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<!DOCTYPE html>
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<title>GPS :: Global Pneumococcal Sequencing Project</title>
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<h1><i class="fa fa-rocket lblue"></i> Capacity Building </h1>
</header>
<div class="desc">
<p>
Surveillance is an inherently longitudinal process so sustainability
in the future is vital. A key focus of the second phase of the GPS project
(GPS2) is to establish a working system for sustainable genomic surveillance
with an emphasis on decentralization of data generation and analysis, especially
in low- and middle- income countries (LMICs) where the burden of pneumococcal
disease is high. In view of variation in local infrastructure and resources, the
GPS project devises bespoke support for project partners to cater for different
needs in sequencing, training and mentorship.
</p>
<h2>Sustainable local sequencing</h2>
<p>
At the beginning of GPS2, the GPS team engaged with key partners to discuss the
feasibility of local data generation and resources required, identifying 10
institutes in 8 LMIC countries:
</p>
<ul>
<li>
Bangladesh (<a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="http://chrfbd.org/about-us/">CHRF</a>)
</li>
<li>
India (<a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="https://www.cmch-vellore.edu/">CMC</a> and
<a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="http://www.kimsbangalore.edu.in/">KIMS</a>)
</li>
<li>
Kenya (<a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="https://www.kemri.org/">KEMRI</a>)
</li>
<li>
Malawi (<a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="https://www.mlw.mw/">MLW</a>)
</li>
<li>
Nigeria (<a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="https://www.ui.edu.ng/">University of Ibadan</a> and
<a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="https://run.edu.ng/usite/">Redeemer's University</a>)
</li>
<li>
Pakistan (<a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="https://www.aku.edu/Pages/home.aspx">AKU</a> and
<a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="https://lums.edu.pk/">LUMS</a>)
</li>
<li>
South Africa (<a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="https://www.nicd.ac.za/">NICD</a>)
</li>
<li>
The Gambia (<a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="https://www.lshtm.ac.uk/research/units/mrc-gambia/about">
LSHTM MRC unit</a>)
</li>
</ul>
<h2>Enhancing local capacity for data analysis</h2>
<p>
A key aim of GPS2 is to support the development of skills of local
researchers who become confident to independently analyse genomic data.
Supporting the development of bioinformatics expertise is achieved
through a multi-faceted approach, through a combination of online
training, in person workshops and ongoing mentoring.
</p>
<figure class="row text-center">
<img src="img/2019_writers_workshop-1500px.jpg"
alt="photograph of the participants" style="width:50%" />
<figcaption>
Participants at the 2019 writers workshop at the Wellcome Sanger Institute
</figcaption>
</figure>
<p>
In 2019, collaborators from six LMIC countries joined the GPS team at
the Wellcome Sanger institute for an intensive week focused on analysis
and drafting of country analysis papers for publication, some of which
have been published. Our plans for an in person bioinformatics workshop
are currently on hold due to the pandemic. However, free
<a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="https://training.bactgen.sanger.ac.uk/#/">online training</a>
resources have been developed by the GPS and JUNO training manager
Christine Boinett. We aim to deploy a face-to-face or virtual format 5 day
bioinformatics course to supplement the online courses in partnership with
colleagues from <a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="https://www.wellcomeconnectingscience.org/">
Wellcome Connecting Science</a> (WCS).
<a target="_blank"
title="free courses from Wellcome Connecting Science (opens in a new window)"
aria-label="open free courses from Wellcome Connecting Science in a new window"
href="https://www.futurelearn.com/partners/wellcome-genome-campus">
Other FREE courses</a> from
WCS, in partnership with FutureLearn are currently available online for
anyone to take in their own time. Some of these courses offer
<a target="_blank" title="opens in a new window"
aria-label="open link in a new window"
href="https://cpduk.co.uk/explained">continuing
professional development</a> (CPD) credits.
</p>
<p>
Below is some feedback from two of our partners who attended the writers
workshop. You can also find out more about
<a target="_blank"
title="Samanta Almeida's publication in Microbial Genomics (opens in a new window)"
aria-label="open Samanta Almeida's publication in Microbial Genomics in a new window"
href="https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000635">
Samanta Almeida</a>’s and
<a target="_blank"
title="Paula Gagetti's publication in Microbial Genomics (opens in a new window)"
aria-label="open Paula Gagetti's publication in Microbial Genomics in a new window"
href=""https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000636>
Paula Gagetti</a>’s in-depth country level S. pneumoniae genomic analysis work through
their publications in Microbial Genomics.
</p>
<figure class="clearfix" style="color: darkgreen;">
<blockquote style="min-height:335px;"> <!-- set min-height with reference to img height -->
<p>
<img class="pull-left" style="height:300px; width:auto; padding-right:2ex;"
src="img/Samanta-600px.jpg" alt="photograph of Samanta Almeida" />
“The participation in the GPS project was an experience analysing WGS data and meeting
the challenge of handling a large volume of data. The GPS team made a great effort to
help me with the analysis and to address difficulties. In my opinion, it is a project
that goes far beyond data generation, as there is a real effort to build capacity by
sharing knowledge and providing bioinformatics training. During my participation, I
received many incentives to develop studies and opportunities to present these results.
