A Core Genome Multilocus Sequence Typing Scheme for Streptococcus mutans.

Hongsheng Liu,Zhenfei Guo,Shanshan Liu,Yudong Liu,Shengkai Liao,Kai Zhang,Qinglong Wang,Yu Sun,Xiaoliang Li

doi:10.1128/msphere.00348-20

Hongsheng Liu, Zhenfei Guo + Show 7 more

Open Access

https://doi.org/10.1128/msphere.00348-20

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Abstract

Streptococcus mutans is one of the primary pathogens responsible for the development of dental caries. Recent whole-genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST) approaches have been employed in epidemiological studies of specific human pathogens. However, this approach has not been reported in studies of S. mutans Here, we therefore developed a cgMLST scheme for S. mutans We surveyed 199 available S. mutans genomes as a means of identifying cgMLST targets, developing a scheme that incorporated 594 targets from the S. mutans UA159 reference genome. Sixty-eight sequence types (STs) were identified in this cgMLST scheme (cgSTs) in 80 S. mutans isolates from 40 children that were sequenced in this study, compared to 35 STs identified by multilocus sequence typing (MLST). Fifty-six cgSTs (82.35%) were associated with a single isolate based on our cgMLST scheme, which is significantly higher than in the MLST scheme (11.43%). In addition, 58.06% of all MLST profiles with ≥2 isolates were further differentiated by our cgMLST scheme. Topological analyses of the maximum likelihood phylogenetic trees revealed that our cgMLST scheme was more reliable than the MLST scheme. A minimum spanning tree of 145 S. mutans isolates from 10 countries developed based upon the cgMLST scheme highlighted the diverse population structure of S. mutans This cgMLST scheme thus offers a new molecular typing method suitable for evaluating the epidemiological distribution of this pathogen and has the potential to serve as a benchmark for future global studies of the epidemiological nature of dental caries.IMPORTANCEStreptococcus mutans is regarded as a major pathogen responsible for the onset of dental caries. S. mutans can transmit among people, especially within families. In this study, we established a new epidemiological approach to S. mutans classification. This approach can effectively differentiate among closely related isolates and offers superior reliability relative to that of the traditional MLST molecular typing method. As such, it has the potential to better support effective public health strategies centered around this bacterium that are aimed at preventing and treating dental caries.

Highlights

Streptococcus mutans is one of the primary pathogens responsible for the development of dental caries
We began by identifying genes that were well-suited to incorporation into our core genome multilocus sequence typing (cgMLST) scheme by filtering the S. mutans UA159 (GenBank accession number NC_004350.2) reference genome based upon minimum gene length, gene overlap, and start/stop codon positioning
We extracted the sequences corresponding to the eight housekeeping genes traditionally used for multilocus sequence typing (MLST)-based bacterial typing, and we compared these sequences to the S. mutans MLST database

Summary

Introduction

Streptococcus mutans is one of the primary pathogens responsible for the development of dental caries. A minimum spanning tree of 145 S. mutans isolates from 10 countries developed based upon the cgMLST scheme highlighted the diverse population structure of S. mutans This cgMLST scheme offers a new molecular typing method suitable for evaluating the epidemiological distribution of this pathogen and has the potential to serve as a benchmark for future global studies of the epidemiological nature of dental caries. Genotypic methodologies, including ribotyping, arbitrary primed PCR (AP-PCR), chromosomal DNA restriction fragment polymorphism, repetitive extragenic palindromic PCR (rep-PCR), multilocus enzyme electrophoresis, and pulse-field gel electrophoresis (PFEG), have been used to subtype S. mutans [11,12,13,14,15,16] These phenotypic approaches, are time intensive and have difficulty differentiating between closely related bacterial strains [17]. Another MLST scheme was reported by Do et al in 2010 [18]

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