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PulseNet Africa ONT Feasibility Study 2025 Application
1.
Name:
2.
Organization:
3.
Country:
4.
Select sequencing platforms that you have access to
Illumina iSeq
Illumina MiSeq
Illumina MiniSeq
Illumina NextSeq 1000/2000
ONT Mk1b
ONT Mk1c
ONT Mk1d
ONT Gridion
Other (please specify)
None of the above
5.
How many staff regularly perform sequencing in your laboratory?
0
1
2
3
4
5
More than 5
6.
How many staff regularly perform bioinformatics analysis in your laboratory?
0
1
2
3
4
5
More than 5
7.
Does your laboratory perform in-house bioinformatics analysis?
Yes
No
8.
What bioinformatics tools/programs/pipelines does your lab currently use?
BioEdit
GCE Tools (ResFinder, VirulenceFinder, PlasmidFinder, SerotypeFinder)
CLC Genomics
Command Line
EDGE
EPI2ME
Galaxy
Geneious
MEGA
Pathogenwatch
Terra.bio
Other (please specify)
None of the above
9.
Which public repositories does your lab share data with?
NCBI
EBI
DDBJ
Other (please specify)
None of the above
10.
How are samples obtained for sequencing in your laboratory?
Outbreak samples
special projects
surveillance
biobank
Other (please specify)
11.
What metadata is available for samples that are sequenced?
Sample source
pathogen type
type of infection
collection date
patient data (date of birth, sex, etc.)
AST/phenotypic testing data
Other (please specify)
12.
Will sharing of sequencing data with PulseNet Africa members be possible?
Yes
No
13.
Does your lab participate in national surveillance for AMR of enteric bacteria?
Yes
No
14.
Does your lab participate in External Quality Control System for AST through Global Foodborne Infections Network (GFN)
Yes
No
15.
Does your lab upload data to the following programs? GLASS, WHO-NET
Yes
No
16.
Please describe your laboratory’s role in national enteric disease and AMR surveillance.
17.
Please provide your feasibility study proposal description. This should include the priority pathogen that will be sequenced, the one-health component of the project, any collaboration with other sites or institutions and desired public health impact (2 page limit, standard margins, font size Arial 10.5 or Times New Roman 12).
18.
Provide the source of isolates and % (i.e. 100% clinical, 50% clinical and 50% environmental)
19.
How will isolates be obtained?
Surveillance samples
project samples
biobank samples
Other (please specify)
20.
How many people will be participating in sequencing these isolates?
1
2
3
4
5
More than 5
21.
How many people will plan on becoming PNI certified? (Note: Reagents provided will support certification strain sequencing for up to two staff)
1
2
22.
Do you foresee challenges in being able to complete sequencing of certification strains and feasibility bacterial enteric strains by August 30, 2025.
Yes
No
23.
If yes to previous question, please explain any challenges your laboratory might encounter in completing the sequencing of 100 isolates after receiving the sequencing reagents.
