Assignment of Reference 5’-end 16S rDNA Sequences and Species-Specific Sequence Polymorphisms Improves Species Identification of Nocardia

Fanrong Kong1, Sharon C.A Chen1, *, Xiaoyou Chen1, 2, Vitali Sintchenko1, Catriona Halliday1, Lin Cai3, Zhongsheng Tong1, 4, Ok Cha Lee1, Tania C Sorrell1
1 Centre for Infectious Diseases and Microbiology, The University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia
2 Department of Tuberculosis, Beijing Tuberculosis & Thoracic Tumour Research Institute, Beijing, P. R. China
3 Department of Dermatology, Peking University People’s Hospital, Beijing, P. R. China
4 Research Laboratory for Infectious Skin Diseases, Department of Dermatology, Wuhan First Hospital, Wuhan, P. R. China

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© Kong et al.; Licensee Bentham Open.

open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

* Address correspondence to this author at the Centre for Infectious Diseases and Microbiology, Westmead Hospital, Darcy Road, Westmead, New South Wales, 2145, Australia; Fax: +61-2- 9891 5317; E-mail:


16S rDNA sequence analysis is the most accurate method for definitive species identification of nocardiae. However, conflicting results can be found due to sequence errors in gene databases. This study tested the feasibility of species identification of Nocardia by partial (5’-end 606-bp) 16S rDNA sequencing, based on sequence comparison with “reference” sequences of well-annotated strains. This new approach was evaluated using 96 American Type Culture Collection (n=6), and clinical (n=90) Nocardia isolates. Nucleotide sequence-based polymorphisms within species were indicative of “sequence types” for that species. Sequences were compared with those in the GenBank, Bioinformatics Bacteria Identification and Ribosomal Database Project databases. Compared with the reference sequence set, all 96 isolates were correctly identified using the criterion of ≥99% sequence similarity. Seventy-eight (81.3%) were speciated by database comparison; alignment with reference sequences resolved the identity of 14 (15%) isolates whose sequences yielded 100% similarity to sequences in GenBank under >1 species designation. Of 90 clinical isolates, the commonest species was Nocardia nova (33.3%) followed by Nocardia cyriacigeorgica (26.7%). Recently-described or uncommon species included Nocardia veterana (4.4%), Nocarida bejingensis (2.2%) and, Nocardia abscessus and Nocardia arthriditis (each n=1). Nocardia asteroides sensu stricto was rare (n=1). There were nine sequence types of N. nova, three of Nocardia brasiliensis with two each of N. cyriacigeorgica and Nocardia farcinica. Thirteen novel sequences were identified. Alignment of sequences with reference sequences facilitated species identification of Nocardia and allowed delineation of sequence types within species, suggesting that such a barcoding approach can be clinically useful for identification of bacteria.

Keywords: Nocardia spp, species identification, 16S rDNA, reference sequences, sequence polymorphisms.