Pathogenic Bacteria Identification and Antimicrobial Genetics by Nanopore Sequencing

Nosocomial bacterial infections are a prevalent issue due to pathogenic bacteria having easier access to invade the bloodstream. Over the years pharmaceutical companies have released a variety of antimicrobial drugs to combat this problem, however, the over-prescription, along with bacteria’s innate ability to adapt, has led to increased resistance.¹ Due to current analytical limitations, it is challenging to quickly identify pathogenic bacterial strains and their antibiotic susceptibilities in a clinical setting.² Nanopore sequencing is a newly emerging analytical technique with an efficient design that can aid in the identification of bacteria down to the strain level. Nanopore sequencing involves isolating bacteria from human samples like blood, cerebrospinal fluid, or sputum, DNA and RNA extractions, and real-time genomic sequencing.³ The nanopore sequencing device contains pores where electrodes create an electric current.⁴ As they traverse the flow cell, nucleotides disrupt the electric currents resulting in a real time, near complete genetic sequence of the sample.⁴ Nanopore sequencing has been shown to identify bacterial species with as low as 10²-10⁴ CFU/mL within 2 hours of incubation and determine antimicrobial resistance genes (ARG) with 10³-10⁷ CFU/mL within 9 hours.³ With sequence coverage over 90%, nanopore sequencing rivals current culture-based identification methods in accuracy and speed.³

Citations

(1) Tahmasebi, H.; Arjmand, N.; Monemi, M.; Babaeizad, A.; Alibabaei, F.; Alibabaei, N.; Bahar, A.; Oksenych, V.; Eslami, M. From Cure to Crisis: Understanding the Evolution of Antibiotic-Resistant Bacteria in Human Microbiota. Biomolecules 2025, 15 (1), 93. DOI:10.3390/biom15010093. 

(2) Zhang, L., Yu, X., Zhang, C., Zhang, X., Huang, H., & Peng, J. (2024). Development and Comprehensive Evaluation of Culture-independent, long amplicon-based targeted next-generation sequencing methods for predicting antimicrobial resistance in tuberculosis. Analytical Chemistry, 97(1), 281–289. https://doi.org/10.1021/acs.analchem.4c04166 

(3) Ali, J., Johansen, W., & Ahmad, R. (2024). Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing. Scientific Reports, 14(1). https://doi.org/10.1038/s41598-024-55635-z 

(4) How nanopore sequencing works. Oxford Nanopore Technologies. (2025). https://nanoporetech.com/platform/technology