Sequencing and antimicrobial resistance profiling of clinical isolates from Nairobi, Kenya in a resource-limited setting
About Meenakshi Iyer
Meenakshi Iyer is a postdoctoral fellow in the ‘Indo-Africa dengue sequencing, vaccine design and capacity building’ consortium with Prof. Sudhir Krishna at National Centre for Biological Sciences, TIFR, Bengaluru, Karnataka, India. She is interested in developing pipelines for genomics data analysis, and has also worked on structural biology and the protein sequence-structure-function relationship.
To investigate whether MinION-only sequencing is sufficient for identification, genome sequencing and downstream analysis in resource-limited settings, we sequenced the genomes of fourteen clinical isolates suspected to be Neisseria gonorrhoeae from Nairobi, Kenya. Using whole-genome sequencing, we identified N. gonorrhoeae and N. meningitidis. Computational AMR prediction could be used along with routine susceptibility tests in clinics. The workflow for genome identification followed in the study, assembly and analysis could be used for any clinical isolate. Further studies are required to determine the utility of real-time sequencing in outbreak investigations, diagnosis and management of infections, especially in resource-limited settings.