Comparison of the Vitek 2, API 20A, and 16s rRNA Gene Sequencing for the Identification of Anaerobic Bacteria

Gyun Cheol Park; Sook Jin Jang; Min Jung Lee; Joong-Ki Kook; Min Jung Kim; Young Sook Kim; Nam Woong Yang; Hye Soo Lee; Seong Ho Kang; Geon Park; Dae Soo Moon

doi:10.5145/ACM.2015.18.1.20

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Park, Jang, Lee, Kook, Kim, Kim, Yang, Lee, Kang, Park, and Moon: Comparison of the Vitek 2, API 20A, and 16s rRNA Gene Sequencing for the Identification of Anaerobic Bacteria

Original Article

Ann Clin Microbiol 2015;18(1):20-26.

Published online: 5 March 2015

DOI: https://doi.org/10.5145/ACM.2015.18.1.20

Comparison of the Vitek 2, API 20A, and 16s rRNA Gene Sequencing for the Identification of Anaerobic Bacteria

Gyun Cheol Park¹, Sook Jin Jang^1,², Min Jung Lee², Joong-Ki Kook³, Min Jung Kim³, Young Sook Kim⁴, Nam Woong Yang⁵, Hye Soo Lee^6,⁷, Seong Ho Kang¹, Geon Park¹, Dae Soo Moon¹

¹Department of Laboratory Medicine, Chosun University College of Medicine, Jeonju, Korea

²Research Center for Resistant Cells, Chosun University College of Medicine, Jeonju, Korea

³Department of Oral Biochemistry, College of Dentistry, Chosun University, Jeonju, Korea

⁴Departments of Radiology, Chosun University College of Medicine, Jeonju, Korea

⁵Department of Microbiology, College of Medicine, Chosun University, Gwangju, Jeonju, Korea

⁶Department of Laboratory Medicine, Chonbuk National University Medical School, Jeonju, Korea

⁷Chonbuk National University Hospital Branch of National Culture Collection of Pathogens, Jeonju, Korea

Correspondence: Sook Jin Jang, Department of Laboratory Medicine, Chosun University College of Medicine, 365, Pilmun-daero, Dong-gu, Gwangju 501-717, Korea. (Tel) 82-62-220-3259, (Fax) 82-62-232-2063, (E-mail) sjbjang@chosun.ac.kr

Received 23 December 20149 January 2015 Accepted 10 January 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

초록

Background

Recently, genotypic identification of an-aerobes is emerging as an alternative to the phenotypic method. In this study, we evaluated the performance of Vitek 2, API 20A and 16s rRNA gene sequencing for the identification of anaerobic bacteria.

Methods

A total of 35 anaerobe reference strains were identified using Vitek 2, API 20A and 16s rRNA gene sequencing. We evaluated the performance of three methods on the basis of the accurate identification rates.

Results

The Vitek 2, API 20A and 16s rRNA gene sequencing identified 54.3, 15.4, and 94.3% of test strains correctly at the species level and identified 77.1, 42.3, and 100% at the genus level, respectively. Results of the McNemar's test showed that there was a significant difference between each of the three identification methods in species level identification (P value＜0.05).

Conclusion

16s rRNA gene sequencing showed bet-ter performance than Vitek 2 or API 20A for anaerobic bacteria. Considering its excellent performance, 16s rRNA gene sequencing may be useful for accurate identification of anaerobic bacteria that cannot be correctly identified by phenotypic methods.

Keywords: Anaerobic bacteria, API 20A, Comparison, Vitek 2, 16s rRNA Gene sequence

REFERENCES

1.Park Y., Lee Y., Kim M., Choi JY., Yong D., Jeong SH, et al. Recent trends of anaerobic bacteria isolated from clinical specimens and clinical characteristics of anaerobic bacteremia. Infect Chemother. 2009. 41:216–23.

2.Wilson JR., Limaye AP. Risk factors for mortality in patients with anaerobic bacteremia. Eur J Clin Microbiol Infect Dis. 2004. 23:310–6.

3.Lassmann B., Gustafson DR., Wood CM., Rosenblatt JE. Reemer-gence of anaerobic bacteremia. Clin Infect Dis. 2007. 44:895–900.

4.Summanen P., Jousimies-Somer H. Comparative evaluation of RapID ANA and API 20 A for identification of anaerobic bacteria. Eur J Clin Microbiol Infect Dis. 1988. 7:771–5.

5.Lee EH., Degener JE., Welling GW., Veloo AC. Evaluation of the Vitek 2 ANC card for identification of clinical isolates of anaerobic bacteria. J Clin Microbiol. 2011. 49:1745–9.

6.Blairon L., Maza ML., Wybo I., Piérard D., Dediste A., Vandenberg O. Vitek 2 ANC card versus BBL Crystal Anaerobe and RapID ANA II for identification of clinical anaerobic bacteria. Anaerobe. 2010. 16:355–61.

