Phenotypic and molecular characterisation of a novel species, Mycobacterium hubeiense sp., isolated from the sputum of a patient with secondary tuberculosis in Hubei of China

Abstract

A new fast-growing mycobacterium, designated strain QGD101T, was isolated from the sputum of an 84-year-old man suspected of tuberculosis in Wuhan Medical Treatment Center, Hubei, China. This strain was a gram-staining-negative, aerobic, non-spore-forming and catalase-positive bacterium, which was further identified as the NTM by PNB and TCH tests. The moxifloxacin and levofloxacin exhibited strong suppressing function against QGD101T with MIC values of 0.06 and 0.125 µg/ml after drug susceptibility testing of six main antimicrobial agents on mycobacteria. Based on the sequence analysis of 16S rRNA, rpoB, hsp65 and 16S-23S rRNA internal transcribed spacer, the strain QGD101T could not be identified to a species level. Mycobacterium moriokaense ATCC43059T that shared the highest 16S rRNA gene sequence similarity (98%) with strain QGD101T was actually different in genomes average nucleotide identity (78.74%). In addition, the major cellular fatty acids of QGD101T were determined as C18:1ω9c, C16:0 and C18:2ω6c. The DNA G + C content was 64.9% measured by high performance liquid chromatography. Therefore, the phenotypic and genotypic characterisation of this strain led us to the conclusion that it represents a novel species of mycobacteria, for which the name Mycobacterium hubeiense sp. nov. (type strain QGD101T = CCTCCAA 2017003T = KCTC39927T) was proposed. Thus, the results of this study are very significant for the clinical diagnosis of tuberculosis and future personalised medicine.

Keywords: 16S rRNA; genomic analysis; nontuberculous mycobacteria; phenotype; rpoB.

Fig. 1.

Neighbour-joining trees based on 16S rRNA gene sequences of strain QGD101^T and some type strains. The tree was rooted with N. farcinica ATCC3318T. Percentages indicated at nodes represent bootstrap levels supported by 1000 resampled datasets; values <50% are not shown. The significance of the branching order was estimated by the bootstrap method calculated 1000 replications. Bar, 0.01 substitutions per nucleotide position.

Fig. 2.

Neighbour-joining trees based on rpoB sequences of strain QGD101^T and some type strains. Percentages indicated at nodes represent bootstrap levels supported by 1000 resampled datasets; values <50% are not shown. The significance of the branching order was estimated by the bootstrap method calculated 1000 replications. Bar, 0.1 substitutions per nucleotide position.

Fig. 3.

Correlation plot based on QGD101^T and reference strains ANI values.

Fig. 4.

Fatty acid chromatogram of QGD101^T.