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Case Study on Genomic Epidemiology

It is important to consider the participants' background when designing learning activities.
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Hi, my name is Monica Abrudan and here with me is Mihir Kekre, a laboratory implementation manager, in the Global Health Research Unit, where antimicrobial resistance surveillance. Today, we are going to talk about course design for wet lab and bioinformatics training. Thanks Monica for having me, it’s great to be here. So you’ve been an instructor on the train the trainer course which focused on capacity building or genomic surveillance of AMR, in low and middle income countries. Could you please give us more details on what was of course about? Yeah, absolutely The train the trainer course was a unique capacity building initiative in collaboration with the National Institute for Health Research.
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The aim and goals of this course was mainly to create a cohort of instructors that could deliver AMR genomics expertise in a concise way in their local ecosystems, for both the wet lab laboratory and the bioinformatics aspects. That sounds like a very complicated set up. So, who was your target audience and how were the participants selected for this course? So we had exceptional applications from all over the world because we wanted to make this a genuinely global cause. We had applications from the South East Asia, from the far East, Central, and South America as well as the entire African continent. Now, in my view, selecting these candidates was quite a challenge. In fact, because the goal we wanted was fourfold.
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So, the first thing we wanted was obviously we wanted to pick a cohort that had a strong interest in genomics and AMR. And also, was part of some surveillance systems in their home country. The second one obviously, was to pick an equal representation. We wanted to make this a truly global course, so we wanted to pick from every single continent that has a significant prevalence of AMR. Thirdly, the model we went with was pairing wet lab scientists with bioinformaticians.
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Now, the reason we did this, was because, we wanted to – genomic surveillance is a concerted effort, so wet lab and bioinformatics cross collaborate a lot and we wanted to make sure that we mimic that scenario on the course so we paired lab scientists with bioinformaticians, to work together throughout the course. And I think, lastly, in the vein of true public health, the roles that these chosen people were doing, should be stretched across the whole public health spectrum because we want different perspectives. And, in the end, I feel that we got a really diverse mix of wet lab scientists, computational scientists, data experts, epidemiologists, and the like.
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So, we had different perspectives from all over the world that could bounce off each other and the other participants could take back with them. Thank you Mihir, so if I understand correctly in this course there were multiple instructors and you run modules addressed the two types of audiences. So first you worked with a mixed audience of bioinformaticians and wet lab scientists, and then you trained an audience consisting of only laboratory scientists. So this is quite interesting and unique, so how did you adapt the learning objectives to fit different target audiences? Yeah, that’s a really good question.
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So as I said, genomic surveillance is a concerted national effort of building a system to do so and there’s a lot of collaboration and sharing of ideas between various streams like the scientists who work in the lab, to the people who analyse the data, to the epidemiologists who make conclusions. So I think initially what we wanted to do with a mixed audience, people who aren’t familiar with every single stream or they have their specialist streams, work to give them a grounding in the fundamentals. So there was a bridge to communicate with the other streams. So if they’re strong with the fundamentals, that becomes very easy to collaborate on.
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And then as we moved along with the course, we went into more detail with, for example, for me I went into the technical depth with the wet lab scientists where we would not just show them how to do practical hands-on things but also give them the tools to assemble and manage an entire surveillance system. Because we have to bear in mind that it’s not just– we’re not teaching them technical proficiency, we’re teaching them how to relay those technical concepts to others in their ecosystem. So that’s why we went a bit deeper into– with the wet lab cohort. What resources did you use in the activity design and did you design specific activities for different audiences?
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Yeah, absolutely, I mean this was an all encompassing course. So, we had to strike a balance between– you had your usual traditional lecture learning, which was introducing people to the concepts of genomics and AMR. And then beyond that point, we obviously had practical hands on sessions where we would teach people wet lab concepts, but also how to relay those concepts onto other beginners. So things like– in the lab for example, we would plate bacteria, like anyone would, and identify them and characterise their AMR profile. This is something you do on a technical course.
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But what we did differently, was to be able to teach them how you would structure that activity and how you would make people get the most value out of it. The other thing we did was to build team based simulation exercises. I remember this very clearly because we worked with Illumina, who are a sequencing company that allow for short read sequencing. And they– in collaboration with them, we help built a simulation exercise but people were looking at real data, that was generated off the sequencers and they would help troubleshoot the errors and the QC artefacts that we find in them.
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So it gave them a real feel for what they would do in the real world when they were developing their own surveillance systems back in their home countries. So just a curiosity regarding this course, did you have to adapt your language when you talk to different audiences, did you have to use different vocabularies in some situations? Yes we had a mix of audience who some of whom were experts, whereas others weren’t introduced to genomics weren’t as familiar with genomics when they first arrived. So, this is where the fundamental modules helped, because we tried to bring that grounding in the first couple of days. So they were familiar with the job and familiar with the terminology.
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And then, they could then be on par with the other participants, to then go ahead with the course and the hands on training. So, it looked like everything went fine. So would you change anything in the course design? That’s really interesting question. I mean it’s a pilot course isn’t it? So I feel that having led the training for the wet lab, one of the overwhelming pieces of advice and feedback that I got, and in some ways I do resonate with, is that people wanted the course to be a lot longer. So, organising laboratory activities can take a lot of time, at the very time consuming and they take almost whole days.
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So, one of the things was that if we could space the activities a bit more, then people would get time to analyse and reflect between the practical sessions and the theory that we taught them. So that was one thing if feasible I would try and change. I would definitely add more experiential content. So, this is a very unique course where we teach people how to build a surveillance system in the real world not just learn something on a course and go back and try and apply it but we give them tools where they can apply it. So I think giving them more simulation based scenarios, would be incredible, because it would test their decision making and troubleshooting a lot better.
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And this would in turn make the course a bit longer as well. So, it kind of ties into where we want to be. Also, it would try and accelerate the fact that how they would share their skills with others, so it would definitely help that. One of the key factors, I don’t think this is something I would change necessarily, but it’s something I would hope would continue in future versions, which is, the course already offered several travel bursaries and was completely free of charge and I’m glad that that’s going to continue with this collaboration, because the people attending this course where are coming from organisations that are in the most remotest and resource limited settings and don’t always have the support to attend the courses abroad.
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So I would definitely want that to continue, from a personal point of view. So you already touched on this, give us some specific points you’ve learned from teaching mixed audiences? Yeah, I think one of the main things I’ve learned, is that genomic surveillance in general, having done it myself, is a streamlined effort. So, I almost compare it sometimes to like a symphony being synthesised where there are so many different specialists moving parts and you have a coming together, so the symphony comes together like a concerted national effort and there’s so much collaboration and so much sharing of ideas.
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So, the success of such a course, I think, teaching several different expertise levels and several different specialists, it shows that there’s definitely like a universal need for this nature of course that teaches how to teach forward. So it’s a very innovative style and I think this knowledge transfer should be– this teaching transfer model should be applied to several courses around the world. And I think that’s something I would definitely take away for future iterations of this. Thank you Mihir, it was great talking to you. I’m sure our learners have a lot to learn from what you’ve talked about. Absolutely it’s my pleasure. Thank you.

