Infective endocarditis due to a novel Gemella species revealed by metagenomic sequencing
- 1Department of Infectious Diseases, Japanese Red Cross Musashino Hospital, Tokyo, Japan
- 2Laboratory of Microbial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo, Japan
- 3Department of Pharmacy, Japanese Red Cross Musashino Hospital, Tokyo, Japan
Abstract
Background: Gemella species are rare causes of infective endocarditis, and accurate species identification can be challenging with routine diagnostic methods. We report infective endocarditis caused by a novel Gemella species, highlighting the diagnostic value of sequencing-based approaches for bacteria not registered in public databases and the risk of misclassification when novel species are not represented in reference databases.
Case Summary: A 55-year-old Japanese man presented with fatigue, anorexia, and altered mental status. Echocardiography revealed vegetations on the mitral and tricuspid valves with severe mitral regurgitation, and imaging demonstrated multiple systemic embolic events. Blood cultures grew gram-positive cocci that were initially identified as Gemella bergeri by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The patient received antimicrobial therapy and underwent mitral valve replacement and tricuspid valve repair. Culture of the excised valve tissue was negative. Metagenomic sequencing of the valve vegetation detected a Gemella species distinct from G. bergeri. Genome assembly from sequencing data showed 94.5% average nucleotide identity with a reference G. bergeri genome, supporting classification as a novel species. Whole-genome sequencing of the blood culture isolate demonstrated near-complete concordance with the organism detected in the valve tissue. The patient recovered with a 6-week course of intravenous penicillin G after blood cultures became sterile.
Conclusion: This case demonstrates that rare Gemella infections may be misidentified by routine mass spectrometry. It underscores the importance of sequencing-based methods for accurate pathogen identification and highlights a diagnostic pitfall associated with database-dependent identification in infective endocarditis.
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BibTeX
@article{sekikawa2026infective,
title = {{Infective endocarditis due to a novel Gemella species revealed by metagenomic sequencing}},
author = {Yoshiyuki Sekikawa and Kazuhiro Horiba and Masanori Hashino and Keiko Soneda and Tomoyuki Kato},
journal = {ASM case reports},
year = {2026},
month = aug,
doi = {10.1128/asmcr.00057-26},
url = {https://europepmc.org/article/PMC/PMC13729745},
note = {CC BY},
}
RIS
TY - JOUR
TI - Infective endocarditis due to a novel Gemella species revealed by metagenomic sequencing
AU - Yoshiyuki Sekikawa
AU - Kazuhiro Horiba
AU - Masanori Hashino
AU - Keiko Soneda
AU - Tomoyuki Kato
PY - 2026
DA - 2026/08/10
JO - ASM case reports
DO - 10.1128/asmcr.00057-26
UR - https://europepmc.org/article/PMC/PMC13729745
AB - Background: Gemella species are rare causes of infective endocarditis, and accurate species identification can be challenging with routine diagnostic methods. We report infective endocarditis caused by a novel Gemella species, highlighting the diagnostic value of sequencing-based approaches for bacteria not registered in public databases and the risk of misclassification when novel species are not represented in reference databases. Case Summary: A 55-year-old Japanese man presented with fatigue, anorexia, and altered mental status. Echocardiography revealed vegetations on the mitral and tricuspid valves with severe mitral regurgitation, and imaging demonstrated multiple systemic embolic events. Blood cultures grew gram-positive cocci that were initially identified as Gemella bergeri by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The patient received antimicrobial therapy and underwent mitral valve replacement and tricuspid valve repair. Culture of the excised valve tissue was negative. Metagenomic sequencing of the valve vegetation detected a Gemella species distinct from G. bergeri. Genome assembly from sequencing data showed 94.5% average nucleotide identity with a reference G. bergeri genome, supporting classification as a novel species. Whole-genome sequencing of the blood culture isolate demonstrated near-complete concordance with the organism detected in the valve tissue. The patient recovered with a 6-week course of intravenous penicillin G after blood cultures became sterile. Conclusion: This case demonstrates that rare Gemella infections may be misidentified by routine mass spectrometry. It underscores the importance of sequencing-based methods for accurate pathogen identification and highlights a diagnostic pitfall associated with database-dependent identification in infective endocarditis.
SN - 2996-2684
ER -