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Pakistan-US Science and Technology Cooperation Program
Phase 7 (2017 Deadline)

Rapid bacteria identification in rural communities of Pakistan via cloud storage
US Partner: Ya-Hong Xie, University of California, Los Angeles (UCLA)
Pakistan Partner: Khalid Mahmood, Government College University, Faisalabad
Project summary
This project will establish a protocol for fast and low cost identification of bacteria for use in rural areas of Pakistan and in the US using a nano-engineered assay developed by UCLA. Commercialization efforts are planned with Sensorem, LLC, a US-based company.

Progress Reports

The project aim is to provide a fast diagnosis technology alternative in bacteria diagnosis to rural communities in Pakistan through the usage of an online cloud system. The project explored the major challenges in Pakistan and focused on the bacteria involved with the Tuberculosis disease and the antibiotic resistance strains typically found in developing countries. The project saw a unique collaboration between the US university of UCLA and the Pakistani university of GCUF where UCLA provided the nanochip (shipped to GCUF), GCUF provided the bacteria and spectroscopy measurement, and then UCLA finally provided the data analysis with AI provided through the online cloud system. The project was successful in showing the feasibility of such a platform and had great accuracy in separating one of the prevalent multi-drug resistant strains of pulmonary Tuberculosis.

2019: We have proposed and developed the Surface-enhanced Raman Scattering based technique combined with principal component analysis and deep neural network to realize biological entities identification which are able to serve as biomarkers in many diseases including proteins, bacteria, exosomes, and cells at clinical valuable level. By cooperating with Pakistan group and providing assistance to them, we are able to build a preliminarily system to collect bacteria induced diseases sample data from local patients. This project will help local area to monitor diseases situation and make diagnostic report in the future.

Also, the basic theoretical research carried out by Prof. Xie’s group, such as orientation dependence of the Raman spectral feature study offers a plausible explanation of high level of specificity of SERS in identification of biological entities including proteins, exosomes and cells. This work provides a solid foundation for SERS to become an important tool for bio-medical applications. With the help from innovative techniques including machine learning, deep neural network and principle component analysis, rapid and precise database of biological samples examination can be realized.

2018: The project aims to develop a nano-technology enabled platform for rapid identification of bacteria in the rural regions of Pakistan. It is also expected to be a vehicle for enhancing the educational infrastructure in Pakistani universities (Government College University Faisalabad, GCUF) through collaboration with UCLA.
During the first full year of the project, significant progress was made in the direction laid out in the original proposal at both GCUF and UCLA.

The GCUF team has all the team members trained at a local hospital (Bahawal Victoria Hospital BVH) in terms of how to collect and handle patient samples and properly dispose of these samples after the measurements. They have taken delivery of a brand-new Raman spectrometer and are expecting the delivery of a scanning electron microscope, thereby significantly enhanced the experimental infrastructure of the university. One of the female faculty members, Ms. Salma Irfan is currently visiting UCLA where she is receiving training by the UCLA group for proper usage of the unique nano-technology platform invented by the UCLA group for analyzing patient blood samples for bacterial infection.

The UCLA team has been improving the nano-technology platform via computer aided design followed by nano-fabrication. A number of nano-structured plasmonic substrates has been supplied to the GCUF team. While waiting for the delivery of the Raman spectrometer at GCUF, the UCLA team has made headway in establishing the capability of the nano-technology platform in analyzing patient cerebrospinal fluid (CSF) for the purpose of being potentially used as biology-based test method for diagnosing Alzheimer’s disease, Parkinson’s disease and other neurodegenerative diseases. Studies have also been conducted for successful identification of exosomes with tremendous potential in the diagnosis of an array of disorders including cancer. Finally, successful identification of colon cancer cells has been demonstrated. These accomplishments have resulted in five manuscripts with three of them published so far.