Abstract
Rapid and accurate etiologic diagnosis accelerates targeted antimicrobial therapy. Metagenomic analysis has played a critical role in pathogen identification. In this study, we leveraged the advantages of both the MinION and BGISEQ-500 platforms to make a bacteriologic diagnosis from a culture-negative lung tissue sample from an immunocompromised patient with severe pneumonia. Real-time nanopore sequencing rapidly identified Klebsiella pneumoniae by an 823 bp specific sequence within 1 min. Genomic analysis further identified blaSHV-12, blaKPC-2, blaTEM-1, blaCTX-M-65, and other resistance genes. The same sample was further sequenced on the BGISEQ-500 platform, which presented consistent results regarding the most top dominant pathogens and provided additional information of resistance genes. Revised antibiotic treatment was followed by the patient's clinical recovery. Though sample preparation and the interpretation of final results still need to be improved further, metagenomic sequencing contributes to the accurate diagnosis of culture-negative infections and facilitates the rational antibiotic therapy.
Highlights
Infectious diseases are major causes of morbidity and mortality (Simner et al, 2017)
The predominant pathogen detected by both platforms was K. pneumoniae
No K. pneumoniae was isolated in standard cultures of the lung biopsy tissue
Summary
Infectious diseases are major causes of morbidity and mortality (Simner et al, 2017). Pathogen Diagnosis by the MinION with more rapid and accurate diagnostic advantages than traditional methods, especially in culture-negative samples (Greninger et al, 2015; Schmidt et al, 2016; Gong et al, 2018; Li et al, 2018). By combining the advantages of both Nanopore and NGS platforms, metagenomic sequencing can achieve a rapid pathogenic diagnosis, even in culture-negative samples, and maximize genomic information. We identified Klebsiella pneumoniae in a culture-negative lung tissue sample by combining the MinION and BGISEQ-500 sequencing platforms during the treatment of an immunocompromised patient with severe pneumonia. Analysis of antibiotic resistance genes provided valuable data to guide rational antibiotic therapy These results indicate that metagenomic sequencing has the potential to improve pathogen identification in clinical samples, especially in culture-negative cases
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
