Inter- and intra-strain variability of tandem repeats in Mycoplasma pneumoniae based on next-generation sequencing data-Reference-Cited by-同舟云学术

Inter- and intra-strain variability of tandem repeats in Mycoplasma pneumoniae based on next-generation sequencing data

Published:2017-02 Issue:2 Volume:12 Page:119-129
ISSN:1746-0913
Container-title:Future Microbiology
language:en
Short-container-title:Future Microbiology

Author:

Zhang Jing¹²,Song Xiaohong²³,Ma Marella J⁴,Xiao Li⁵,Kenri Tsuyoshi⁶,Sun Hongmei⁷,Ptacek Travis⁸,Li Shaoli⁷,Waites Ken B⁹,Atkinson T Prescott¹⁰,Shibayama Keigo⁶,Dybvig Kevin⁸,Feng Yanmei¹¹

Affiliation:

1. Department of Pathogenic Biology, Chongqing Medical University, Chongqing, China

2. Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA

3. Department of Pharmacology, Sichuan University, Chengdu, Sichuan, China

4. Winston Churchill High School, Potomac, MD, USA

5. Department of Medicine, University of Alabama at Birmingham, AL, USA

6. Department of Bacteriology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan

7. Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China

8. Department of Microbiology, University of Alabama at Birmingham, AL, USA

9. Department of Pathology, University of Alabama at Birmingham, AL, USA

10. Department of Pediatrics, University of Alabama at Birmingham, AL, USA

11. Department of Pulmonary Medicine, The First Affiliated Hospital, Chongqing Medical University, Chongqing, China

Abstract

Aim: To characterize inter- and intra-strain variability of variable-number tandem repeats (VNTRs) in Mycoplasma pneumoniae to determine the optimal multilocus VNTR analysis scheme for improved strain typing. Methods: Whole genome assemblies and next-generation sequencing data from diverse M. pneumoniae isolates were used to characterize VNTRs and their variability, and to compare the strain discriminability of new VNTR and existing markers. Results: We identified 13 VNTRs including five reported previously. These VNTRs displayed different levels of inter- and intra-strain copy number variations. All new markers showed similar or higher discriminability compared with existing VNTR markers and the P1 typing system. Conclusion: Our study provides novel insights into VNTR variations and potential new multilocus VNTR analysis schemes for improved genotyping of M. pneumoniae.

Publisher

Future Medicine Ltd

Subject

Microbiology (medical),Microbiology

Link

https://www.futuremedicine.com/doi/pdf/10.2217/fmb-2016-0111

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