Application of Metagenomic Next-Generation Sequencing in the Etiological Diagnosis of Infective Endocarditis During the Perioperative Period of Cardiac Surgery: A Prospective Cohort Study

Abstract

ObjectiveThe present study aimed to prospectively evaluate the role of metagenomic next-generation sequencing (mNGS) in the etiological diagnosis of patients with perioperative infective endocarditis (IE).MethodsFrom May 1st, 2019 to December 31st, 2020, a total of 99 patients with IE were enrolled in the present study according to the modified Duke criteria, etiological, and pathological results. 11 non-IE patients undergoing heart valve surgery in the same period were selected as the control group. A blood culture test was performed immediately after admission, and the valves harvested operatively were examined by blood culture and mNGS.ResultsIn the IE group, there were 29 cases (29.3%) with positive blood culture, 16 cases (16.2%) with positive valve culture, and 85 cases (85.9%) with positive valve mNGS. Compared to culture-based detection, mNGS achieved better performance with a sensitivity, specificity, area under the curve (AUC) of 0.859, 0.727, and 0.793, respectively. The combined approach using culture and mNGS further improved the diagnostic accuracy (sensitivity 89.9%, specificity 72.7%, AUC 0.813). Preoperative white blood cell (P = 0.029) and neutrophils (P = 0.046) were identified as independent factors affecting the detection rate of mNGS. In the mNGS-positive group, 95 strains of pathogens were found and 10 cases were identified with mixed infection. There were 72 gram-positive bacteria and 14 gram-negative bacteria. mNGS positive group displayed higher species richness than mNGS negative group with enrichment of Streptococcus sanguis, Streptococcus buccalis, and Streptococcus griseus. Proteobacteria and Actinomycetes were enriched in mNGS negative group. Notably, six patients showed disconcordant results between culture and mNGS. Rothia aeria was identified in the blood culture, valve culture, and valve mNGS in one patient. Bartonella Quintana and Coxiella burnetii, which were fastidious intracellular bacteria, were found in two blood and valve culture-negative cases.ConclusionsmNGS outperformed the conventional culture method and displayed high accuracy in detecting pathogens in IE patients. This study provided support for the use of mNGS in the etiological diagnosis of IE.

Utility of Metagenomic Next-Generation Sequencing in Infective Endocarditis: A Systematic Review

“…The average turnaround time, which represents the time between sample collection to the time of availability of test results, was 3.2 days (SD 1.2 days) for mNGS versus 11 days for 16S PCR in a study [ 19 ], and 48 hours versus 1 week for culture method in another study [ 16 ].…”

“…The sensitivity ranged between 85.9 and 100% for cardiac valve mNGS, and between 47% and 80% for plasma mNGS, with a specificity of 72.7% to 100% in patients with cardiac valve mNGS, and a specificity of 71.4% to 100% in patients with plasma mNGS. The PPV of mNGS was only reported in two studies, with a value around 97%; however, the NPV differed between these two studies (85.7 and 36.4%) [ 14 , 16 ]. Sensitivity and PPV of generators and lead tip sonication and NGS were lower for systemic device-related infections (DRI) (Sen: 18%, PPV ~ 50%; Sen: 48%, PPV ~ 90%, respectively) compared to those of blood culture (Sen: 93%, PPV ~ 99%) [ 21 ].…”

“…Although blood cultures have long been the gold standard for pathogen identification in IE, novel diagnostic methods such as mNGS may be more sensitive (see Table 2 ). For example, mNGS with blood or valve cultures improved diagnostic accuracy in one study (Sen 89.9%, Sp 72.7%, AUC 0.813) [ 16 ]. Moreover, although rare, cases due to polymicrobial infection were identified using mNGS, but not in culture-based methods, indicating mNGS may have better performance in identifying polymicrobial infections [ 16 , 17 ].…”

Native valve, prosthetic valve, and cardiac device-related infective endocarditis: A review and update on current innovative diagnostic and therapeutic strategies

“…Considering false culture-negative potential, when suspicion of IE remains then other techniques are emerging as additional diagnostic tools. This includes serological and molecular techniques, to include broad-range polymerase chain reaction (PCR) analysis, next-generation sequencing ( Oberbach et al, 2017 ; Kolb et al, 2019 ; Zeng et al, 2022 ), and mass spectrometry ( Holler et al, 2011 ; Singhal et al, 2015 ). At the same time, false negative PCR results have been reported with positive cultures ( Gauduchon et al, 2003 ; Breitkopf et al, 2005 ) and identifying new isolates with mass spectroscopy relies on pre-existing databases input.…”

The application of metagenomic next-generation sequencing for Angiostrongylus eosinophilic meningitis in a pediatric patient: A case report

“…In addition, the DNA detection of enterovirus and herpes simplex virus 1 and 2 (HSV-1 and 2) were all negative. Thus, we performed an mNGS test with CSF sample in a Clinical Laboratory Improvement Amendments-certified and College of American Pathologists-accredited laboratory (Nanjing Geneseeq Technology, Jiangsu Province, China) as described previously ( 14 ), which revealed A. cantonensis DNA sequences covering 0.0079% of the genome ( Figure 2C ). Sanger sequencing confirmed the presence of A. cantonensis DNA sequences ( Figures 2D,E ).…”