Dr. Beverly Egyir, FAO's Dr. Jeff Lewjene, Dr. Bright Adu, and Marco Van Zwetselaar conducted a workshop at the Noguchi Memorial Institute for Medical Research in Ghana from May 22–25, 2023,. Participants from nine African nations gained expertise in data analysis, ONT sequencing, AMR surveillance, and microbiological risk assessment as a result of the program. After receiving computers, MinION devices, and practical instruction, participants participated in group presentations and closing statements.
WORKSHOP: STRENGTHENING MICROBIAL RISK ASSESSMENT FOR FOOD SAFETY AND ANTIMICROBIAL RESISTANCE USING PORTABLE DNA SEQUENCING TECHNOLOGIES
22ND -25TH MAY 2023
NMIMR, ACCRA-GHANA
INTRODUCTION
The training on strengthening microbial risk assessment for food safety and antimicrobial resistance using portable DNA sequencing technologies began from Monday 22nd – Thursday 25th May 2023. There were participants from nine (9) African countries namely: Benin, Cameroon, Eswatini, Ghana, Kenya, Malawi, Nigeria, Zambia and Zimbabwe. The training was held at the Noguchi Memorial Institute for Medical Research, University of Ghana and funded by SeqAfrica, FAO and the Fleming fund. The training aimed to equip participants with skills needed to tackle the problem of AMR head-on across the African continent as well as have both wet lab and dry lab skills on sequencing using the ONT sequencing platform and analyzing sequenced data. The trainees were given laptops and Minion to use back in their countries.
Day 1
The day began with a welcome address by Dr. Beverly Egyir after facilitators and participants arrived and settled in. There was a brief session of introduction by facilitators and participants where participants stated their expectations at the end of the training. There were also two representatives from FAO. Some expectations of the participants include:
To maximize their knowledge and gain more genomic skills which will be relevant in the fight against AMR
To be equipped with the workflow of ONT
To broaden their knowledge in using bioinformatics tools
Looking forward to see a picture/tree after sequencing the E.coli isolates from the various African countries
Use ONT for AMR surveillance by gaining skills on the bioinformatics tools needed
After the introductions, participants and facilitators stepped out for a group picture
Participants along with facilitators took a group picture after the brief introductions. A facilitator, Dr. Beverly Egyir gave the first presentation for the day on the topic ‘AMR bacteria from food and animals in Ghana.’ She spoke on the indiscriminate use of antibiotics on farmlands, which is fueling the issue of AMR and the complex network between these animals, the environment and humans. The findings of the research she presented proves to highlight the importance of AMR surveillance for safety in one health.
Dr. Bright Adu gave a presentation after the first presentation by Dr. Egyir. He presented on the Oxford Nanopore Technologies (ONT) sequencing platforms. He took the participants briefly through the history of sequencing and how it the concept of sequencing has evolved over the years. He ended his presentation by explaining clearly the process of the ONT workflow.
There was break for snacks after the presentation. Before the snacks, participants were grouped into seven (7) teams. Each team consisted of not more than four (4) individuals to enhance proper hands-on session in the labs.
After snacks, all the team members of group 1 to group 4 moved to the lab for a practical session on preparing libraries for sequencing using the Rapid Barcoding Kit. In the lab, participants took turns in the biosafety hood to have some hands-on experience preparing the libraries using the Rapid sequencing gDNA – barcoding (SQK –RBK 110.96) protocol as guide. Facilitators were also present in the lab to assist participants prepare quality libraries.
While group 1 to group 4 were in the lab, group 5 to 7 were in the conference hall. A facilitator, Marco Van Zwetselaar introduced the participants to analysis on ONT sequenced data entailed. He introduced a few of the many bioinformatics tools available and spoke briefly, on what nanoporins are. The lecture aimed to help participants get familiar with the tools, terms and command lines that would be useful in analysis.
After each of the sessions ended, there was break to have lunch. The first group that was in the lab moved to the conference room after the lunch and vice versa. The day ended after each session.
Day 2
Participants and facilitators arrived and settled in for the day’s activities. The day began with a recap of day one’s activity. A participant, Luria Leslie, led the wet lab session (preparing libraries using the rapid barcoding kit) of the recap and Grey-Areben led the dry lab session. The laptops given by the FAO was distributed after the recap session. The facilitators and the FAO representative Dr. Jeff Lewjene handled over the laptops to every participant.
The participants were then assisted through the process of signing the property loan form from FAO for the item (laptops) received. A facilitator, Marco Van Zwetselaar, began the step-by step process on how to set up the laptops for Minion analysis with participants.
Around mid-morning, there was some time for snack break after which the set-up processes continued until the day ended. The set up process included getting the device to run Ubuntu, some installations were done and the conda environment was set up to install some packages. There was time for lunch the afternoon.
Day 3
On the morning of the third day, participants arrived and settled in. The first activity of the day was to retrieve sequenced data from the Minion. The participants were made to go to the lab in groups to retrieve the data sequenced that had been running since day 1 of the training. Snacks were taken after retrieving each group’s data. Christian Owusu-Nyantakyi taught the participants how to assembly the sequenced data using Flye. After which Grebstad Rabbi Amuasi took over and took the participants through the Centre for Genomic Epidemiology (CGE) platform. He demonstrated how to check for resistant genes, virulence genes, MLSTs using the CGE platform. There was break for lunch after these sessions.
After the lunch break, Marco Van Zwetselaar introduced MOSS (Microbial Outbreak Surveillance System) to the participants. The day ended with the session with Marco.
Day 4
Today being the last day of the training, T-shirts for the training were shared for participants and facilitators first thing in the morning. After everyone settled in with their laptops set up, a facilitator, Marco Van Zwetselaar took participants through final set up processes, which included using the virtual box. There was break for snacks. Participants moved into groups to prepare for their presentations. After hours of working in groups, analyzing the sequenced data from day 3 as well as preparing ppts for the presentation, there was a break for lunch.
The presentation in groups began directly after lunch. Each group took turns presenting their findings after analyzing their data. After the presentations, Dr. Beverly Egyir and Dr. Jeffery Lewjene presentated participants and the facilitators as well.
Dr. Jeffery Lewjene gave the final remarks. He addressed a few things in his remarks. He assured participants the Minion will be shipped to their various countries because there has been a delay at the port in Ghana. He ended by congratulated and thanked participants and facilitators for making it to the training. The day ended with a vote of thanks by Dr. Beverly Egyir. There was time for picture taking and networking at the end of the day before participants departed to their hotel.
