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 Bioinformatics Expert for bioinformatics work. The established microbiology laboratory is focused on enhancing the detection, monitoring, and research of Antimicrobial Resistance (AMR) using advanced Whole Genome Sequencing (WGS) technologies. The bioinformatician will analyze and interpret genomic data and support the laboratory’s efforts to understand and combat AMR. Furthermore, they will ensure the analyzed data is presented at national and international forums and its publication in high-impact factor journals with support from the WGS team. 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 Bioinformatician is to provide expert analysis and interpretation of WGS data related to AMR. The Bioinformatician will develop and maintain bioinformatics pipelines, collaborate closely with the WGS Expert, DAI, and LSTHM team, and contribute to the laboratory's research publications related to Bioinformatics.

The Bioinformatician will be responsible for the following tasks:
Data Analysis and Interpretation:
• Develop and maintain bioinformatics pipelines for the analysis of WGS data with a focus on AMR detection.
• Analyse WGS data to identify resistance genes, mutations, and other relevant genomic features.
• Collaborate with the WGS Expert to ensure seamless integration of sequencing data into bioinformatics workflows.

Tool Development and Optimisation:
• Develop and optimise bioinformatics tools and algorithms to enhance the accuracy and efficiency of WGS data analysis.
• Stay updated on the latest developments in bioinformatics and incorporate new tools and methods into the laboratory’s workflows.

Data Management:
• Ensure proper storage, organisation, and management of large genomic datasets.
• Implement and maintain databases or platforms for efficient data retrieval and analysis.

Collaboration and Training:
• Work closely with laboratory staff to support data analysis needs and provide bioinformatics expertise.
• Train laboratory personnel in essential bioinformatics tools and techniques for WGS data analysis.

Research and Reporting:
• Contribute to research projects by providing bioinformatics analysis and insights.
• Prepare reports on bioinformatics activities, including data analysis outcomes and tool development.
• Contribute to research publications, presentations, and grant proposals.

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
A PhD in Bioinformatics, Computational Biology, Genomics, or a related field with a proven track record of PhD research/sub-search in WGS/informatics.
Preference: Candidates with master’s in microbiology, infectious diseases, molecular biology, or other fields.

Professional Experience
• At least 7+ years of experience in bioinformatics, particularly in analyzing WGS data.
• Experience with bioinformatics tools and pipelines, specifically for AMR detection and genomic data analysis.
• Familiarity with genomic databases, data management, and the development of bioinformatics algorithms.

Technical Skills
• Proficiency in programming languages such as Python, R, or Perl, and experience with bioinformatics software (e.g., BLAST, BWA, SAM tools).
• Strong understanding of AMR mechanisms and the genomic features associated with resistance.
• Experience with high-performance computing environments and data management platforms.
• We have a proven track record of publications related to bioinformatics data sharing in international high-impact journals.

Females, personal from vulnerable/disadvantaged populations, and differently abled personal are highly encouraged to apply