Capacity development in genomic sequencing for AMR

Capacity development in genomic sequencing for AMR

June 2021

Pernille Nilsson

Project Manager SEQAFRICA

The African experience (SEQAFRICA)

June 2021 The Fleming Fund | SEQAFRICA 2

SEQAFRICA – Extending whole genome sequencing capacity for AMR Surveillance

• Led by the Research Group for Global Capacity Building at the National Food Institute (DTU Food), Denmark.

• Established and currently support a consortium of regionaland national sequencing centres

1. Nigeria, University of Ibadan (UI)

2. Tanzania, Kilimanjaro Clinical Research Institute (KCRI)

3. South Africa, National Institute for Communicable Diseases (NICD)

4. Ghana, Noguchi Memorial Institute for Medical Research (NMIMR)

5. South Africa, NICD, SARS-CoV-2


Bringing WGS into AMR surveillance

• Develop and support WGS and bioinformatics capacity for AMR surveillance across Africa

• Sequencing efforts are focused on several key pathogens• E.g. E. coli. Salmonella spp., Klebsiella pneumonia, Acinetobacter spp.• Contemporary (and archived isolates)• Sequence goal of 16.000 genomes

• Contribute to the global pandemic surveillance efforts of SARS-CoV-2


Resources we provide

• WGS and data analysis services to the African region

• Support genomic surveillance efforts and investigation of

• Outbreaks

• Unusual resistance phenotypes

• Delineation of the flow of organisms/genes in a One Health framework

• Training


Long read sequencing training at NICD

SEQAFRICA implementation progress - Overall

Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 Q10 Q11 Q12

On-going support

Kick-off meetingAug 2019 Sept 2021 Spring 2022

NCEInitiated procurement process of sequencers

Conducted training course Module 2

COVID-19 pandemic


Agreement signedJun 2019

Signed agreements for sequencing machines

16.000 genomes

Today

Online need assessment

Consortium established

Initiated procurement process of additional sequencer

Hamilton sequencing robot installed at NICD

MiSeq installed at UI

NextSeq550 installed at KCRI

Advanced bioinformatics and long read sequencing courses at DTU

Sequencing initiated

Sampling initiated

Training course Module 4


12 months


SEQAFRICA implementation progress – Training

Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 Q10 Q11 Q12

On-going support

Sept 2021 Spring 2022

NCE


COVID-19 pandemic


Conducting training course Module 3

Long read sequencing training at NICD

TodayKick-off meetingAug 2019


Advanced bioinformatics and long read sequencing courses at DTU Training course

Module 4


Virtual Training modules

• Module 1 – Introduction to WGS in AMR surveillance 15 Feb – 26 Feb 2021

• Module 2 – WGS workflow – from isolate to analysis 22 March – 29 March 2021

• Module 3 – SARS-CoV-2 – whole genome sequencing17 May – 28 May 2021

• Module 4 – Advanced bioinformatics using command line Fall 2021

The Fleming Fund | Presentation 8June 2021

Module 1: Introduction to Whole Genome Sequencing in AMR surveillance

• The course provided an introduction to Whole Genome Sequencing (WGS) and its use in Antimicrobial resistance (AMR) surveillance.

• The participant will upon completion of the course

• i) know what WGS is and how it can be used and

• ii) be able to use freely available online tools to perform simple bioinformatics analysis and interpret results

Panel discussion on Genomic Surveillance (PGI, WHO, US FDA, DTU and NICD), will be transformed into an opinion piece intended for scientific publishing

Benin 1Cameroon 2Eswatini 3Ghana 10Kenya 21Malawi 3Nigeria 15Senegal 1

South Africa 12Sudan 2Tanzania 1Zambia 6Zimbabwe 6

83

NGS in country

Participants


Module 2: WGS workflow – from isolate to analysis

• The course introduced and covered all aspects of the entire WGS workflow starting with a bacterial isolate and finishing with completely analysed DNA sequence/genome.