I presented abstracts in the most important pneumococcus international events, the
International Symposium on Pneumococcal and Pneumococcal Diseases (ISPPD), Australia
(2018), and Toronto (2020) editions.”
</p>
</blockquote>
<figcaption>
Samanta Almeida, Center of Bacteriology, Adolfo Lutz Institute, São Paulo, Brazil
</figcaption>
</figure>
<figure class="clearfix" style="color: darkgreen;">
<blockquote style="min-height:335px;"> <!-- set min-height with reference to img height -->
<p>
<img class="pull-right" style="height:300px; width:auto; padding-left:2ex;"
src="img/Paula-600px.jpg" alt="photograph of Paula Gagetti" />
“The most exciting thing was that prestigious professionals in the pneumococcal area
dedicated a week of their time to sit down with us, discuss our results and draw
conclusions about the impact of vaccines in different regions of the world. That was
really amazing. Added to the human warmth of each of them that also allowed us to share
beautiful moments drinking a beer in the pubs of Hinxton and Cambridge.
</p>
<p>
From there, a very important link was generated. I worked a lot with Steph, whom I thank
for the recognition and respect for our work and for answering all my questions
immediately. Working with such a prestigious group of experts with the highest level of
responsibility gives us the confidence to do other works in the future”
</p>
</blockquote>
<figcaption>
Paula Gagetti (National Reference Laboratory on AMR of the National Institute of Infectious
Diseases, Buenos Aires, Argentina)
</figcaption>
</figure>
<p></p>
<h2>One-to-one training</h2>
<p>
Nida Javaid is a PhD student from a partner group in the Department of Biology, Lahore
University of Management Sciences, Pakistan. Nida obtained an 8 months research fellowship
funded by Higher Education Commission in Pakistan and joined the Bentley group the Wellcome Sanger
Institute for hands-on training in genomic analyses of S. pneumoniae. Unfortunately, Nida’s
arrival coincided with the UK national lockdown and the switch to working from home. Despite these
challenges, Nida quickly integrated with the team, and learnt how to apply key tools used for
characterising the genomic epidemiology of pneumococci to datasets from South Africa and Pakistan.
Dr. Stephanie Lo is Nida’s main mentor and together they made a great mentor-mentee team. As the
lockdown restrictions started easing, Nida started having weekly in-person meetings with Stephanie,
and joined occasional get-togethers with other team members.
</p>
<figure class="row text-center">
<img src="img/Nida-1500px.jpg"
alt="photograph Nida Javaid and Steph Lo" style="width:50%" />
<figcaption>
Nida Javaid and Steph Lo at the Wellcome Genome campus
</figcaption>
</figure>
<p>
Find out more about Nida’s work with the Bentley team:
</p>
<figure class="clearfix" style="color: darkgreen;">
<blockquote>
<p>
“The original plan was that I will be working on the population genomics analysis of
pneumococcal isolates from Pakistan. However, due to the lockdown, sequencing of isolates
from Pakistan was delayed and I started working on the country analysis of pneumococcal
carriage isolates from South Africa. I started with running quality control analysis of the
sequenced data, followed by in silico serotyping, genotyping, prediction of antimicrobial
resistance and phylogenetic analysis from pneumococcal genomes using a wide range of
command-line tools such as SeroBA and PopPUNK. I then visualized the output using Microreact,
a tool that allows me to interactively explore the phylogeny with temporal and geographical
data. Now almost a year and a half later, this manuscript is ready for submission. I would
like to thank Dr. Shabbir Madhi for allowing me to work on his dataset.
</p>
<p>
After a few months, pneumococcal isolates from Pakistan were sequenced. I then analysed these
data using the approach and tools that I had learnt during my first few months at Sanger, and
am working towards publication of my Pakistan country analysis. We also presented our
preliminary results at the ABPHM online conference. Although I am back in Pakistan now, I am
still actively working with Stephanie and attend the team meetings regularly. I would like to
thank Stephen, Stephanie, and the team for their support and kindness. I would also like to
thank my PhD advisor, Dr. Shaper Mirza, for her support and guidance through my PhD.”
</p>
</blockquote>
<figcaption>
Nida Javid (Department of Biology, Lahore University of Management Sciences, Pakistan)
</figcaption>
</figure>
<p></p>
<h2>Portable pipeline: reducing the bioinformatics burden</h2>
<p>
Ensuring quality control of sequence data and generating succinct, reliable data characterising
genomes can be time consuming and require substantial bioinformatic training. During GPS2 a portable
pipeline is being developed which will enable collaborators to easily input whole genome sequencing
data and generate the in silico typing data required for downstream analysis.
</p>
<figure class="row text-center">
<img src="img/gps2_portable_pipeline_flowchart-1500px.jpg"
alt="GPS2 portable pipeline flow diagram" style="width:50%" />
</figure>
</div>
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</section>
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