Comparative genomic analysis of Mycobacterium intracellulare: implications for clinical taxonomic classification in pulmonary Mycobacterium avium-intracellulare complex disease

Abstract

Background Mycobacterium intracellulare is a representative etiological agent of emerging pulmonary M. avium-intracellulare complex disease in the industrialized countries worldwide. The recent genome sequencing of clinical strains isolated from pulmonary M. avium-intracellulare complex disease has provided insight into the genomic characteristics of pathogenic mycobacteria, especially for M. avium; however, the genomic characteristics of M. intracellulare remain to be elucidated. Results In this study, we performed comparative genomic analysis of 55 M. intracellulare and related strains such as M. paraintracellulare (MP), M. indicus pranii (MIP) and M. yonogonense. Based on the average nucleotide identity, the clinical M. intracellulare strains were phylogenetically grouped in two clusters: (1) the typical M. intracellulare (TMI) group, including ATCC13950 and virulent M.i.27 and M.i.198 that we previously reported, and (2) the MP-MIP group. The alignment of the genomic regions was mostly preserved between groups. Plasmids were identified between groups and subgroups, including a plasmid common among some strains of the M.i.27 subgroup. Several genomic regions including those encoding factors involved in lipid metabolism (e.g., fadE3, fadE33), transporters (e.g., mce3), and type VII secretion system (genes of ESX-2 system) were shown to be hypermutated in the clinical strains. M. intracellulare was shown to be pan-genomic at the species and subspecies levels. The mce genes were specific to particular subspecies, suggesting that these genes may be helpful in discriminating virulence phenotypes between subspecies. Conclusions Our data suggest that genomic diversity among M. intracellulare, M. paraintracellulare, M. indicus pranii and M. yonogonense remains at the subspecies or genovar levels and does not reach the species level. Genetic components such as mce genes revealed by the comparative genomic analysis could be the novel focus for further insight into the mechanism of human pathogenesis for M. intracellulare and related strains.

High genetic heterogeneity of Mycobacterium intracellulare isolated from respiratory specimens

“…On the other hand, the VNTR analysis, which has proved to be a very useful and highly discriminatory tool in molecular epidemiology studies, is unable to recognize species related to M. intracellulare , such as Mycobacterium paraintracellulare and Mycobacterium indicus pranii . The identification of clinical isolates genetically close to M. intracellulare , addressed by multigene sequence-based analysis [ 18 ] or comparative genomic analysis [ 19 ], is important to define virulence determinants and evolution of MAC strains causing pulmonary disease.

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Novel Screening System of Virulent Strains for the Establishment of a Mycobacterium avium Complex Lung Disease Mouse Model Using Whole-Genome Sequencing

“…Our understanding of the mechanism underlying MAC pathogenicity has been hindered by the lack of a universal animal model that reflects human progressive MAC-LD. Since MAC is generally less virulent than M. tuberculosis and has high genetic and virulence diversity ( 16 – 18 ), selecting a suitable strain is an important process for model establishment. In the present study, we developed a screening method for identifying virulent strains in immunocompetent mice by combining mixed infection and WGS analysis.…”

“…Since NTM are generally less virulent than M. tuberculosis , the difficulty in inducing a productive and sustained infection in immunocompetent mice is the current hurdle for the development of an experimental model ( 14 , 15 ). In addition, because there is high genetic diversity ( 16 , 17 ) and corresponding large diversity in virulence among MAC strains ( 18 ), choosing suitable strains could be an important process.…”

The resistomes of Mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer

“…Besides efflux proteins, the ABC-F ATP-binding cassette ribosomal protection proteins (RPPs), excluding lsaB and poxtA, were also prevalently detected in MABC (> 1,575 strains). In addition, fourteen 23S rRNA methyltransferases (Erm (33), Erm (43), Erm (44), Erm (45), Erm (46), Erm (48), ErmA, ErmB, ErmC, ErmG, ErmH, ErmO, ErmT and ErmY) were also abundant. A betalactamase, blaLAP-1 which is also responsible for fluoroquinolone, aminoglycoside, tetracycline and rifamycin resistance [35], was detected in all but one (1,580) strain.…”

“…Before studying phylogenetic relatedness and evolutionary pressure on MABC resistomes, recombination in ARPs was first excluded as recombination can confound a selection analysis by causing mutation rate heterogeneity among sites [39]. After recombination analysis, 14 ARPs (arr-8, Erm (33), Erm (43), Erm (44), Erm (45), Erm (48), ErmA, ErmB, ErmC, ErmG, ErmT, ErmY, sul1 and sul2) were found to show recombination signals (homoplasies, recombination breakpoints and non-uniform distribution of sequence variations in alignments) in all three recombination detection methods (Additional file 1: Table S11) and were excluded from selection analysis.…”