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

Tateishi Y., Ozeki Y., Nishiyama A., Miki M., Maekura R., Fukushima Y., Nakajima C., Suzuki Y., Matsumoto S.

Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan; Department of Respiratory Medicine, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan; Graduate School of Health Care Sciences, Jikei Institute, Osaka, Japan; Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan; Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Kampus C Jl. Mulyorejo, Surabaya, Indonesia


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. © 2021, The Author(s).

Comparative genomics; Mammalian cell entry genes; Mycobacterium indicus pranii; Mycobacterium intracellulare; Mycobacterium paraintracellulare


BMC Microbiology

Publisher: BioMed Central Ltd

Volume 21, Issue 1, Art No 103, Page – , Page Count

Journal Link:

doi: 10.1186/s12866-021-02163-9

Issn: 14712180

Type: All Open Access, Gold, Green


Brode, S.K., Caley, C.L., Marras, T.K., The epidemiologic relationship between tuberculosis and non-tuberculous mycobacterial disease: a systematic review (2014) Int J Tuberc Lung Dis, 18 (11), pp. 1370-1377; Adjemian, J., Olivier, K.N., Seitz, A.E., Holland, S.M., Prevots, D.R., Prevalence of nontuberculous mycobacterial lung disease in U.S. Medicare beneficiaries (2012) Am J Respir Crit Care Med, 185 (8), pp. 881-886; Raju, R., Raju, S.M., Zhao, Y., Rubin, E.J., Leveraging advances in tuberculosis diagnosis and treatment to address nontuberculous mycobacterial disease (2016) Emerg Infect Dis, 22 (3), pp. 365-369; Cowman, S., van Ingen, J., Griffith, D.E., Loebinger, M.R., Non-tuberculous mycobacterial pulmonary disease (2019) Eur Respir J, 54 (1), p. 1900250; Namkoong, H., Kurashima, A., Morimoto, K., Hoshino, Y., Hasegawa, N., Ato, M., Mitarai, S., Epidemiology of pulmonary nontuberculous mycobacterial disease, Japan (2016) Emerg Infect Dis, 22 (6), pp. 1116-1117; Periwal, Y., Patowary, A., Vellarikkal, S.K., Gupta, A., Singh, M., Mittal, A., Comparative whole-genome analysis of clinical isolates reveals characteristic architecture of Mycobacterium tuberculosis pangenome (2015) PLoS One, 10 (4); Yang, T., Zhong, J., Zhang, J., Li, C., Yu, X., Xiao, J., Jia, X., Chen, F., Pan-genomic study of Mycobacterium tuberculosis reflecting the primary/secondary genes, generality/individuality, and the interconversion through copy number variations (2018) Front Microbiol, 9, p. 1886; Das, S., Pettersson, B.M.F., Behra, P.R.K., Mallick, A., Cheramie, M., Ramesh, M., Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing (2020) Sci Rep, 10, p. 5246. , COI: 1:CAS:528:DC%2BB3cXlvFClu78%3D; Uchiya, K., Tomida, S., Nakagawa, T., Asahi, S., Nikai, T., Ogawa, K., Comparative genome analyses of Mycobacterium avium reveal genomic features of its subspecies and strains that cause progression of pulmonary disease (2017) Sci Rep, 7 (1), p. 39750; Rindi, L., Garzelli, C., Genetic diversity and phylogeny of Mycobacterium avium (2014) Infect Genet Evol, 21, pp. 375-383; Mijs, W., de Haas, P., Rossau, R., Van der Laan, T., Rigouts, L., Portaels, F., Molecular evidence to support a proposal to reserve the designation Mycobacterium avium subsp avium for bird-type isolates and ‘M. avium subsp. hominissuis’ for the human/porcine type of M. avium (2002) Int. J. Syst. Evol. Microbiol., 52, pp. 1505-1518. , COI: 1:CAS:528:DC%2BD38XnvFyiur4%3D, PID: 12361252; Thorel, M.F., Krichevsky, M., Lévy-Frébault, V.V., Numerical taxonomy of mycobactin-dependent mycobacteria, emended description of Mycobacterium avium, and description of Mycobacterium avium subsp. avium subsp. nov., Mycobacterium avium subsp. paratuberculosis subsp. nov., and Mycobacterium avium subsp. silvaticum subsp. nov (1990) Int J Syst Bacteriol, 40 (3), pp. 254-260; Lee, S.-Y., Kim, B.-J., Kim, H., Won, Y.-S., Jeon, C.O., Jeong, J., Lee, S.H., Kim, B.J., Mycobacterium paraintracellulare sp. nov., for the genotype INT-1 of Mycobacterium intracellulare (2016) Int J Syst Evol Microbiol, 66 (8), pp. 3132-3141; Kim, B.-J., Math, R.K., Jeon, C.O., Yu, H.-K., Park, Y.-G., Kook, Y.