Jing Zhang1,2, Xiaohong Song2,3, Marella J Ma4, Li Xiao5, Tsuyoshi Kenri6, Hongmei Sun7, Travis Ptacek8, Shaoli Li7, Ken B Waites9, T Prescott Atkinson10, Keigo Shibayama6, Kevin Dybvig8, Yanmei Feng11. 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.
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.
Entities:
Keywords:
Mycoplasma pneumoniae; next-generation sequencing; tandem repeats
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