Bacterial identification in clinical diagnostic laboratories using 16S rRNA sequences

[Tutorial] How to identify bacteria using a single Sanger sequence
01/10/2018

Bacterial identification in clinical diagnostic laboratories using 16S rRNA sequences

Bacterial infection may be caused by either new species or novel genetic variants in known bacteria that cannot be identified by conventional methods. 16S rRNA (16S) sequencing can provide a cost-effective means of bacterial identification in clinical diagnostic laboratories.

Identification accuracy though, is highly dependent on the quality of the 16S database.  A database for this purpose needs to be comprehensive, maintained with frequent updates, and importantly, properly organized with regards to taxonomy.

The EzBioCloud 16S database (formerly EzTaxon and EzTaxon-e) has been widely used in clinical laboratories worldwide. The current public version is free for academic and non-profit institutions.

For clinical interpretations, please consult the guideline below:

CLSI. Interpretive Criteria for Identification of Bacteria and Fungi by DNA Target Sequencing; Approved Guideline. CLSI document MM18-A. Wayne, PA: Clinical and Laboratory Standards Institute; 2008.

 

Selected publications related to clinical diagnostics and Veterinary medicine using the EzBioCloud 16S Identify service [Learn more].

  • Martinez-Anton, L., Marenda, M., Firestone, S. M., Bushell, R. N., Child, G., Hamilton, A. I., Long, S. N. & Le Chevoir, M. A. R. (2018). Investigation of the Role of Campylobacter Infection in Suspected Acute Polyradiculoneuritis in Dogs. J Vet Intern Med 32, 352-360. [Learn more]
  • Aoki, K., Harada, S., Yahara, K., Ishii, Y., Motooka, D., Nakamura, S., Akeda, Y., Iida, T., Tomono, K.& other authors (2018). Molecular Characterization of IMP-1-Producing Enterobacter cloacae Complex Isolates in Tokyo. Antimicrob Agents Chemother 62. [Learn more]

  • Kim, M. S., Chang, J., Kim, M. N., Choi, S. H., Jung, S. H., Lee, J. W. & Sung, H. (2017). Utility of a Direct 16S rDNA PCR and Sequencing for Etiological Diagnosis of Infective Endocarditis. Ann Lab Med 37, 505-510. [Learn more]

  • Aguilera-Arreola, M. G., Martinez-Pena, M. D., Hernandez-Martinez, F., Juarez Enriques, S. R., Rico Verdin, B., Majalca-Martinez, C., Castro-Escarpulli, G., Albarran-Fernandez, E. & Serrano-Lopez, S. C. (2016). Cultivation-independent approach for the direct detection of bacteria in human clinical specimens as a tool for analysing culture-negative samples: a prospective study. Springerplus 5, 332.

  • Pasciak, M., Dacko, W., Sikora, J., Gurlaga, D., Pawlik, K., Miekisiak, G. & Gamian, A. (2015). Creation of an In-House Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Corynebacterineae Database Overcomes Difficulties in Identification of Nocardia farcinica Clinical Isolates. J Clin Microbiol 53, 2611-2621.

  • Uwamino, Y., Muranaka, K., Hase, R., Otsuka, Y. & Hosokawa, N. (2016). Clinical Features of Community-Acquired Helicobacter cinaedi Bacteremia. Helicobacter 21, 24-28.

  • Sydenham, T. V., Arpi, M., Klein, K. & Justesen, U. S. (2014). Four cases of bacteremia caused by Oscillibacter ruminantium, a newly described species. J Clin Microbiol 52, 1304-1307.

  • Srinivasan, S., Munch, M. M., Sizova, M. V., Fiedler, T. L., Kohler, C. M., Hoffman, N. G., Liu, C., Agnew, K. J., Marrazzo, J. M.& other authors (2016). More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria. J Infect Dis 214 Suppl 1, S21-28.

  • Buss, S. N., Starlin, R. & Iwen, P. C. (2014). Bacteremia caused by Microbacterium binotii in a patient with sickle cell anemia. J Clin Microbiol 52, 379-381.

  • Sohn, K. M., Huh, K., Baek, J. Y., Kim, Y. S., Kang, C. I., Peck, K. R., Lee, N. Y., Song, J. H., Ko, K. S. & Chung, D. R. (2015). A new causative bacteria of infective endocarditis, Bergeyella cardium sp. nov. Diagn Microbiol Infect Dis 81, 213-216.

  • Benga, L., Benten, W. P., Engelhardt, E., Kohrer, K., Gougoula, C. & Sager, M. (2014). 16S ribosomal DNA sequence-based identification of bacteria in laboratory rodents: a practical approach in laboratory animal bacteriology diagnostics. Lab Anim 48, 305-312.

  • Jeon, Y., Kim, T. S., Kim, H. B., Park, K. U., Song, J. & Kim, E. C. (2012). First Korean case of Robinsoniella peoriensis bacteremia in a patient with aspiration pneumonia. Ann Lab Med 32, 370-374.

  • Duus, L. M., Hoiby, N., Wang, M., Schiotz, O. & Norskov-Lauritsen, N. (2013). Bacteria of the genus Dyella can chronically colonise the airways of patients with cystic fibrosis and elicit a pronounced antibody response. Int J Med Microbiol 303, 267-269.

  • Jung, A., Teske, L. & Rautenschlein, S. (2014). Enterococcus cecorum infection in a racing pigeon. Avian Dis 58, 654-658.

  • Thorasin, T., Hoyles, L. & McCartney, A. L. (2015). Dynamics and diversity of the ‘Atopobium cluster’ in the human faecal microbiota, and phenotypic characterization of ‘Atopobium cluster’ isolates. Microbiology 161, 565-579.

  • Park, K. S., Ki, C. S., Kang, C. I., Kim, Y. J., Chung, D. R., Peck, K. R., Song, J. H. & Lee, N. Y. (2012). 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 50, 1792-1795.

  • Loncaric, I., Stalder, G. L., Mehinagic, K., Rosengarten, R., Hoelzl, F., Knauer, F. & Walzer, C. (2013). Comparison of ESBL–and AmpC producing Enterobacteriaceae and methicillin-resistant Staphylococcus aureus (MRSA) isolated from migratory and resident population of rooks (Corvus frugilegus) in Austria. PLoS One 8, e84048.

 

 


The EzBioCloud team / Last edited on Mar 17, 2018