• The participant will upon completion of the course

• i) know all the steps included in preparing and conducting WGS using Illumina short read technology and

• ii) similarly know the steps included in preparing and conducting long read sequencing using the MinIonfrom Oxford NanoporeTechnologies (ONT).

Benin 1Cameroon 2Eswatini 3Ghana 8Kenya 15Malawi 2Nigeria 14Senegal 1South Africa 11Sudan 2Zambia 6Zimbabwe 4

69

NGS in country

Participants


Module 3: SARS-CoV-2 – whole genome sequencing

• The course introduced and covered all aspects of the entire WGS workflow for SARS-CoV-2 starting with a respiratory sample and finishing with completely analysed genomes.

• The participant will upon completion of the course know

• i) all the steps included in preparing and conducting WGS using Illumina short read technology

including the

1. wet laboratory procedures

2. computational genome assembly

3. use of online tools to assess phylogenies and mutations in the global context.

French interpretation option added

Ghana 2

Kenya 5

Mauritius 1

Morocco 1

Nigeria 2

South Africa 10

Sudan 2

Tunisia 3

26

NGS in country

Participants


Virtual Training modules

85.71%

100%

92.31%

90.48%

100% 100%

95.24%

100% 100%

75%

80%

85%

90%

95%

100%

Module 1 Module 2 Module 3

Agree or Strongly Agree

Fulfilled my learning expectations Course was overall well organized Online material was informative

“I can understand my own data, use online tools and do basic interpretation confidently.”

“The exercises were a good tool to measure the depth of what was taught during the course”


SEQAFRICA implementation progress – Sampling and WGS

Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 Q10 Q11 Q12

On-going support

Sequencing initiated

Sept 2021 Spring 2022

NCE

Today

COVID-19 pandemic

16.000 genomes

Samples in-house:~8500 isolates/samples53 %

Sampling initiated

WGS completed:~4400 isolates/samples27 %

Sampling ongoing at all 5 partners

Kick-off meetingAug 2019



Countries SEQAFRICA has/will be providing WGS services to


Countries SEQAFRICA has/will be providing WGS services to

Fleming Fund partner countries


Sample inventory

NMIMR:Bacterial: 533SARS-CoV-2: 100

UI: Bacterial: 866

KCRI:Bacterial: 1429

NICD:Bacterial: 3777

Number of countries serviced: 14Total accepted: 8549

NICD COVID19:SARS-CoV-2: 1844


Sequence inventory

NMIMR:Bacterial: 217SARS-CoV-2: 90Of goal: 30.7 %

UI: Bacterial: 1

KCRI:Bacterial:

NICD:Bacterial: 3020Of goal: 60.4 %Total sequenced: 4369

Percent of goal: 27 %NICD COVID19:SARS-CoV-2: 1041Of goal: 104.1 %


Major challenges

1. Procurement

2. Supply chaini. Stable supply of reagents and consumables

3. Logistics

4. ”Brain drain”


Major Lessons learned

1. Follow-up till you drop

2. ‘No man is an island’ – Collaborations/Synergy/Alignment

3. Country-specific barriers require country-specific solutions• However, regional/continental solutions would/could/are necessary for

sustainability on the continent. Import regulations vary among countriesand equipment can be harder to import to some countries than others, having compentent and knowledgeable people to assist in import and customs clearance is key

4. Virtual training can be a valuable asset


Contact us for more information

Reference sequencing opportunities

WGS Training modules

Coursera E-learning courses

[email protected]

[email protected]

(Pernille Nilsson, Project Manager)

[email protected]

(Rene S. Hendriksen, Technical Lead)

antimicrobialresistance.dk/seqafrica.aspx

@AfricaSeq

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mailto:[email protected]



https://antimicrobialresistance.dk/seqafrica.aspx

Thank you

This programme is being funded by the UK Department of Health and Social Care.

The views expressed do not necessarily reflect the UK Government’s official policies.

Documents

Capacity development in genomic sequencing for AMR