-H., Kim, B.J., Mycobacterium yongonense sp. nov., a slow-growing non-chromogenic species closely related to Mycobacterium intracellulare (2013) Int J Syst Evol Microbiol, 63 (Pt_1), pp. 192-199; Saini, V., Raghuvanshi, S., Talwar, G.P., Ahmed, N., Khurana, J.P., Hasnain, S.E., Tyagi, A.K., Tyagi, A.K., Polyphasic taxonomic analysis establishes Mycobacterium indicus pranii as a distinct species (2009) PLoS One, 4 (7); Saini, V., Raghuvanshi, S., Khurana, J.P., Ahmed, N., Hasnain, S.E., Tyagi, A.K., Tyagi, A.K., Massive gene acquisitions in Mycobacterium indicus pranii provide a perspective on mycobacterial evolution (2012) Nucleic Acids Res, 40 (21), pp. 10832-10850; Kim, B.-J., Choi, B.-S., Lim, J.-S., Choi, I.-Y., Kook, Y.-H., Kim, B.-J., Complete genome sequence of Mycobacterium intracellulare clinical strain MOTT-64, belonging to the INT1 genotype (2012) J Bacteriol, 194 (12), p. 3268; Kim, S.-Y., Park, H.Y., Jeong, B.-H., Jeon, K., Huh, H.J., Ki, C.-S., Lee, N.Y., Koh, W.J., Molecular analysis of clinical isolates previously diagnosed as Mycobacterium intracellulare reveals incidental findings of “Mycobacterium indicus pranii” genotypes in human ling infection (2015) BMC Infect Dis, 15 (1), p. 406; Tortoli, E., Fedrizzi, T., Meehan, C.J., Trovato, A., Grottola, A., Giacobazzi, R., The new phylogeny of the genus Mycobacterium: the old and the news (2017) Infect Genet Evol, 56, pp. 19-25; Matsumoto, Y., Kinjo, T., Motooka, D., Nabeya, D., Jung, N., Uechi, K., Horii, T., Nakamura, S., Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles (2019) Emerg Microbes Infect, 8 (1), pp. 1043-1053; Tateishi, Y., Hirayama, Y., Ozeki, Y., Nishiuchi, Y., Yoshimura, M., Kang, J., Shibata, A., Matsumoto, S., Virulence of Mycobacterium avium complex strains isolated from immunocompetent patients (2009) Microb Pathog, 46 (1), pp. 6-12; Tateishi, Y., Kitada, S., Miki, K., Maekura, R., Ogura, Y., Ozeki, Y., Whole-genome sequence of the hypervirulent clinical strain Mycobacterium intracellulare M.i.198 (2012) J Bacteriol, 194, p. 6336. , COI: 1:CAS:528:DC%2BC38Xhs1Cju7bO; Uchiya, K., Takahashi, H., Yagi, T., Moriyama, M., Inagaki, T., Ishikawa, K., Comparative genome analysis of Mycobacterium avium revealed genetic diversity in strains that cause pulmonary and disseminated disease (2013) PLoS One, 8 (8); Bannantine, J.P., Wu, C.W., Hsu, C., Zhou, S., Schwartz, D.C., Bayles, D.O., Paustian, M.L., Talaat, A.M., Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association (2012) BMC Genomics, 13 (1), p. 89; Casali, N., Riley, L.W., A phylogenomic analysis of the Actinomycetales mce operons (2007) BMC Genomics, 8 (1), p. 60; Hemati, Z., Derakhshandeh, A., Haghkhah, M., Chaubey, K.K., Gupta, S., Singh, M., Singh, S.V., Dhama, K., Mammalian cell entry operons; novel and major subset candidates for diagnosis with special reference to Mycobacterium avium subspecies paratuberculosis infection (2019) Vet Quartery, 39 (1), pp. 65-75; Zao, J.-W., Sim, Z.-Q., Zhang, X.-Y., Zhang, Y., Liu, J., Ye, J., Mycobacterial 3-hydroxyacyl-l-thioester dehydratase Y derived from Mycobacterium tuberculosis induces COX-2 expression in mouse macrophages through MAPK-NF-κB pathway (2014) Immunol Lett, 161 (1), pp. 125-132; Tettelin, H., Riley, D., Cattuto, C., Medini, D., Comparative genomics: the bacterial pan-genome (2008) Curr Opin Microbiol, 11 (5), pp. 472-477; Chaudhari, N.M., Gupta, V.K., Dutta, C., BPGA- an ultra-fast pan-genome analysis pipeline (2016) Sci Rep, 6 (1), p. 24373; van Ingen, J., Turenne, C.Y., Tortoli, E., Wallace, R.J., Jr., Brown-Elliott, B.A., A definition of the Mycobacterium avium complex for taxonomical and clinical purposes, a review (2018) Int J Syst Evol Microbiol, 68 (11), pp. 3666-3677; Nouioui, I., Carro, L., García-López, M., Meier-Kolthoff, J.P., Woyke, T., Kyrpides, N.C., Pukall, R., Göker, M., Genome-based taxonomic classification of the phylum Actinobacteria (2018) Front Microbiol, 9, p. 2007; Tortoli, E., Meehan, C.J., Grottola, A., Fregni Serpini, G., Fabio, A., Trovato, A., Pecorari, M., Cirillo, D.M., Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium (2019) Infect Genet Evol, 75, p. 