Title : Development of AMR reference reagents for AMR gene detection and surveillance
Abstract:
Antimicrobial resistance (AMR) is responsible for 4.95 million human deaths per year and is estimated to rise to 10 million deaths annually, if left uncontrolled. Accurate, sensitive and synchronised national and global AMR detection and surveillance efforts are crucial now more than ever and provide vital data that will help determine how we address this threat. Metagenomic sequencing has the potential to revolutionise AMR gene detection and surveillance. However, each step in the sequencing and analytical workflow is met with a variety of commonly used methods. Our previous work on validated World Health Organization Reference reagents for complex microbial communities has shown that different methodologies can lead to discrepant results. Furthermore, there are currently no means of standardisation in AMR detection and surveillance using genomic approaches, which renders the ground truth unknown amongst the plethora of available data.
With this in mind, we conducted a study with the following aims: (i) to develop and validate two AMR DNA bacterial community reference materials and (ii) to use these reagents to reveal any differences in community species and AMR gene representation, when sequenced using three different approaches: (1. Illumina 150bp and 2. 300bp metagenomic sequencing and 3. hybrid-Oxford Nanopore-Illumina metagenomic sequencing) and analysed by eight different bioinformatic pipelines. This work will shed light on the advantages and shortcomings of the different sequencing and analytical approaches and provide urgently required reference materials that can help establish the ground truth in future genomic studies.
