AUTHOR=Nogueira Christiane L. , de Almeida Luiz G. P. , Menendez Maria C. , Garcia Maria J. , Digiampietri Luciano A. , Chimara Erica , Cnockaert Margo , Palomino Juan C. , Portaels Françoise , Martin Anandi , Vandamme Peter , Leão Sylvia C. 

TITLE=Characterization of Mycobacterium chelonae-Like Strains by Comparative Genomics

JOURNAL=Frontiers in Microbiology

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.00789

DOI=10.3389/fmicb.2017.00789

ISSN=1664-302X

ABSTRACT=<p>Isolates of the <italic>Mycobacterium chelonae</italic>-<italic>M. abscessus</italic> complex are subdivided into four clusters (CHI to CHIV) in the INNO-LiPA® <italic>Mycobacterium</italic> spp DNA strip assay. A considerable phenotypic variability was observed among isolates of the CHII cluster. In this study, we examined the diversity of 26 CHII cluster isolates by phenotypic analysis, drug susceptibility testing, whole genome sequencing and single-gene analysis. Pairwise genome comparisons were performed using several approaches, including average nucleotide identity (ANI) and genome-to-genome distance (GGD) among others. Based on ANI and GGD the isolates were identified as <italic>M. chelonae</italic> (14 isolates), <italic>M. franklinii</italic> (2 isolates) and <italic>M. salmoniphium</italic> (1 isolate). The remaining 9 isolates were subdivided into three novel putative genomospecies. Phenotypic analyses including drug susceptibility testing, as well as whole genome comparison by TETRA and delta differences, were not helpful in separating the groups revealed by ANI and GGD. The analysis of standard four conserved genomic regions showed that <italic>rpoB</italic> alone and the concatenated sequences clearly distinguished the taxonomic groups delimited by whole genome analyses. In conclusion, the CHII INNO-LiPa is not a homogeneous cluster; on the contrary, it is composed of closely related different species belonging to the <italic>M. chelonae-M. abscessus</italic> complex and also several unidentified isolates. The detection of these isolates, putatively novel species, indicates a wider inner variability than the presently known in this complex.</p>