MGS2AMR: a gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile

BACKGROUND: Identification of pathogenic bacteria from clinical specimens and evaluating their antimicrobial resistance (AMR) are laborious tasks that involve in vitro cultivation, isolation, and susceptibility testing. Recently, a number of methods have been developed that use machine learning algorithms applied to the whole-genome sequencing data of isolates to approach this problem. However, making AMR assessments from more easily available metagenomic sequencing data remains a big challenge. RESULTS: We present the Metagenomic Sequencing to Antimicrobial Resistance (MGS2AMR) pipeline, which detects antibiotic resistance genes (ARG) and their possible organism of origin within a sequenced metagenomics sample. This in silico method allows for the evaluation of bacterial AMR directly from clinical specimens, such as stool samples. We have developed two new algorithms to optimize and annotate the genomic assembly paths within the raw Graphical Fragment Assembly (GFA): the GFA Linear Optimal Path through seed segments (GLOPS) algorithm and the Adapted Dijkstra Algorithm for GFA (ADAG). These novel algorithms improve the sensitivity of ARG detection and aid in species annotation. Tests based on 1200 microbiome samples show a high ARG recall rate and correct assignment of the ARG origin. The MGS2AMR output can further be used in many downstream applications, such as evaluating AMR to specific antibiotics in samples from emerging intestinal infections. We demonstrate that the MGS2AMR-derived data is as informative for the entailing prediction models as the whole-genome sequencing (WGS) data. The performance of these models is on par with our previously published method (WGS2AMR), which is based on the sequencing data of bacterial isolates. CONCLUSIONS: MGS2AMR can provide researchers with valuable insights into the AMR content of microbiome environments and may potentially improve patient care by providing faster quantification of resistance against specific antibiotics, thereby reducing the use of broad-spectrum antibiotics. The presented pipeline also has potential applications in other metagenome analyses focused on the defined sets of genes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-023-01674-z.