Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles

Yuki Matsumoto,Takeshi Kinjo,Daisuke Motooka,Daijiro Nabeya,Nicolas Jung,Kohei Uechi,Toshihiro Horii,Tetsuya Iida,Jiro Fujita,Shota Nakamura

doi:10.1080/22221751.2019.1637702

Yuki Matsumoto, Takeshi Kinjo + Show 8 more

Open Access

https://doi.org/10.1080/22221751.2019.1637702

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Abstract

ABSTRACT The prevalence of nontuberculous mycobacteria (NTM) pulmonary diseases has been increasing worldwide. NTM consist of approximately 200 species and distinguishing between them at the subspecies level is critical to treatment. In this study, we sequenced 63 NTM genomes, 27 of which were newly determined, by hybrid assembly using sequencers from Illumina and Oxford Nanopore Technologies (ONT). This analysis expanded the available genomic data to 175 NTM species and redefined their subgenus classification. We also developed a novel multi-locus sequence typing (MLST) database based on 184 genes from 7547 assemblies and an identification software, mlstverse, which can also be used for detecting other bacteria given a suitable MLST database. This method showed the highest sensitivity and specificity amongst conventional methods and demonstrated the capacity for rapid detection of NTM, 10 min of sequencing of the ONT MinION being sufficient. Application of this methodology could improve disease epidemiology and increase the cure rates of NTM diseases.

Highlights

The Mycobacterium genus belongs to the Actinobacteria phylum and includes three major human pathogens: Mycobacterium tuberculosis (MTB), Mycobacterium leprae, and nontuberculous mycobacteria (NTM) species
We expanded the number of NTM species with known genomic sequences to 175 and substantially improved the quality of genome assemblies
Comparative analysis using core and pan genomes constructed from 175 NTM genomes revealed the subgenera of the newly sequenced NTM species

Summary

Introduction

The Mycobacterium genus belongs to the Actinobacteria phylum and includes three major human pathogens: Mycobacterium tuberculosis (MTB), Mycobacterium leprae, and nontuberculous mycobacteria (NTM) species. Bolletii) are the major causative agents of NTM-PD [7,12]. These two complexes are further classified into many subspecies that show different susceptibilities to chemotherapies [13,14,15]. This diversity of NTM subspecies represents a significant obstacle against successful treatment, and current therapies require prolonged treatment and often lead to insufficient clinical outcomes due to the lack of subspecies identification [16]. Identifying NTM at a subspecies level is an essential step prior to treatment [14,15]

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