Comparison of Blood-Based Shotgun and Targeted Metagenomic Sequencing for Microbiological Diagnosis of Infective Endocarditis

Abstract

Background Shotgun and targeted metagenomic sequencing have been shown in separate studies to be potentially useful for culture-free pathogen identification in blood and/or plasma of patients with infective endocarditis (IE). However, the 2 approaches have not been directly compared. The aim of this study was to compare shotgun metagenomic sequencing with targeted metagenomic sequencing (tMGS) for organism identification in blood or plasma of patients with IE. Methods Patients with possible or definite IE were prospectively enrolled from October 2020 to July 2021. Shotgun metagenomic sequencing was performed with the Karius test, which uses microbial cell-free DNA (mcfDNA) sequencing to detect, identify, and quantitate DNA-based pathogens in plasma. tMGS was performed using a 16S ribosomal RNA (rRNA) polymerase chain reaction assay targeting the V1 to V3 regions of the 16S rRNA gene. Results were compared using the McNemar test of paired proportions. Results Samples from 34 patients were investigated. The Karius test was positive in 24/34 (71%), including 3/6 (50%) with blood culture–negative endocarditis (BCNE), which was not significantly different from the positivity rate of tMGS (P = .41). Results of the Karius test were concordant with tMGS in 75% of cases. The Karius test detected 2 cases of methicillin-resistant Staphylococcus aureus among the 7 S. aureus detections, in accordance with results of phenotypic susceptibility testing. The combination of blood cultures, the Karius test, and tMGS found a potential causative pathogen in 33/34 (97%), including 5/6 with BCNE. Conclusions The Karius test and tMGS yielded comparable detection rates; however, beyond organism identification, the Karius test generated potentially useful antibiotic resistance data.

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“…A positive impact of KT in establishing unexpected diagnosis in 5/43 (11.6%) patients, as we showed, should be seen as an improvement in an era where the microbiological diagnostic tools are vast and potentially allow for pathogen identification in nearly all infective cases now [ 28 ]. These results are in line with previous published research in other settings, such as pneumonia, where Bergin et al [ 14 ].…”

“…Similarly, our cohort has a high percentage of patients with concomitant infective endocarditis or endovascular infection. KT has already shown promising results in these settings [ 15 , 16 , 27 , 28 ]. The strong association found between concordance of KT results with standard microbiological testing and NVO diagnosis or the presence of infective endocarditis (IE) and/or endovascular infection has plausible biological explanation (eg, higher bacterial burden in peripheral blood) and strengthen the hypothesis that KT might be especially useful in infectious syndromes where hematogenous seeding is the main pathogenic mechanism.…”

“…The help of KT in this setting is also underscored by the fact that metagenomic techniques are theoretically independent from antibiotic administration [ 15 ]. Our study was not powered enough to study the impact of timing of KT relative to blood cultures on concordance and yield, as hypothesized by some authors [ 15 , 22 , 28 ]—specifically because the vast majority of our patient cohort was sampled only once because of logistic constraints and clinical decision, or the correlation between microbial burden and metastatic infections [ 27 , 29 , 30 ]. Moreover, how the discordance in positivity and lower diagnostic yield increases over time as time on antibiotics elapses or how KT can be used to track infection clearance over the course of treatment, still must be determined in this setting.…”

Novel Diagnostic Methods for Infective Endocarditis

“…Moreover, the results of the Karius test were consistent with the results of tMGS in 75% of cases. In conclusion, by combining the methods together (blood cultures, Karius test, and tMGS), it was possible to find a potential causative agent in 97% of patients, including 5 out of 6 with BCNIE [72].…”

“…Detects microbial cell-free DNA, it can also detect fungal species and resistent microorganisms, contrarly to tMGS [72].…”