Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study

Abstract

Background Early and accurate diagnosis of microorganism(s) is important to optimize antimicrobial therapy. Shotgun metagenomic sequencing technology, an unbiased and comprehensive method for pathogen identification, seems to potentially assist or even replace conventional microbiological methodology in the diagnosis of infectious diseases. However, evidence in clinical application of this platform is relatively limited. Methods To evaluate the capability of shotgun metagenomic sequencing technology in clinical practice, both shotgun metagenomic sequencing and conventional culture were performed in the PCR-positive body fluid specimens of 20 patients with suspected infection. The sequenced data were then analyzed for taxonomic identification of microbes and antibiotic resistance gene prediction using bioinformatics pipeline. Results Shotgun metagenomic sequencing results showed a concordance of 17/20 compared with culture results in bacterial detection, and a concordance of 20/20 compared with culture results in fungal detection. Besides, drug-resistant types annotated from antibiotic resistance genes showed much similarity with antibiotic classes identified by susceptibility tests, and more than half of the specimens had consistent drug types between shotgun metagenomic sequencing and culture results. Conclusions Pathogen identification and antibiotic resistance gene prediction by shotgun metagenomic sequencing identification had the potential to diagnose microorganisms in infectious diseases, and it was especially helpful for multiple microbial co-infections and for the cases where standard culture approached failed to identify microorganisms.

Cellulosimicrobium Infections in Humans—A Narrative Review

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“…These new diagnostic modalities have led to the accurate and more frequent identification of relatively rare microorganisms [ 1 , 2 ]. Such microorganisms may have been very difficult identify with classical microbiological tools that assess the morphology and biochemical profile of these microorganisms [ 3 ].…”

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“…This untargeted sequencing approach leads to the generation of taxonomic information from conserved genes, such as the 16S rRNA gene, as well as a complete overview of the panoply of genomes present, including information on virulence, antimicrobial resistance and metabolic potential [69]. Theoretically, the identification of pathogens and antimicrobial susceptibility testing (AST) could be determined using the same test [69,150]. Barraud et al demonstrated this by using shotgun metagenomics to correctly profile bacteria in urine samples from sepsis patients, while also detecting antimicrobial resistance (AMR) genes that corresponded with standard AST results [151].…”

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