Introduction

The Fleming Fund (FF) is a U.K. Department of Health and Social Care programme to help low and middle-income countries fight Antimicrobial Resistance (AMR). AMR poses a severe global threat, expected to cause 10 million deaths annually by 2050. With potential costs reaching $100 trillion, its impact on the global economy is significant. Fleming Fund Grants aim to tackle the AMR challenge in developing countries including Pakistan. The grants are funded by the UK Department of Health and Social Care and managed by Mott MacDonald for the country, regional and fellowship grants. Pakistan has received Fleming Fund support since 2019 in the form of two Country Grants, 9 Fellowships, and central and local procurement of equipment, reagents, and consumables. Between 2017 and the end of phase-1 of the program in March 2023, the program has provided financial support to grantees to establish and support local development of national AMR surveillance systems.

In partnership with the Fleming Fund, DAI's programme in Pakistan collaborates with the Pakistani government to strengthen systems using a “One Health” (OH) approach – a multisectoral approach to complex health problems that reaches across human health, animal health, and environment sectors. As global leaders in One Health, the DAI team helps incorporate One Health across programme interventions. DAI is helping Pakistan become a leader in combating antimicrobial resistance, and a model for better management of antimicrobials in human and animal populations. DAI and its consortium partners have successfully secured an additional round, Phase 2, of the Fleming Fund Country Grant in Pakistan which spans from January 2024 to December 2025. The Phase 2 of the FFCG programme focuses on achieving four intermediate outcomes: 1) Production of quality AMR/U/C and burden of disease data; 2) Conducting quality data analysis; 3) Sharing quality data analysis with decision-makers; and 4) Contributing to sustainable investments at both the country and global levels to counter AMR.

Position Summary

The Fleming Fund Country Grant Pakistan (FFCGP) requires a Whole Genome Sequencing Expert (WGS) Expert. FFCGP is working with the National Institute of Health to start the WGS related to AMR, and such required support in the area of WGS will be provided. The established microbiology (bacteriology) laboratory aims to strengthen the detection, monitoring, and research of Antimicrobial Resistance (AMR) through advanced Whole Genome Sequencing (WGS) technologies. The WGS Expert will be instrumental in assisting in setting up and optimising WGS workflows, ensuring high-quality sequencing output, and supporting the laboratory's staff on-spot orientations and further development of training modules. WGS Expert will ensure the success of WA2.03 WGS data incorporated into the national surveillance data deliverable.

Scope of Work
The primary objective of the WGS Expert is to establish, validate, and maintain WGS methodologies within the laboratory, ensuring that the sequencing processes are robust, reproducible, and aligned with international standards. The expert will also be responsible for training laboratory staff on WGS techniques and supporting Bioinformatics in ensuring high-quality testing.

The WGS Expert will be responsible for the following tasks:

Establishment and Optimization:
• Support developing, optimizing, and validating WGS protocols specifically for AMR detection.
• Provide technical assistance in Implementing quality control and quality assurance procedures for the WGS process.
• Technical guidance on maintaining laboratory equipment required for WGS, ensuring adherence to best practices.
• Support Liverpool School of Tropical Medicine (LSTM) for developing SOPs and other documents with the National Institute of Health (NIH).

Capacity Building:
• Train laboratory staff in WGS techniques, covering all steps from sample preparation to sequencing.
• Provide ongoing technical support to laboratory personnel in troubleshooting and improving WGS workflows.
• Whenever required, perform WGS for quality assessment OR whenever requested by NIH.

Collaboration:
• Work closely with the bioinformatics team at NIH, DAI, and LSTH to ensure seamless integration of WGS data into downstream analysis pipelines.
• Engage with external partners and stakeholders to share knowledge and develop collaborative WGS projects on AMR.

Documentation and Reporting:
• Maintain detailed records of WGS protocols, experiments, and results.
• Prepare technical reports on WGS activities and contribute to research publications as needed.
• Ensure WGS results comply with international standards

Research Publications:
• Work closely with the bioinformatics team at NIH, DAI, and LSTH to ensure seamless integration of WGS data into downstream analysis pipelines.
• Engage with external partners and stakeholders to share knowledge and develop collaborative WGS projects on AMR.

Note: Candidate will be assigned any other activity apart from above activities by supervisor if he/she deems necessary.

Requirements (Education, Experience, Skills, Languages etc.):

Qualifications
PhD in Microbiology, Molecular Biology with proven research work in WGS.
Preference: Candidates with an extensive proven track record of WGS laboratory performance and, as such, will be preferred.

Professional Experience
• At least 8+ years of experience in a microbiology laboratory setting, focusing on WGS.
• Proven expertise in WGS methodologies, including sample preparation, sequencing, and quality control.
• Experience in the development and optimization of laboratory protocols.

Technical Skills
• Hands-on experience with WGS platforms such as Illumina and Thermo Fisher Scientific is mandatory. While expertise in Oxford Nanopore or others relevant to AMR detection will be an added advantage
• Strong understanding of AMR mechanisms and the importance of WGS in identifying resistance genes.
• Proven record of published papers on WGS Females, personal from vulnerable/disadvantaged populations, and differently-abled personal are highly encouraged to apply