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Table 1 Pathogenic microorganisms detected by using next-generation sequencing in original and follow-up urine specimen

From: Identification of Enterococcus faecalis in a patient with urinary-tract infection based on metagenomic next-generation sequencing: a case report

Original urine specimen Follow-up urine specimen
Species Category Number of detected reads Species Category Number of detected reads
Homo sapiens Human 26,263,435 Homo sapiens Human 15,341,902
Enterococcus faecalis Bacteria 163 Enterococcus faecalis Bacteria 2
JC polyomavirus Virus 91 JC polyomavirus Virus 202
Human herpesvirus 6 Virus 3 Human herpesvirus 6 Virus 1
Malassezia globosa fungus 77 Streptococcus pneumoniae Bacteria 129
Actinomyces neuii Bacteria 32 Streptococcus mitis Bacteria 59
Staphylococcus haemolyticus Bacteria 8 Ureaplasma parvum Bacteria 56
Cutibacterium avidum Bacteria 6 Streptococcus pseudopneumoniae Bacteria 51
Other species: Meiothermus ruber, Comamonas testosteroni, Yarrowia lipolytica, Acinetobacter ursingii, etc. Streptococcus oralis Bacteria 26
Staphylococcus lugdunensis Bacteria 3
Other species: Xanthomonas campestris, Cutibacterium acnes, Delftia acidovorans, Acinetobacter ursingii, Meiothermus ruber, etc.
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