Journal: Frontiers in Microbiology

Article Title: Non-tuberculous mycobacteria isolates from patients with chronic pulmonary disease and no epidemiological relationship show sequence clusters through whole-genome sequencing

doi: 10.3389/fmicb.2025.1549030

Figure Lengend Snippet: Classification of NTM isolates in this study into species and subspecies using well-annotated reference type genomes. The figures show the maximum likelihood of the SNV tree inferred from core-genome alignment for all SGM first isolates and type strain genomes. SNVs were identified from core-genome Roary alignment, based on blastp 90% identity. Samples are colored based on WGS strain identification. M. avium subsp. avium strains in red; M avium subsp. paratuberculosis, and M. avium subsp. silvaticum reference strains in pink; M. marseillense and M. parascrofulaceum reference genomes used as outgroups in yellow; M. intracellulare subsp. intracellulare genomes in dark green; M. paraintracellulare in orange; M. intracellulare subsp. yongonense reference genome in purple; M. intracellulare subsp. chimaera genomes in blue; and M. intracellulare sp. strains in light green. The scale bar indicates the average number of substitutions per site (23,640 SNVs).

Article Snippet: M. intracellulare is formed by M. intracellulare subsp. intracellulare, M. intracellulare subsp. c himaera and M. intracellulare subsp. yongonense (list of prokaryotic names with standing in nomenclature is available at https://lpsn.dsmz.de/ ).

Techniques:

Journal: Frontiers in Microbiology

Article Title: Non-tuberculous mycobacteria isolates from patients with chronic pulmonary disease and no epidemiological relationship show sequence clusters through whole-genome sequencing

doi: 10.3389/fmicb.2025.1549030

Figure Lengend Snippet: Phylogenetic tree of M. intracellulare s ubsp. chimaera isolates with sequence clustering data, patient information, and Sequence Type (ST) information annotated. This figure shows the maximum likelihood SNV tree for all M. intracellulare subsp. chimaera isolates. The SNVs were identified from mapping reads to M. intracellulares subsp. chimaera reference genome DSM 44,623. Highlighted samples correspond to the sequence cluster calculated using the SNV threshold from the upper boundary of the SNV pairwise distance within patient diversity. The scale bar shows the number of SNVs per site (6.9 SNVs) and node bootstrap scores are shown when below 75 (with 1,000 bootstrap sampling). The tree figure was annotated with additional information in columns: Patient, from which the strain was isolated; rPinecone, cluster number generated from rPinecone R analysis; SKA cluster, cluster number generated from SKA analysis; and ST, sequence type profile number obtained from the pubMLST Mycobacteria spp. scheme.

Article Snippet: M. intracellulare is formed by M. intracellulare subsp. intracellulare, M. intracellulare subsp. c himaera and M. intracellulare subsp. yongonense (list of prokaryotic names with standing in nomenclature is available at https://lpsn.dsmz.de/ ).

Techniques: Sequencing, Sampling, Isolation, Generated

Journal: Journal of Clinical Microbiology

Article Title: This is giving me a complex: a practical attempt to streamline nontuberculous mycobacteria nomenclature for clinical purposes

doi: 10.1128/jcm.01531-23

Figure Lengend Snippet: Suggested nomenclature of common nontuberculous mycobacteria a

Article Snippet: MALDI-TOF-MS: matrix-assisted laser desorption ionization-time-of-flight mass spectrometry and M. = Mycobacterium . b Unproven human or animal pathogen. c M. intracellulare subsp. yongonense is a heterotypic synonym; correct name is M. intracellulare subsp. chimaera. d The validity of this species is currently unclear. e Due to taxonomical reclassification, these are now considered synonyms of other taxa ( https://lpsn.dsmz.de/ ) but may still be reported depending on methods/databases used.

Techniques: Sequencing