Mihir Kekre is the Laboratory Operations Lead for the Global Health Research Unit on Antimicrobial Resistance Surveillance. He was an educator on the Train the Trainer course on capacity building for Genomic Surveillance of AMR (described by Prof David Aanensen in Step 2.4, Case study on Train the trainer courses), as lead instructor on the laboratory modules.

The curriculum of this course was divided into genomics laboratory training and bioinformatics. The morning sessions of the course were focussed on pedagogy and how to train, and then the afternoons were devoted to learning specific topic areas, and framing those into ways to forward train. The course was attended by wet lab scientists, computational scientists, data experts and epidemiologists from around the world. In this interview, Mihir addresses important questions on how to approach a mixed audience from all over the world and how to adapt the training to different levels of expertise and different professional backgrounds.

Genomic surveillance of AMR is a concerted effort and requires multiple specialties to work together and to understand each other’s work.

Mihir stresses on the fact that the introductory modules of the Train the Trainer course aimed to create a bridge between participants’ different backgrounds.

Genomic Laboratory experts were paired up with bioinformaticians and encouraged to discuss, approach exercises together and in this way, develop a common language.

The training course implemented exercises that aimed to mimic the real world and included team-based simulation activities. For example, a simulation exercise was run along with representatives from the Illumina company. Course participants worked with real data, troubleshooting errors, and quality checking sequencing artefacts, just as they do in the real world. Similarly, activities were also designed around generating antibiograms and susceptibility profiles for resistant microbes plated in real-time.

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Train the Trainer: Design Genomics and Bioinformatics Training

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