7.Mory F., Alauzet C., Matuszeswski C., Riegel P., Lozniewski A. Evaluation of the new Vitek 2 ANC card for identification of medi-cally relevant anaerobic bacteria. J Clin Microbiol. 2009. 47:1923–6.

8.Rennie RP., Brosnikoff C., Turnbull L., Reller LB., Mirrett S., Janda W, et al. Multicenter evaluation of the Vitek 2 anaerobe and Cory-nebacterium identification card. J Clin Microbiol. 2008. 46:2646–51.

9.Schreckenberger PC., Celig DM., Janda WM. Clinical evaluation of the Vitek ANI card for identification of anaerobic bacteria. J Clin Microbiol. 1988. 26:225–30.

10.Kierzkowska M., Majewska A., Kuthan RT., Sawicka-Grzelak A., Mł ynarczyk G. A comparison of Api 20A vs MALDI-TOF MS for routine identification of clinically significant anaerobic bacterial strains to the species level. J Microbiol Methods. 2013. 92:209–12.

11.Li Y., Gu B., Liu G., Xia W., Fan K., Mei Y, et al. MALDI-TOF MS versus VITEK 2 ANC card for identification of anaerobic bacteria. J Thorac Dis. 2014. 6:517–23.

12.Song Y., Liu C., McTeague M., Finegold SM. 16S ribosomal DNA sequence-based analysis of clinically significant gram-positive anaerobic cocci. J Clin Microbiol. 2003. 41:1363–9.

13.Petti CA., Polage CR., Schreckenberger P. The role of 16S rRNA gene sequencing in identification of microorganisms misidentified by conventional methods. J Clin Microbiol. 2005. 43:6123–5.

14.Downes J., King A., Hardie J., Phillips I. Evaluation of the Rapid ID 32A system for identification of anaerobic Gram-negative bacilli, excluding the Bacteroides fragilis group. Clin Microbiol Infect. 1999. 5:319–26.

15.Clarridge JE 3rd. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev. 2004. 17:840–62. table of contents.

16.Justesen US., Skov MN., Knudsen E., Holt HM., S⊘gaard P., Justesen T. 16S rRNA gene sequencing in routine identification of anaerobic bacteria isolated from blood cultures. J Clin Microbiol. 2010. 48:946–8.

17.Song Y., Liu C., Bolanos M., Lee J., McTeague M., Finegold SM. Evaluation of 16S rRNA sequencing and reevaluation of a short biochemical scheme for identification of clinically significant Bacteroides species. J Clin Microbiol. 2005. 43:1531–7.

18.Lau SK., Woo PC., Fung AM., Chan KM., Woo GK., Yuen KY. Anaerobic, non-sporulating, Gram-positive bacilli bacteraemia chara-cterized by 16S rRNA gene sequencing. J Med Microbiol. 2004. 53:1247–53.

19.Yang NW., Kim JM., Choi GJ., Jang SJ. Development and evaluation of the quick anaero-system-a new disposable anaerobic culture system. Korean J Lab Med. 2010. 30:133–7.

20.Simmon KE., Mirrett S., Reller LB., Petti CA. Genotypic diversity of anaerobic isolates from bloodstream infections. J Clin Microbiol. 2008. 46:1596–601.

21.CLSI. Interpretive criteria for identification of bacteria and fungi by DNA target sequencing. CLSI document MM18-A. Wayne, PA; Clinical and Laboratory Standards Institute. 2008.

22.Park KS., Ki CS., Kang CI., Kim YJ., Chung DR., Peck KR, et al. Evaluation of the GenBank, EzTaxon, and BIBI services for molecular identification of clinical blood culture isolates that were unidentifiable or misidentified by conventional methods. J Clin Microbiol. 2012. 50:1792–5.

23.Mellmann A., Cloud JL., Andrees S., Blackwood K., Carroll KC., Kabani A, et al. Evaluation of RIDOM, MicroSeq, and Genbank services in the molecular identification of Nocardia species. Int J Med Microbiol. 2003. 293:359–70.

Table 1.

