MinION Whole-Genome Sequencing in Resource-Limited Settings: Challenges and Opportunities

Abstract

Purpose of Review The introduction of MinION whole-genome sequencing technology greatly increased and simplified complete genome sequencing in various fields of science across the globe. Sequences have been generated from complex organisms to microorganisms and are stored in genome databases that are readily accessible by researchers. Various new software for genome analysis, along with upgrades to older software packages, are being generated. New protocols are also being validated that enable WGS technology to be rapidly and increasingly used for sequencing in field settings. Recent Findings MinION WGS technology has been implemented in developed countries due to its advantages: portability, real-time analysis, and lower cost compared to other sequencing technologies. While these same advantages are critical in developing countries, MinION WGS technology is still under-utilized in resource-limited settings. Summary In this review, we look at the applications, advantages, challenges, and opportunities of using MinION WGS in resource-limited settings.

Next-generation sequencing metabarcoding assays reveal diverse bacterial vector-borne pathogens of Mongolian dogs

“…These assays confer a substantial benefit over previously developed mNGS assays on the Illumina platform as the hardware required is relatively cheap (1000 USD), easy-to-use and with per sample analysis costs reaching below ∼6.5 USD, depending on the number of samples multiplexed ( Huggins et al, 2022a , 2023b ). In addition, the MinION™ is a small USB-sized device that is portable and can be used within the field to provide vector-borne pathogen diagnosis even if laboratory access is not available, thereby providing a viable pathogen surveillance methodology for countries such as Mongolia ( Quick et al, 2016 ; Gigante et al, 2020 ; Wasswa et al, 2022 ). Nevertheless, now that this study has acquired key data on canine BVBPs in Mongolia, more detailed and specific pathogen-targeting epidemiological studies can be conducted.…”

Molecular and clinical epidemiology of carbapenem resistant Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacterales in Fiji: a multicentre prospective observational study

“…This entails integrating passive surveillance techniques, utilising available data, and implementing targeted surveillance initiatives to collect data and isolates specifically for AMR surveillance. Moreover, the establishment of a reference laboratory equipped with cost-effective and sustainable sequencing platforms, such as those from Oxford Nanopore Technology, 107 would benefit Fiji. This reference laboratory would play a pivotal role in establishing genome surveillance, seamlessly integrating with epidemiological data to enhance AMR monitoring and management.…”

Future Perspectives on the Application of the Oxford Nanopore® MinION™ Sequencer in Cultural Heritage Biodeterioration Studies

“…Due to the sequencer portability, handling features, adaptability and its analysis speed, the platform allows for an on-site analysis. In fact, multiple reports of such applications are currently available and the technique has been applied for real-time sequencing in differential environmental contexts, such as Ebola surveillance in West Africa, water quality monitoring, environmental microbe analysis, coronavirus SARS-CoV-2 diagnosis and even aboard the ISS [63][64][65][66][67][68][69][70][71]. The technique has also demonstrated to be reliable in resource-limited settings [69], a condition that is also verified for some cultural heritage monuments Worldwide.…”

“…In fact, multiple reports of such applications are currently available and the technique has been applied for real-time sequencing in differential environmental contexts, such as Ebola surveillance in West Africa, water quality monitoring, environmental microbe analysis, coronavirus SARS-CoV-2 diagnosis and even aboard the ISS [63][64][65][66][67][68][69][70][71]. The technique has also demonstrated to be reliable in resource-limited settings [69], a condition that is also verified for some cultural heritage monuments Worldwide. In addition, Oxford Nanopore ® WGS analysis can also contribute to developing countries study of their historical properties' microbial threats.…”

“…While the Oxford Nanopore ® MinION™ sequencer presents numerous advantages for studying microbial communities in cultural heritage materials, several limitations must also be acknowledged. Among them it should be highlighted that: the occurrence of sequencing errors; high cost and difficulties to attain reagent storage in low-resource or remote settings; and the need for strong internet connections for analysis, can hamper new applications of the method [69]. Moreover, the complexity of bioinformatics pipelines required for data analysis can also present further challenges for researchers.…”