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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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Characterization of Mycobacterium chelonae-Like Strains by Comparative Genomics.

Christiane L Nogueira1, Luiz G P de Almeida2, Maria C Menendez3

  • 1Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São PauloSão Paulo, Brazil.

Frontiers in Microbiology
|May 24, 2017
PubMed
Summary

The INNO-LiPA® assay

Keywords:
M. chelonae-M. abscessus complexidentificationmycobacteriumtaxonomywhole genome sequencing

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Area of Science:

  • Microbiology
  • Genomics
  • Taxonomy

Background:

  • The Mycobacterium chelonae-M. abscessus complex is classified into four clusters (CHI-CHIV) using the INNO-LiPA® DNA strip assay.
  • Significant phenotypic variation exists within the CHII cluster isolates.

Purpose of the Study:

  • To investigate the genetic and phenotypic diversity within the CHII cluster of the Mycobacterium chelonae-M. abscessus complex.
  • To re-evaluate the taxonomic classification of CHII cluster isolates using whole genome sequencing and comparative genomics.

Main Methods:

  • Phenotypic analysis and drug susceptibility testing were performed on 26 CHII isolates.
  • Whole genome sequencing was employed for all isolates.
  • Pairwise genome comparisons utilized average nucleotide identity (ANI) and genome-to-genome distance (GGD).
  • Analysis of conserved genomic regions, including rpoB, was conducted.

Main Results:

  • ANI and GGD analyses identified M. chelonae (14 isolates), M. franklinii (2 isolates), and M. salmoniphium (1 isolate).
  • Nine isolates were classified into three novel putative genomospecies.
  • Standard phenotypic and whole genome comparison methods (TETRA, delta differences) did not effectively differentiate these groups.
  • Analysis of the rpoB gene and concatenated conserved regions successfully distinguished the taxonomic groups.

Conclusions:

  • The CHII cluster is taxonomically diverse, containing multiple closely related species within the M. chelonae-M. abscessus complex.
  • Several unidentified isolates within the CHII cluster represent putative novel species.
  • The study highlights a greater intra-complex variability than previously recognized, underscoring the need for refined diagnostic and taxonomic approaches.