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

ABSTRACT: 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.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.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.Our study provides novel insights into VNTR variations and potential new multilocus VNTR analysis schemes for improved genotyping of M. pneumoniae.

SUBMITTER: Zhang J

PROVIDER: S-EPMC5551932 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

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

Zhang Jing J Song Xiaohong X Ma Marella J MJ Xiao Li L Kenri Tsuyoshi T Sun Hongmei H Ptacek Travis T Li Shaoli S Waites Ken B KB Atkinson T Prescott TP Shibayama Keigo K Dybvig Kevin K Feng Yanmei Y

Future microbiology 20161012

<h4>Aim</h4>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.<h4>Methods</h4>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.<h4>Results</h4>We identified 13 VNTRs inc ...[more]

PMID: 27728978

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Dataset Information

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

Publications

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

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