1887

Microbial Genomics logo

Volume 7, Issue 10

The open pan-genome architecture and virulence landscape of Open Access

Abstract

Animal tuberculosis (TB) is an emergent disease caused by , one of the animal-adapted ecotypes of the complex (MTC). In this work, whole-genome comparative analyses of 70 . were performed to gain insights into the pan-genome architecture. The comparison across predicted genome composition enabled clustering into the core- and accessory-genome components, with 2736 CDS for the former, while the accessory moiety included 3897 CDS, of which 2656 are restricted to one/two genomes only. These analyses predicted an open pan-genome architecture, with an average of 32 CDS added by each genome and show the diversification of discrete subpopulations supported by both core- and accessory-genome components. The functional annotation of the pan-genome classified each CDS into one or several COG (Clusters of Orthologous Groups) categories, revealing ‘transcription’ (total average CDSs, =258), ‘lipid metabolism and transport’ (=242), ‘energy production and conversion’ (=214) and ‘unknown function’ (=876) as the most represented. The closer analysis of polymorphisms in virulence-related genes in a restrict group of from a multi-host system enabled the identification of clade-monomorphic non-synonymous SNPs, illustrating clade-specific virulence landscapes and correlating with disease severity. This first comparative pan-genome study of a diverse collection of encompassing all clonal complexes indicates a high percentage of accessory genes and denotes an open, dynamic non-conservative pan-genome structure, with high evolutionary potential, defying the canons of MTC biology. Furthermore, it shows that can shape its virulence repertoire, either by acquisition and loss of genes or by SNP-based diversification, likely towards host immune evasion, adaptation and persistence.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): comparative genomics , core-genome , Mycobacterium bovis , pan-genome , virulence and WGS
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000664
2021-10-29
2024-05-06
Loading full text...

Full text loading...

/deliver/fulltext/mgen/7/10/mgen000664.html?itemId=/content/journal/mgen/10.1099/mgen.0.000664&mimeType=html&fmt=ahah

