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Molecular identification and phylogenetic relationships of clinical Nocardia isolates

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Abstract

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.

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Acknowledgements

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.

Funding

This work was supported by the National Science and Technology Major Project (Grant No. 2015ZX10003003).

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Author notes

  1. Ming Wei and Peng Wang have contributed equally to this work.

Authors and Affiliations

  1. Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital, Capital Medical University, 8 Gongren Tiyuchang Nanlu, Chaoyang District, Beijing, 100020, People’s Republic of China

    Ming Wei, Peng Wang, Chunxia Yang & Li Gu

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  1. Ming Wei
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  2. Peng Wang
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  3. Chunxia Yang
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  4. Li Gu
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Contributions

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.

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Correspondence to Li Gu.

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Wei, M., Wang, P., Yang, C. et al. Molecular identification and phylogenetic relationships of clinical Nocardia isolates. Antonie van Leeuwenhoek 112, 1755–1766 (2019). https://doi.org/10.1007/s10482-019-01296-2

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