Table 2.

Agreement of genotypic (MicroSeq 500) identification with phenotypic identification of bacteria grown in blood culture bottles

Sequencing result% of sequence homologyConventional identification
Streptococcus pneumoniae (3 isolates)96.5–100  S. pneumoniae
Streptococcus vestibularis 100 Streptococcus spp., viridans group
Streptococcus pyogenes 100 S. pyogenes
Staphylococcus epidermidis 100 Staphylococcus spp., coagulase negative
Staphylococcus hominis 99.4 Staphylococcus spp., coagulase negative
Staphylococcus aureus (3 isolates)97.9–99.8 S. aureus
Corynebacterium jeikeium 100 Corynebacterium sp.
Micrococcus luteus 99.3 Micrococcus sp.
Enterococcus faecalis 99.8 E. faecalis
Enterococcus faecium 99.8 E. faecium
Enterococcus gallinarum 99.8 E. gallinarum
Enterococcus flavescens 99.8 E. casseliflavus or E. flavescensa
Brevibacterium casei 95.4 Brevibacterium sp.
Escherichia coli (3 isolates)99.4–100  E. coli
Haemophilus influenzae 100 H. influenzae
Enterobacter cloacae 99.9 E. cloacae
Enterobacter aerogenes 99.9 E. aerogenes
Pseudomonas aeruginosa (2 isolates)99.8–100  P. aeruginosa
Klebsiella pneumoniae 99.0 K. pneumoniae
Proteus mirabilis 99.9 P. mirabilis
Cardiobacterium hominis 100 Cardiobacterium sp.
Serratia marcescens 99.4 S. marcescens
Stenotrophomonas maltophilia 98.9 S. maltophilia
Capnocytophaga ochracea 92.2 C. sputigena or C. ochraceaa
Citrobacter youngae 99.6 C. freundii complex
Citrobacter freundii 98.0 C. freundii
Acinetobacter junii 100 Acinetobacter sp.
Ralstonia(Alcaligenes)eutropha 96.3 Ralstonia sp.
Sphingomonas paucimobilis 100 S. paucimobilis
Morganella morganii 99.8 M. morganii
Propionibacterium acnes 100 Propionibacterium sp.
Fusobacterium nucleatum 97.6 F. nucleatum
Fusobacterium necrophorum 99.5 F. necrophorum
Bacteroides fragilis 99.6 B. fragilis
Bacteroides fragilis 99.8 B. necrophorum
Lactobacillus fermentum 97.2 Lactobacillus sp.
Porphyromonas salivosa 87.8 P. gingivalisb
Ruminococcus(Peptostreptococcus) productus 83.2 Peptostreptococcus prevotiib
  • a The biochemical pattern could not differentiate between the two species.

  • b The genotypic identification disagreed with the phenotypic identification.