Portable In-Field DNA Sequencing for Rapid Detection of Pathogens and Antimicrobial Resistance: A Proof-of-Concept Study

Abstract

Purpose: Infectious diseases represent a major global health threat due to the rapid spread of pathogens, leading to widespread outbreaks. Concurrently, antimicrobial resistance (AMR) is increasing, making standard treatments less effective and complicating infection management. Effective surveillance systems are essential to address these challenges. Methods: We conducted a proof-of-concept study to evaluate a portable in-field microbial lab against a traditional molecular lab for DNA isolation, sequencing, microbial detection, antibiotic resistance gene identification, and plasmid classification. Samples from lake water, wastewater treatment plant sludge, and retail meat were selected to reflect relevant surveillance vectors. This approach provides valuable data for environmental monitoring, public health, and food safety, aiding in outbreak preparedness. We compared results using five metrics: DNA yield and purity, read N50, taxonomic classification, antibiotic resistance gene identification (ARGs), and plasmid classification. Results: Our study found that metagenomic bacterial DNA isolation from environmental and food sources is feasible with portable lab technology, producing >800ng of DNA, suitable for Nanopore sequencing. DNA from retail meat, lake, and sludge samples resulted in similar read numbers and read N50 values. Taxonomic classification was achieved at the genus and species levels. A Jaccard similarity of over 50% was observed in the top 20 most abundant species between chicken samples, and lake samples. ESKAPE pathogens were detected in chicken and lake samples. ARGs and plasmids were also identified in both retail meat and lake samples. Conclusion: This study demonstrates that in-field DNA isolation and sequencing are feasible with minimal equipment, yielding results comparable to traditional lab methods.