Molecular identification and phylogenetic relationships of clinical Nocardia isolates
- 71 Downloads
Species identification of Nocardia is difficult because of a complex and rapidly evolving taxonomy. In this study, gene sequencing (16S rRNA, gyrB, secA1, hsp65, rpoB), single 16S rRNA gene sequence phylogenetic analysis, and MALDI-TOF analysis were used to accurately identify 46 clinical Nocardia isolates to the species level. This provided a basis for establishing a routine method of multi-locus sequence analysis (MLSA) for molecular identification of Nocardia species. Genetic polymorphism analysis showed that MLSA was a powerfully discriminating method compared with the 16S rRNA gene to identify clinical Nocardia isolates. However, five-locus (gyrB-16S rRNA-secA1-hsp65-rpoB) MLSA led to misidentifications of all of the five Nocardia abscessus, which were confirmed by digital DNA-DNA hybridization (DDH) analysis. Interestingly, four strains identified as Nocardia beijingensis by a 16S rRNA gene phylogenetic tree may be novel species as suggested by DDH studies. For the purpose of achieving both accuracy and discrimination, the data of MLSA were reanalyzed. A three-locus MLSA with concatenated gyrB-16S rRNA-secA1 sequences was used to construct the phylogenetic tree with high accuracy and powerful discrimination. Therefore, a routine method of MLSA was developed to identify clinical Nocardia species.
KeywordsNocardia Identification MLSA Phylogenetic relationships 16S rRNA gene DNA-DNA hybridization
The authors thank all staff members of the Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital (Beijing, China), for their contribution to this work.
LG and MW conceived the study. MW, PW, and CY performed the research. LG, MW, and PW analyzed data and wrote the paper. All authors read and approved the manuscript.
This work was supported by the National Science and Technology Major Project (Grant No. 2015ZX10003003).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
- Carrasco G, de Dios Caballero J, Garrido N, Valdezate S, Cantón R, Sáez-Nieto JA (2016) Shortcomings of the Commercial MALDI-TOF MS database and use of MLSA as an arbiter in the identification of Nocardia species. Front Microbiol 7:542. https://doi.org/10.3389/fmicb.2016.00542 CrossRefPubMedPubMedCentralGoogle Scholar
- Goodfellow M, Kämpfer P, Busse HJ, Trujillo M, Suzuki KI, Ludwig W, Whitman W (2012) Bergey’s manual® of systematic bacteriologyGoogle Scholar
- Michael G, Kämpfer P,Busse H-J, Trujillo M, Suzuki K-I, Ludwig W, Whitman W (2012) Bergey's manual® of systematic bacteriology. Google Scholar
- Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Truper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evolut Microbiol 37(4):463–464CrossRefGoogle Scholar