103983; Castejon, M., Menéndez, M.C., Comas, I., Vicente, A., Garcia, M.J., Whole-genome sequence analysis of the Mycobacterium avium complex and proposal of the transfer of Mycobacterium yongonense to Mycobaterium intracellulare subsp. yonogense susbp (2018) Int J System Evol Microbiol, 68 (6), pp. 1998-2005; Tortoli, E., Rindi, L., Garcia, M.J., Chiaradonna, P., Dei, R., Garzelli, C., Kroppenstedt, R.M., Scarparo, C., Proposal to elevate the genetic variant MAC-A, included in the Mycobacterium avium complex, to species rank as Mycobacterium chimaera sp. nov (2004) Int J Syst Evol Microbiol, 54 (4), pp. 1277-1285; Kasperbauer, S.H., Daley, C.L., Mycobacterium chimaera infections related to the heater-cooler unit outbreak: A guide to diagnosis and management (2019) Clin Infect Dis, 68 (7), pp. 1244-1250; Riojas, M.A., McGough, K.J., Rider-Riojas, C.J., Rastogi, N., Hazbón, M.H., Phylogenomic analysis of the species of the Mycobacterium tuberculosis complex demonstrates that Mycobacterium africanum, Mycobacterium bovis, Mycobacterium caprae, Mycobacterium microti and Mycobacterium pinnipedii are later heterotypic synonyms of Mycobacterium tuberculosis (2018) Int J Syst Evol Microbiol, 68 (1), pp. 324-332; Kim, S.-Y., Shin, S.H., Moon, S.M., Yang, B., Kim, H., Kwon, O.J., Huh, H.J., Koh, W.J., Distribution and clinical significance of Mycobacterium avium complex species isolated from respiratory specimens (2017) Diag Microb Infect Dis, 88 (2), pp. 125-137; Dumas, E., Boritsch, E.C., Vandenbogaert, M., de la Vega, R.C.R., Thiberge, J.-M., Caro, V., Mycobacterial pan-genome analysis suggests important role of plasmids in the radiation of type VII secretion systems (2016) Genome Biol Evol, 8 (2), pp. 387-402; Daley, C.L., Iaccarino, J.M., Jr., Lange, C., Cambau, E., Wallace, R.J., Andrejak, C., Treatment of nontuberculous mycobacterial pulmonary disease: an official ATS/ERS/ESCMID/IDSA clinical practice guideline: executive summary (2020) Eur Respit J, 71, pp. e1-e36; Griffith, D.E., Aksamit, T., Brown-Elliott, B.A., Catanzaro, A., Daley, C., Gordin, F., Holland, S.M., Winthrop, K., An official ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases (2007) Am J Respir Crit Care Med, 175 (4), pp. 367-416; Maekura, R., Okuda, Y., Hirotani, A., Kitada, S., Hiraga, T., Yoshimura, K., Yano, I., Ito, M., Clinical and prognostic importance of serotyping Mycobacterium avium-Mycobacterium intracellulare complex isolates in human immunodeficiency virus-negative patients (2005) J Clin Microbiol, 43 (7), pp. 3150-3158; Pandey, A.K., Sassetti, C.M., Mycobacterial persistence requires the utilization of host cholesterol (2008) Proc Natl Acad Sci U S A, 105 (11), pp. 4376-4380; Forrellad, M.A., McNeil, M., Santangelo Mde, L., Blanco, F.C., García, E., Klepp, L.I., Role of the Mce1 transporter in the lipid homeostasis of Mycobacterium tuberculosis (2014) Tuberculosis(Edinb), 94, pp. 170-177. , COI: 1:CAS:528:DC%2BC2cXisFSnsb0%3D; Tateishi, Y., Minato, Y., Baughn, A.D., Ohnishi, H., Nishiyama, A., Ozeki, Y., Matsumoto, S., Genome-wide identification of essential genes in Mycobacterium intracellulare by transposon sequencing – implication for metabolic remodeling (2020) Sci Rep, 10 (1), p. 5449; Kim, B.-J., Hong, S.-H., Kook, Y.-H., Kim, B.-J., Molecular evidence of lateral gene transfer in rpoB gene of Mycobacterium yongonense strains via multlilocus sequence analysis (2013) PLoS One, 8 (1); Fedrizzi, T., Meehan, C.J., Grottola, A., Giacobazzi, E., Fregni Serpini, G., Tagliazucchi, S., Fabio, A., Segata, N., Genomic characterization of nontuberculous mycobacteria (2017) Sci Rep, 7 (1), p. 45258; Stinear, T.P., Seemann, T., Harrison, P.F., Jenkin, G.A., Davies, J.K., Johnson, P.D., Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis (2008) Genome Res, 18 (5), pp. 729-741; van Helden, P., Victor, T., Warren, R., van Helden, E., Isolation of DNA from Mycobacterium tuberculosis (2001) Mycobacterium Tuberculosis Protocols, pp. 19-30. , Parish T, Stoker NG, Humana Press; Tanizawa, Y., Fujisawa, T., Nakamura, Y., DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication (2018) Bioinformatics., 34 (6), pp. 1037-1039

Indexed by Scopus

Leave a Comment