Identification of clinical bacterial isolates with ambiguous biochemical profiles by conventional 16S rRNA gene sequencing, commercially available bacterial identification systems, and the Microseq 500 16S rDNA-based bacterial identification system

Strain no. (reference)Sexa/age (yr) of patientClinical specimen or specimen sourceIdentification by conventional 16S rRNA gene sequencingIdentification by commercially available bacterial identification systemIdentification by MicroSeq 500 16S rDNA-based bacterial identification system
VitekAPIIdentityPercentage difference between sequence of isolates and that of identified bacterium in database
Card used for identificationIdentitycStrips for identificationIdentity
1 (20)F/43Blood Staphylococcus aureus GPI95% Staphylococcus simulans, 3% Staphylococcus haemolyticusSTAPH87% Staphylococcus aureus, 5% Staphylococcus warneri Staphylococcus aureus 0
2M/3Cochlear implant Staphylococcus epidermidis GPI53% Staphylococcus epidermidis, 27% Staphylococcus capitisSTAPH99% Staphylococcus chromogenes Staphylococcus epidermidis 0
3F/3Blood Micrococcus luteus GPI99.9% Micrococcus sp.STAPH99% Staphylococcus auricularis Micrococcus luteus 0.2
4 (16)F/69Blood Streptococcus dysgalactiae GPIUnidentified20 STREP77% Streptococcus dysgalactiae Streptococcus dysgalactiae 0.6
5 (6)M/81Blood Streptococcus iniae GPIUnidentified20 STREP99% Streptococcus dysgalactiae Streptococcus iniae 0
6M/33Bronchoalveolar lavage Streptococcus salivarius GPIUnidentified20 STREPUnidentified Streptococcus salivarius 0.4
7F/31Blood Streptococcus anginosus GPIUnidentified20 STREP70% Streptococcus intermedius, 30% Streptococcus anginosus Streptococcus anginosus 0
8 (19)M/62Blood Granulicatella adiacens GPI98% Gemella morbillorum or Streptococcus agalactiae or Streptococcus acidominimus20 STREP80% Granulicatella adiacens, 16% Gemella morbillorum Abiotrophia defectiva 9.9
9 (19)M/15Blood Abiotrophia defectiva GPIUnidentified20 STREPUnidentified Abiotrophia defectiva 1.1
10M/66Blood Gemella morbillorum GPI63% Gemella morbillorum or Streptococcus agalactiae or Streptococcus acidominimus, 22% Streptococcus pneumoniae20 STREP60% Leuconostoc sp., 28% Streptococcus mitis Gemella morbillorum 0.1
11F/41Blood Gemella haemolysans GPI68% Gemella morbillorum or Streptococcus agalactiae or Streptococcus acidominimus, 24% Streptococcus pneumoniae20 STREP95% Gemella haemolysans, 6% Gemella morbillorum Gemella haemolysans 0.6
12M/41Blood Helcococcus kunzii GPIUnidentified20 STREP50% Gemella haemolysans, 30% Gemella morbillorum, 18% Abiotrophia adiacens Clostridium hastiforme 13.9
13 (4)F/39Blood Microbacterium sp.GPIUnidentifiedCORYNE99% Aureobacterium or Corynebacterium aquaticum Microbacterium liquefaciens 0.8
14M/22Blood Gordona terrae GPIUnidentifiedCORYNE98% Rhodococcus sp. Gordona terrae 0
15M/38Pus swab Tsukamurella sp.GPIUnidentifiedCORYNE83% Rhodococcus sp., 12% Aureobacterium or Corynebacterium aquaticum Tsukamurella pulmonis 0.2
16M/71Blood Clostridium ramosum ANI86% Clostridium barati, 7% Lactobacillus catenaforme, 2% Clostridium paraputrificum20A97% Bifidobacterium sp. Clostridium ramosum 0
17 (18)F/36Intrauterine contraceptive device Actinomyces odontolyticus ANI99% Propionibacterium granulosum20A78% Actinomyces meyeri or odontolyticus, 19% Actinomyces naeslundii Actinomyces meyeri 2.1
18 (15)M/70Blood Lactobacillus salivarius ANIUnidentified20A70% Actinomyces naeslundii, 30% Bifidobacterium sp. Lactobacillus salivarius
19M/43Blood Olsenella uli ANI81% Propionibacterium granulosum, 11% Corynebacterium pseudotuberculosis20A43% Gemella morbillorum, 37% Lactobacillus fermentum, 10% Proionibacterium propionicum or avidum Atopobium rimae 11.1
20F/87Blood Eggerthella lenta ANI83% Corynebacterium jeikeium, 7% Clostridium hastiforme, 7% Clostridium histolyticum20A92% Eggerthella lenta, 8% Actinomyces viscosus Eggerthella lenta 0
21M/69Blood Eubacterium tenue ANI98% Clostridium difficile20A76% Clostridium bifermentens, 18% Clostridium cadaveris Eubacterium tenue 0
22F/70Blood Leptotrichia buccalis ANI99% Propionibacterium granulosum20A98% Bifidobacterium sp. Fusobacterium mortiferum 14.6
23M/36Blood Neisseria elongata NHI91% Kingella denitrificansNH99% Neisseria gonorrhoeae Neisseria elongata 0
24 (28)M/31Stool Escherichia coli GNI+73% Salmonella arizonae, 17% Salmonella spp.20E76% Escherichia coli, 23% Salmonella arizonae Escherichia coli 0.1
25M/48Stool Kluyvera ascorbata GNI+57% Kluyvera sp., 36% Enterobacter intermedius20E57% Enterobacter amnigenus, 24% Enterobacter intermedius, 19% Kluyvera sp. Kluyvera ascorbata 0.2
26M/60Bile Shewanella alga GNI+76% nonfermenting gram-negative bacillus, 11% Comamonas acidovorans20NEUnidentified Shewanella alga 0.4
27M/4Pus Bergeyella zoohelcum GNI+53% nonfermenting gram-negative bacillus (asaccharolytic), 39% Myroides sp.20NE51.2% Psychrobacter phenylpyruvicus, 36.5% Bergeyella zoohelcum, 8.5% Methylobacterium mesophilicum Riemerella anatipestifer 7.4
28 (3)M/32Blood Haemophilus segnis NHI56% Actinobacillus actinomycetemcomitansNH58% Haemophilus aphrophilus or Haemophilus paraphrophilus Haemophilus segnis 0.2
29 (26)M/66Blood Campylobacter fetus NDbNDNDND Campylobacter fetus 0
30M/9mStool Campylobacter jejuni NDNDNDND Campylobacter jejuni or Campylobacter coli0
31F/41Stool Campylobacter hyointestinalis NDNDNDND Campylobacter hyointestinalis 0
32 (25)M/7Blood Arcobacter cryaerophilus NDNDNDND Arcobacter butzleri 2.6
33 (5)F/69Blood Arcobacter butzleri NDNDNDND Arcobacter butzleri 0
34 (27)F/79Tissue biopsy Mycobacterium chelonae NDNDNDND Mycobacterium chelonae or Mycobacterium abscessus0
35 (24)F/9Blood Mycobacterium neoaurum NDNDNDND Mycobacterium neoaurum 0
36 (27)M/62Tissue biopsy Mycobacterium nonchromogenicum NDNDNDND Mycobacterium nonchromogenicum 1.6
37M/77Pus Mycoplasma hominis NDNDNDND Mycoplasma hominis 0.1
  • a M, male; F, female.

  • b ND, not done.

  • c Percent identity and organism name are given. In cases where identity with more than one organism was found, both or all are listed.