Metagenomic Sequencing as a Pathogen-Agnostic Clinical Diagnostic Tool for Infectious Diseases: a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies

Abstract

Background: Metagenomic sequencing is frequently claimed to have the potential to revolutionise microbiology through rapid species identification and antimicrobial resistance (AMR) prediction. We assess progress towards this. Methods: We perform a systematic review and meta-analysis of all published literature on culture-independent metagenomic sequencing for pathogen-agnostic infectious disease diagnostics to August 12, 2020. Methodologic bias and applicability were assessed using QUADAS-2. (PROSPERO CRD42020163777) Results: A total of 2023 clinical samples from 13/21 eligible diagnostic test accuracy studies were included in the meta-analysis. Reference standards were culture, molecular testing, clinical decision or a composite measure. Sensitivity and specificity in the most widely investigated sample types were 90%(78-96%) and 86%(45-98%) for blood, 75%(95%CI, 54-89%) and 96%(72-100%) for CSF, and 84%(79-88%) and 67%(38-87%) for orthopaedic samples respectively. We identified limited use of controls, especially negative controls which were used in only 62%(13/21) studies. AMR prediction and comparison to phenotypic results was undertaken in four studies: categorical agreement was 88%(80%-97%), very major and major error rates were 24%(8-40%) and 5%(0-12%) respectively. Better human DNA depletion methods are required: a median 91%(IQR 82-98%)[range 76-98%] of sequences were classified as human. The median(IQR)[range] time from sample to result was 29(24-94)[4-144] hours. The reported consumables cost per sample ranged from $130-$685. Conclusions: There is scope for improving the quality of reporting in clinical metagenomic studies. Although our results are limited by the heterogeneity displayed, our results reflect a promising outlook for clinical metagenomics. Methodological improvements, and convergence around protocols and best practises may improve performance in future.

Clinical Application and Influencing Factor Analysis of Metagenomic Next-Generation Sequencing (mNGS) in ICU Patients With Sepsis

“…( Zheng et al., 2022 ). Highlighting the clinical advantages of NGS in finding particular fastidious pathogenic bacteria that can guide the clinical treatment better ( Kruppa et al., 2018 ; Duan et al., 2021b ; Govender et al., 2021 ; Tsang et al., 2021 ; Zhan et al., 2022 ).…”

Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopedic Device Infection

“…Metagenomic sequencing for AMR determinant detection has also been applied to PPT samples for bone and joint infections ( 9 ), with the correct susceptibility inferred in 94.1% of monomicrobial and 76.5% of polymicrobial samples. Recent reviews also highlight the use of metagenomic sequencing for AMR detection ( 35 , 36 ).…”

Shotgun-metagenomics based prediction of antibiotic resistance and virulence determinants in Staphylococcus aureus from periprosthetic tissue on blood culture bottles

“…We did not calculate the turnaround time since it was not the focus of the study. However, other studies have estimated the time for SMg using the Illumina technology estimating the total time to 29 h (24-94) from sample extraction to identification and AMR profile 56 . Our protocol would probably also fall into similar turnaround time from BCB positivity to pathogen ID.…”