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. 2010 Dec 31;4:123–131. doi: 10.2174/1874285801004010123

Table 1a.

Identification Results Obtained By partial 16S rRNA Gene Sequence Analysis and by Vitek 2 NH Characterization of 45 Strains Included in the Vitek 2 NH Database

Strains Strain Designationsa,b 16S rRNA Gene Analysis Resultsc Difference Between Max Scoresd NCBI–BLAST Species Interpretation Vitek 2 NH Identificatione
A. ureae NCTC 10219T 893 / 879 (A. arthritidis) // 502 14 Probable Misidentified
A. ureae SSI: P 524 881 / 877 (A. arthritidis) // 498 4 Probable Correct
A. actinomycetemcomitans NCTC 9710T 755 / 704 (A. aphrophilus) // 425 51 Confirmed Low Discrimination
A. actinomycetemcomitans HK 666 830 / 731 (H. influenzae) // 463 99 Confirmed Correct
A. actinomycetemcomitans HK 1662 805 / 713 (H. segnis) // 448 92 Confirmed Correct
A. aphrophilus/paraphrophilus NCTC 5906T 762 / 739 (H. parainfluenzae) // 431 41 Confirmed Correct
A. aphrophilus/paraphrophilus SSI: P 536, AB 1635 706 / 673 (A. actinomycetemcomitans) // 407 33 Confirmed Correct
A. aphrophilus/paraphrophilus CCUG 14858T 710 / 675 (H. parainfluenzae) // 413 35 Confirmed Correct
A. aphrophilus/paraphrophilus CCUG 49494 818 / 789 (H. parainfluenzae) // 468 29 Confirmed Correct
A. segnis ATCC 33393T 856 / 740 (Pasteurella aerogenes) // 477 116 Confirmed Unidentified
A. segnis SSI: P 1292 847 / 782 (H. influenzae) // 497 65 Confirmed Low Discrimination
A. segnis SSI: P 1351 825 / 782 (H. influenzae) // 499 43 Confirmed Low Discrimination
C. canimorsus CCUG 19190 657 / 657 (C. cynodegmi) // 492 0 Probable Unidentified
C. canimorsus CCUG 19141 857 (C. cynodegmi) // 854 (C. canimorsus) // 494 -3 Possible Unidentified
C. canimorsus CCUG 19140 829 / 661 (C. cynodegmi) // 485 168 Confirmed Correct
C. canimorsus SSI: 4642/2006 838 / 751 (C. cynodegmi) // 488 87 Confirmed Misidentified
C. canimorsus SSI: 140/2006 587 / 533 (C. cynodegmi) // 365 54 Confirmed Misidentified
C. canimorsus SSI: 187/2006 856 / 780 (C. cynodegmi) // 485 76 Confirmed Misidentified
C. gingivalis CCUG 9715T 893 / 852 (C. granulosa) // 503 41 Confirmed Unidentified
C. ochracea SSI: 3435/04 859 / 852 (C. sputigena) // 491 7 Probable Correct
C. sputigena CCUG 9714T 785 / 765 (C. ochracea) // 481 18 Confirmed Unidentified
C. hominis CCUG 31207 841 / 753 (C. valvarum) // 496 88 Confirmed Correct
C. hominis CCUG 2711T 893 / 761 (C. valvarum) // 502 132 Confirmed Correct
C. hominis SSI: AB 2089 708 / 663 (C. valvarum) // 407 45 Confirmed Correct
E. corrodens ATCC 23834T 780 / 646 (N. denitrificans) // 436 134 Confirmed Correct
E. corrodens SSI: 13794/1992 623 / 541 (K. denitrificans) // 416 82 Confirmed Correct
E. corrodens SSI: 13897/1992 747 / 659 (K. denitrificans) // 425 88 Confirmed Correct
H. haemolyticus NCTC 10659T 856 / 856 (H. influenzae) // 500 0 Probable Misidentified
H. influenzae NCTC 8143T 832 / 736 (H. haemolyticus) // 462 96 Confirmed Correct
H. influenzae SSI: P 1227 756 / 680 (H. haemolyticus) // 418 76 Confirmed Correct
H. influenzae ATCC 49247 906 / 837 (H. haemolyticus) // 508 69 Confirmed Correct
H. parahaemolyticus NCTC 8479T 838 / 838 (A. pleuropneumoniae) // 486 0 Probable Correct
H. parahaemolyticus CCUG 48512 901 / 893 (A. pleuropneumoniae) // 499 8 Probable Misidentified
H. parainfluenzae NCTC 7857T 889 /841  (A. paraphrophilus) // 481 48 Confirmed Correct
H. parainfluenzae SSI: P 1538 870 / 756 (A. paraphrophilus) // 471 114 Confirmed Correct
H. parainfluenzae CCUG 49489 929 / 837 (A. paraphrophilus) // 445 92 Confirmed Correct
H. pittmaniaef CCUG 48703T 686 / 676 (H. parainfluenzae) // 400 10 Probable Low Discrimination
K. denitrificans    CCUG 6516T 838 / 838 (N. weaveri) // 469 0 Probable Low Discrimination
K. denitrificans CCUG 14999 883 / 767 (N. elongata) // 512 116 Confirmed Low Discrimination
K. kingae SSI: A 303T 886 / 762 (N. weaveri) // 495 114 Confirmed Unidentified
K. kingae CCUG 13025 879 / 758 (N. weaveri) // 499 111 Confirmed Unidentified
K. kingae SSI: 4541/05 904 / 785 (N. weaveri) // 509 119 Confirmed Correct
M. catarrhalis CCUG 353T 816 / 758 (M. canis) // 462 58 Confirmed Correct
M. catarrhalis SSI: RH 56295/84 805 / 747 (M. canis) // 460 58 Confirmed Correct
M. catarrhalis CCUG 11766 760 / 729 (M. nonliquefaciens) // 424 31 Confirmed Low Discrimination
a

ATCC, American Type Culture Collection, Bethesda, Md., USA; CCUG, Culture Collection of the University of Göteborg, Sweden; HK, Mogens Kilian, Institute of Microbiology, Aarhus, Denmark; NCTC, National Collection of Type Cultures; SSI, Statens Serum Institut, Copenhagen, Denmark.

b

T denotes type strain.

c

Max score best taxon match / Max score next best taxon match (taxon of next best match) // base pairs examined. If best taxon match 16S identification is not identical to gold standard identification, the 16S rRNA identification is given before the first /

d

Difference between best taxon match (most commonly same identification as gold standard identification) and next best match; in cases when gold standard identification was the same as next best match, the difference is negative.

e

See Table 3 for details of Vitek 2 NH card examination.

f

Formerly H.parahaemolyticus.