Metagenomic Sequencing for Pathogens Detection in a Critically Ill Patient

  Objective  To detect pathogens in a critically ill patient using metagenomic sequencing.

  Methods  A critically ill patient with severe acute pancreatitis suffered from abdominal pain and progressed into unconsciousness. Tissue smear, culture, automated biochemical identification and antibiotic susceptibility test, viral load determination by real-time fluorescence quantitative PCR, and immunohistochemical pathological tests were performed to detect pathogens, in addition to metagenomic sequencing based on the BGISEQ-100 high throughput sequencing platform. The sequences exclusive of host sequences were searched in the microbial genome database including viruses, bacteria, fungi and parasites.

  Results  The patient was infected with methicillin-resistant Staphylococcus aureus, carbapenem-resistant Klebsiella pneumoniae and carbapenem-resistant Acinetobacter baumannii, verified by both the routine methods and the metagenomic sequencing. The metagenomic sequencing also detected cytomegalovirus (CMV) with a turn-around time of 5 days. Real-time fluorescent quantitative PCR confirmed 189 000 copies/mL CMV load.

  Conclusion  In this case, three species of bacteria and one virus were detected by metagenomic sequencing quickly and accurately. Metagenomic sequencing may be helpful for diagnosing infectious diseases in critically ill patients.