The results of identification using API 20A, Vitek 2 and 16S rRNA sequencing of 35 anaerobic reference strains

Strain	Species	Vitek 2	API 20A	16S rRNA gene sequencing
ATCC 33384	Aggregatibacter actinomycetemcomitans	Fusobacterium mortiferum	A. viscosus	A. actinomycetemcomitans
ATCC 35568	Actinomyces meyeri	A. meyeri	A. meyerii/odontolyticus	A. meyeri
CCUG 35333	Actinomyces naeslundii	A. naeslundii	Bifidobacterium spp.	Actinomyces spp.
ATCC 17929	Actinomyces odontolyticus	A. meyeri	A. meyeri/odontolyticus	A. odontolyticus
ATCC 15987	Actinomyces viscosus	A. meyeri	Bifidobacterium spp., Actinomyces israelii	Actinomyces spp.
ATCC 25285	Bacteroides fragilis	B. fragilis	Bacteroides distasonis, P. melaninogenica/oralis, Bifidobacterium spp., Clostridium clostridioforme	B. fragilis
KBN06P00386	Bacteroides fragilis	B. fragilis	NT	B. fragilis
KBN06P00387	Bacteroides fragilis	B. fragilis	NT	B. fragilis
KBN06P00388	Bacteroides fragilis	B. fragilis	NT	B. fragilis
KBN06P00389	Bacteroides fragilis	B. fragilis	NT	B. fragilis
KBN06P00390	Bacteroides fragilis	B. fragilis	NT	B. fragilis
ATCC 8482	Bacteroides vulgatus	B. vulgatus	Bifidobacterium spp.	B. vulgatus
ATCC 13124	Clostridium perfringens	C. perfringens	C. perfringens	C. perfringens
ATCC 12464	Clostridium septicum	C. septicum	Clostridium beijerinckii/butyricum	C. septicum
ATCC 3584	Clostridium sporogenes	C. sporogenes	C. botulinum/sporogenes, Clostridium bifermentans	C. sporogenes
ATCC 8486	Eubacterium limosum	E. limosum	E. limosum, P. acnes	E. limosum
ATCC 33693	Fusobacterium periodonti	cum Fusobacterium variu Fusobacterium nucl m,	F. necrophorum/nucleatum, leatum Porphyromonas asaccharolytica	F. periodonticum
ATCC 25286	Fusobacterium necrophorum	F. necrophorum	P. asaccharolytica, F. necrophorum/nucleatum	F. necrophorum
ATCC 25599	Lactobacillus paracasei	Lactobacillus gasseri	i Bifidobacterium spp., A. israelii	L. paracasei
CCUG 51858	Peptostreptococcus stomattis	No identification	NT	P. stomatis
ATCC 33277	Porphyromonas gingivalis	No identification	NT	P. gingivalis
ATCC 29303	Prevotella bivia	P. bivia	P. bivia	P. bivia
ATCC 19188	Prevotella brevis	No identification	Propionobacterium propionicus/avidum, A. israelii, B. vulgatus, Bacteroides ovatus/thetaiotaomicron Bacteroides stercoris/eggerthii	P. brevis
ATCC 33574	Prevotella buccae	P. buccae	Bacteroides uniformis	P. buccae
ATCC 25611	Prevotella intermedia	No identification	NT	P. intermedia
1109/ChDC KB5	53 Prevotella intermedia	P. bivia, Prevotella P. melaninogenica	disiens, P. asaccharolytica, F. necrophorum/nucleatum	P. intermedia
ATCC 15930	Prevotella loescheii	No identification	P. melaninogenica/oralis, B. vulgatus	P. loescheii
ATCC 25845	Prevotella melaninogenica	No identification	P. intermedia/disiens	P. melaninogenica
ATCC 43324	Prevotella oulorum	P. melaninogenica	P. melaninogenica/oralis	P. oulorum
ATCC 19189	Prevotella ruminicola	No identification	P. intermedia/disiens	P. ruminicola
ATCC 6919	Propionibacterium acnes	P. acnes	P. acnes	P. acnes
KBN06P00391	Propionibacterium acnes	P. acnes	NT	P. acnes
1542/ChDC B715	Propionibacterium acnes	P. acnes	P. acnes	P. acnes
ATCC 17745	Veillonella Parvula	Veillonella spp.	No identification	V. parvula
1035/ChDC B273	Veillonella Parvula	Veillonella spp.	No identification	V. parvula

Abbreviation: NT, not tested.

Table 2.

Performance of Vitek 2, API 20A and 16S rRNA gene sequencing in the identification of 35 anaerobic reference strain*

Performance of identification	Vitek 2		API 20A		16S rRNA gene sequencing
Performance of identification	No	%	No	%	No	%
Correct identification at the species level	19	(54.3)	4	(15.4)	33	(94.3)
Correct identification at the genus level	27	(77.1)	11	(42.3)	2	(100)
Incorrect identification	1	(2.9)	13	(50.0)	0	(0.0)
No identification	7	(20.0)	2	(7.7)	0	(0.0)
Sum	35	(100)	26	(100)	35	(100)

^∗ Comparison pairs showing statistically significant differences (P＜0.05) by McNemar's test: VITEK 2 versus API 20A, VITEK 2 versus 16S rRNA gene sequencing, and API 20A versus 16S rRNA gene sequencing at the genus and species level.

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