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Genotyping of Nocardia farcinica with multilocus sequence typing

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European Journal of Clinical Microbiology & Infectious Diseases Aims and scope Submit manuscript

Abstract

Nocardia are aerobic Gram-positive saprophytes that are widely distributed in nature, but some species cause nocardiosis, especially opportunistic infections that affect immunocompromised patients mostly. In this study, we developed a multilocus sequence typing (MLST) scheme using seven housekeeping genes (gyrB, hsp65, secA1, rpoB, rpoA, recA, and trpB) for genotyping the most common clinical species, Nocardia farcinica (37 clinical isolates from the patients with nocardiosis and seven from animals in China and 15 reference strains). The results showed that using these loci could perform accurate identification among different species, and high discriminative power within the N. farcinica species. Of the 59 N. farcinica isolates, 44 sequence types have been identified; 32 STs covering 46 isolates could be assigned to six clonal complexes that encompassed most of the collected strains. The results showed that these strains displayed a sufficiently informative population structure using this method. Our study also provided a suitable approach for epidemiological studies of N. farcinica. A large clonal complex comprising 16 strains was identified, and was notable for its wide distribution and host adaptation. This complex should be monitored closely and merits further study.

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Author notes

    Authors and Affiliations

    1. Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing Key Laboratory of Emerging infectious Diseases, Beijing, 100015, China

      P. Du

    2. State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, P.O. Box 5, Changping, Beijing, 102206, China

      X. Hou, S. Xu, L. Li, J. Zhang, K. Wan & Z. Li

    3. Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China

      X. Hou, S. Xu, J. Zhang, K. Wan & Z. Li

    4. Xiangya Hospital, Central South University, Changsha, 410008, China

      Y. Xie

    5. School of Laboratory Medicine, Wenzhou Medical University, Chashan University Town, Wenzhou, Zhejiang, 325035, China

      Y. Lou

    Authors
    1. P. Du
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    2. X. Hou
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    3. Y. Xie
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    4. S. Xu
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    Corresponding authors

    Correspondence to Y. Lou or Z. Li.

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    Funding

    This work was supported by the National High Technology Research and Development Program (“863” Program, grant no. 2014AA021404) and the National Key Program of Mega Infectious Diseases (grant no. 2013ZX10004221 and 2013ZX10004607) from the Ministry of Science and Technology and National Health and Family Planning Commission, P. R. China.

    Conflict of interest

    The authors declare that they have no conflict of interest.

    Ethical approval

    This article does not contain any studies with human participants or animals performed by any of the authors.

    Informed consent

    This article does not contain any studies with human participants, and informed consent is not applicable.

    Additional information

    P. Du, X. Hou, and Y. Xie contributed equally to this work.

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    Supplementary Table 1

    Background information on strains used in this study and the results of the MLST. (PDF 66 kb)

    Supplementary Table 2

    HGI of each combination with more than four loci. (PDF 38.5 kb)

    Supplementary Fig. 1

    Multilocus sequence analysis using concatenated sequences of the following four genes: gyrB-16S-secA1-hsp65. The 59 N. farcinica strains collected in this study, four other N. farcinica strains (OAHPP2695, NRRLB2089, OAHPP10250, and OAHPP10380), and 72 strains from another 36 species from a previous study were included. N. farcinica strains were clustered and compressed together in the N. farcinica node. (PDF 429 kb)

    Supplementary Fig. 2

    Phylogenetic analysis of each single gene. (PDF 680 kb)

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    Du, P., Hou, X., Xie, Y. et al. Genotyping of Nocardia farcinica with multilocus sequence typing. Eur J Clin Microbiol Infect Dis 35, 771–778 (2016). https://doi.org/10.1007/s10096-016-2596-x

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    • DOI: https://doi.org/10.1007/s10096-016-2596-x

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