Antibiotic resistance is a global problem in healthcare. Whole-genome sequencing is a novel approach for rapid identification of bacterial resistance genes from clinical samples. Knowing which resistance genes are present facilitates rapid selection of appropriate treatment options for patients. Scientists at Quadram Institute Bioscience (QIB) are internationally recognised for research on antibiotic resistance. By sharing expertise in advanced genomic techniques for the identification, tracking and spread of resistance, the Quadram Institute is helping to build research capacity in less developed nations and contribute to improved health outcomes for vulnerable people.

The project

Whole genome sequencing is not available everywhere. For example, in Pakistan current patient screening methods rely on more conventional tools that are expensive and not sufficiently sensitive to identify resistance genes in bacteria. In this project, PhD student Samyyia Abrar from the University of Punjab undertook a Higher Education Commission of Pakistan-funded, six-month placement at QIB to establish a collaborative network and gain experience in cutting edge genomics techniques applicable to her research in Pakistan. Working with QIB’s Professor Mark Pallen, she used the latest whole-genome sequencing techniques to identify the resistance genes present in clinical isolates from patients in Pakistan.

The trend in antibiotic resistance in Pakistan is similar to that observed in other countries. However, it has been compounded by a weaker health system, less effective infection controls, increased over-the-counter drug sales and limited access to quality diagnostic facilities. This makes Pakistan a high impact target for supporting a reduction in improper and repeated antibiotic use. Antibiotic resistance is linked to increased mortality and disease rates as well as aggravated suffering through prolonged hospital stays and increased financial burdens to both patients and medical institutions in Pakistan. Patients with limited ability to fight infections, such as those undergoing cancer treatment, are more vulnerable to the impact of drug resistance and this project represents an opportunity to make a significant contribution to their health and wellbeing as well as potentially saving lives.

The outcome

Samyyia sequenced over 200 clinical isolates from Pakistan and identified a unique combination of resistance genes that were present in all her samples. These findings will underpin the development of a prototype identification kit based on multiplex Polymerase Chain Reaction (PCR) methodology. This kit represents a practical and affordable diagnostic tool for use in hospital laboratories in Pakistan; it will accelerate the identification of antibiotic resistance genes in bacteria from patient samples and thereby increase treatment efficacy.

“The placement at Quadram Institute Bioscience has improved my knowledge and experience in genome sequencing. This will support my career development as I hope to achieve a researcher position in the near future. The visit will help to open a new horizon of collaboration between institutes”. Samyyia Abrar, University of the Punjab, Lahore, Pakistan

The development of the prototype kit is underway in collaboration with CitiLab & Research Centre (CLRC), Lahore and funding has been sought from the Technology Development Fund (Higher Education Commission funding scheme) by Samyyia’s PhD supervisor at the University of Punjab to develop the prototype further.

In summary

Increased research capability can be achieved through training in genome sequencing. In this case, Quadram Institute scientists are enabling researchers, like Samyyia, to establish research careers in microbial genomics and make significant contributions to the development of improved diagnosis tools that improve treatment efficacy for vulnerable patients in Pakistan.