Early diagnosis of streptococcus cristatus in blood culture-negative infective endocarditis by capture-based metagenomic next-generation sequencing: a case report

Abstract

Background: Infective endocarditis (IE) is a life-threatening infectious cardiac condition characterized by therapeutic complexity and high mortality rates, for which precise pathogen identification is critical to guide accurate treatment. Although this disease is frequently caused by commensal microorganisms of the oral flora, including Streptococcus cristatus (S. cristatus); however, S. cristatus is not a common pathogen associated with IE.

Case presentation: A 59-year-old male patient was admitted to our intensive care unit due to chest tightness and shortness of breath persisting for 10 days, with symptoms worsening over the last 6 h, including dyspnea and an inability to lie down. After the patient was admitted to the hospital for comprehensive examinations, a preliminary clinical diagnosis of IE, aortic valve vegetation formation, acute non-ST-segment elevation myocardial infarction, and heart failure was established. The patient had negative preoperative blood culture results and received empiric therapy with moxifloxacin combined with piperacillin-tazobactam for infection control, subsequently undergoing cardiac surgery. Intraoperatively obtained valve vegetations were sent for pathological testing, tissue bacterial culture, and capture-based mNGS (metagenomic next-generation sequencing) testing. The capture-based mNGS results for the vegetation was returned as S. cristatus within 24 h, with 250,119 sequences detected and 54.56% coverage, which facilitated the rapid identification of the pathogenic microorganism of IE in the early stage. The tissue culture result of the vegetation was returned on the 5th day of delivery, confirming the presence of S. cristatus. The patient was successfully discharged after comprehensive treatment and returned to the hospital 3 weeks post-discharge for a follow-up examination, which suggested a good recovery.

Conclusions: This case highlights a rare instance of S. cristatus endocarditis, which was ultimately confirmed at an early stage through capture-based mNGS performed on valvular vegetation. This suggests that for postoperative patients with persistent infection and blood culture-negative IE, valvular capture-based mNGS serves as a rapid and efficient diagnostic tool to expedite pathogen identification and guide targeted antimicrobial therapy.

Keywords: Streptococcus cristatus; capture-based metagenomic nextgeneration sequencing; case report; infective endocarditis; valve vegetations.

Figure 1

Timeline of patient's clinical management progression, including timing of clinical histoury, diagnostic testing and antimicrobial therapy. ICU admission is used as the day 0 reference point.

Figure 2

Protocol for capture-based mNGS assay. Sample Processing and Nucleic Acid Extraction: Blood samples (3 ml each) were centrifuged at 1,600 × rcf for 10 min at 4°C. Nucleic acid was extracted from 300 μl of the resulting plasma using the MasterPure DNA & RNA Extraction Kit (KingCreate) according to the manufacturer's instructions. The extracted nucleic acid was then used for library construction; Library Construction, Enrichment, and Sequencing: Following RNA conversion to complementary DNA (cDNA), libraries were constructed through fragmentation, end repair, adapter ligation, and PCR amplification. After library generation, eight uniquely barcoded libraries were pooled and hybridized with specific biotinylated probes for 2 h using the MetaCAP Pathogen Capture Metagenomic Assay Kit (KingCreate), according to the manufacturer's protocol. This captured library pool was then sequenced on an Illumina MiniSeq platform.

Figure 3

The capture-based mNGS results of pathogens detected in aortic valve vegetation.

Figure 4

Aortic valve vegetation and pathological analysis. (A) A grayish-white vegetation measuring 0.5 cm × 0.5 cm was observed on the aortic valve. (B) Hematoxylin and eosin (H&E) staining at 10 × 10 magnification revealed a thrombotic vegetation, with bacterial clusters identified within the thrombus.