Mycobacterium polyniensis sp.nov, a non-tuberculous mycobacterium clinical isolate from Tahiti, French Polynesia

TL;DR

A new species of non-tuberculous mycobacterium, Mycobacterium polyniensis, was discovered in Tahiti using a combination of genomic and phenotypic methods.

Contribution

The discovery and classification of a new mycobacterium species, Mycobacterium polyniensis, within the M. terrae complex.

Findings

The isolate CSUR_Q5927 was identified as a new species with 35.8% DNA-DNA hybridization similarity to Mycobacterium terrae.

Genomic analysis revealed a CG-content of 68.5% and 4337 protein-coding genes.

The isolate showed susceptibility to eight antimicrobials and resistance to five others.

Abstract

In this study, we investigated a previously unidentified respiratory tract isolate, CSUR_Q5927, collected in Tahiti, French Polynesia. Through a comprehensive polyphasic approach combining phenotypic traits with whole genome sequencing, we sought to elucidate the identity and characteristics of this isolate. After cultivating colonies in Middlebrook 7H10 at 37 °C for nine days, we observed acid-fast bacilli under microscopic examination and Ziehl-Neelsen staining. Additionally, electron microscopy revealed the presence of unsporulated bacilli, approximately 1.27 μm ± 0.26 μm in size, displaying morphology consistent with that of a mycobacterium. Matrix-assisted laser desorption/ionization mass spectrometry provided an identification score of 1.42, indicating a low confidence level. However, clustering analysis grouped isolate CSUR_Q5927 within the Mycobacterium terrae complex. Whole genome sequencing unveiled a CG-content of 68.5 % and a coding ratio of 93.6 %, comprising 4337 genes encoding proteins, 55 tRNA genes, and two rRNA. Further comparison with reference strain Mycobacterium terrae NCTC 10856 using DNA-DNA hybridisation values revealed a similarity of 35.8 %, confirming the presence of a new species within the M. terrae complex. In vitro susceptibility testing demonstrated the isolate's susceptibility to eight antimicrobials and resistance to five others. After meticulously conducting appropriate negative controls and analysing all the data, we propose the name Mycobacterium polyniensis for this novel M. terrae species, with isolate CSUR_Q5927 serving as the prototype strain. This discovery expands our understanding of the microbial diversity in the Polynesian region and highlights the importance of combining advanced techniques to accurately characterise and classify previously unknown mycobacteria species.

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