the remaining columns of the data collection sheet, next to where you have entered your email. 

Required information includes:

•  Bacteria origin: Select one among animal, environment, food & agriculture or quality control. No bacteria of human origin will be accepted.
•  Bacteria species: Select one among the full official list of over 2500 species.
•  Link to pictures folder: Paste the link where pictures were uploaded.
• # of uploaded pictures: Enter the number of times this antibiotic is present on your AST pictures. This number should be 20.

Again, note there are two tabs on the data collection sheets:

•  Oxoid tab: JOGL_Golden_Oxoid 
•  Bio-Rad tab: JOGL_Golden_Bio-rad

❗️Note: every contribution will be manually checked and approved. All requirements are mandatory to ensure the usefulness of this collection.

STEP 7 - Reimbursement

To thank you for your volunteer effort and reduce your personal costs we designed a refund policy. Refunds will work as follows. For every validated batch of 200 pictures of 6+ antibiotics, and their sheet information the MSF Foundation will pay you 230€. If the cost is higher for you, contact us, as long as you can share the invoices of your order, you will be fully reimbursed.

Its calculation is based on the average price of a typical setup for one AST including a 90mm Petri dish, enough growth medium, a tube for bacterial suspension, a sterile swab and 6 antibiotics.

While the refund only concerns the AST setup, both the picture and filling the sheet are mandatory.

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Contact Louis Laroche at louis.laroche@paris.msf.org when you have completed all the steps. 

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