References

  1. Gagneux S. Ecology and evolution of Mycobacterium tuberculosis. Nat Rev Microbiol 2018202–213 [View Article]
     [Google Scholar]
  2. WHO Global tuberculosis report 2019
     [Google Scholar]
  3. Reis AC, Ramos B, Pereira AC, Cunha M. Global trends of epidemiological research in livestock tuberculosis for the last four decades. Transbound Emerg Dis 2020; 1–14:
     [Google Scholar]
  4. Reis AC, Ramos B, Pereira AC, Cunha M. The hard numbers of tuberculosis epidemiology in wildlife: A meta-regression and systematic review. Transbound Emerg Dis 2020; 9:1–20
     [Google Scholar]
  5. Corner LAL. The role of wild animal populations in the epidemiology of tuberculosis in domestic animals: How to assess the risk. Vet Microbiol 2006; 112:303–312 [View Article] [PubMed]
     [Google Scholar]
  6. Palmer M, Thacker TC, Waters WR, Gortázar C, Corner LAL. Mycobacterium bovis: A model pathogen at the interface of livestock, wildlife, and humans. Vet Med Int 2012; 2012:236205 [View Article] [PubMed]
     [Google Scholar]
  7. Cunha M, Monteiro M, Carvalho P, Mendonça P, Albuquerque T et al. Multihost tuberculosis: insights from the portuguese control program. Vet Med Int 2011; 2011:795165 [View Article] [PubMed]
     [Google Scholar]
  8. Luciano SA, Roess A. Human zoonotic tuberculosis and livestock exposure in low- and middle-income countries: A systematic review identifying challenges in laboratory diagnosis. Zoonoses Public Health 2020; 67:97–111 [View Article]
     [Google Scholar]
  9. Riojas MA, McGough KJ, Rider-Riojas CJ, Rastogi N, Hazbón MH. 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 mycob. Int J Syst Evol Microbiol 2018; 68:324–332 [View Article] [PubMed]
     [Google Scholar]
  10. Jia X, Yang L, Dong M, Chen S, Lv L et al. The bioinformatics analysis of comparative genomics of Mycobacterium tuberculosis complex (MTBC) provides insight into dissimilarities between intraspecific groups differing in host association, virulence, and epitope diversity. Front Cell Infect Microbiol 20177
     [Google Scholar]
  11. Brosch R, Gordon S, Marmiesse M, Brodin P, Buchrieser C et al. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A 2002; 99:3684–3689 [View Article] [PubMed]
     [Google Scholar]
  12. Smith NH, Berg S, Dale J, Allen A, Rodriguez S et al. European 1: A globally important clonal complex of Mycobacterium bovis. Infect Genet Evol 2011; 11:1340–1351 [View Article] [PubMed]
     [Google Scholar]
  13. Rodriguez-Campos S, Schürch AC, Dale J, Lohan AJ, Cunha M et al. European 2 – A clonal complex of Mycobacterium bovis dominant in the Iberian Peninsula. Infect Genet Evol 2012; 12:866–872 [View Article] [PubMed]
     [Google Scholar]
  14. Muller B, Hilty M, Berg S, Garcia-Pelayo MC, Dale J et al. African 1, an Epidemiologically Important Clonal Complex of Mycobacterium bovis Dominant in Mali, Nigeria, Cameroon, and Chad. J Bacteriol 2009; 191:1951–1960 [View Article] [PubMed]
     [Google Scholar]
  15. Berg S, Garcia-Pelayo M, Muller B, Hailu E, Asiimwe B et al. African 2, a Clonal Complex of Mycobacterium bovis Epidemiologically Important in East Africa. J Bacteriol 2011; 193:670–678 [View Article] [PubMed]
     [Google Scholar]
  16. Branger M, Loux V, Cochard T, Boschiroli ML, Biet F et al. The complete genome sequence of Mycobacterium bovis Mb3601, a SB0120 spoligotype strain representative of a new clonal group. Infect Genet Evol 2020; 82:104309 [View Article] [PubMed]
     [Google Scholar]
  17. Rodriguez-Campos S, Smith NH, Boniotti MB, Aranaz A. Overview and phylogeny of Mycobacterium tuberculosis complex organisms: Implications for diagnostics and legislation of bovine tuberculosis. Res Vet Sci 2014; 97:S5–19 [View Article] [PubMed]
     [Google Scholar]
  18. É S, de Alencar A, Hodon M, Filho S, de Souza-Filho A et al. Identification of clonal complexes of Mycobacterium bovis in Brazil. Arch Microbiol 2019; 201:1047–1051 [View Article]
     [Google Scholar]
  19. Vernikos G, Medini D, Riley DR, Tettelin H. Ten years of pan-genome analyses. Curr Opin Microbiol 2015; 23:148–154 [View Article] [PubMed]
     [Google Scholar]
  20. Golby P, Nunez J, Witney A, Hinds J, Quail MA et al. Genome-level analyses of Mycobacterium bovis lineages reveal the role of SNPs and antisense transcription in differential gene expression. BMC Genomics 2013; 14:710 [View Article] [PubMed]
     [Google Scholar]
  21. Cheng G, Hussain T, Sabir N, Ni J, Li M et al. Comparative study of the molecular basis of pathogenicity of M. Bovis strains in a mouse model. Int J Mol Sci 2019
     [Google Scholar]
  22. Dong H, Lv Y, Sreevatsan S, Zhao D, Zhou X. Differences in pathogenicity of three animal isolates of Mycobacterium species in a mouse model. PLoS One 2017; 12:e0183666
     [Google Scholar]
  23. Vargas-Romero F, Mendoza-Hernández G, Suárez-Güemes F, Hernández-Pando R, Castañón-Arreola M. Secretome profiling of highly virulent mycobacterium bovis 04-303 strain reveals higher abundance of virulence-associated proteins. Microbial Pathogenesis 2016; 100:305–311 [View Article]
     [Google Scholar]
  24. Mattow J, Schaible UE, Schmidt F, Hagens K, Siejak F et al. Comparative proteome analysis of culture supernatant proteins from virulent Mycobacterium tuberculosis H37Rv and attenuated M. bovis BCG Copenhagen. Electrophoresis 2003; 24:3405–3420 [View Article]
     [Google Scholar]
  25. Pelayo MCG, Uplekar S, Keniry A, Lopez PM, Garnier T et al. A Comprehensive Survey of Single Nucleotide Polymorphisms (SNPs) across Mycobacterium bovis Strains and M. bovis BCG Vaccine Strains Refines the Genealogy and Defines a Minimal Set of SNPs That Separate Virulent M. bovis Strains and M. bovis BCG Strains. Infect Immun 2009; 77:2230–2238 [View Article] [PubMed]
     [Google Scholar]
  26. Forrellad MA, Klepp LI, Gioffré A, Sabio y García J, Morbidoni HR et al. Virulence factors of the Mycobacterium tuberculosis complex. Virulence 2013; 4:3–66 [View Article] [PubMed]
     [Google Scholar]
  27. Zimpel CK, Patané JSL, Guedes ACP, de Souza RF, Silva-pereira TT et al. Global Distribution and Evolution of Mycobacterium bovis Lineages. Front Microbiol 2020; 11:843 [View Article] [PubMed]
     [Google Scholar]
  28. Reis AC, Tenreiro R, Albuquerque T, Botelho A, Cunha M. Long-term molecular surveillance provides clues on a cattle origin for mycobacterium bovis in Portugal. Sci Rep 2020; 10:1–18
     [Google Scholar]
  29. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  30. Walker B, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS One 2014; 9:e112963
     [Google Scholar]
  31. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  32. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: A modular and extensible implementation of the RAST algorithm for annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article] [PubMed]
     [Google Scholar]
  33. Li H, Durbin R. Fast and accurate short read alignment with Burrows – Wheeler transform. Bioinformatics 2009; 25:1754–1760 [View Article] [PubMed]
     [Google Scholar]
  34. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. The Sequence Alignment / Map format and SAMtools. Bioinformatics 2009; 25:2078–2079 [View Article] [PubMed]
     [Google Scholar]
  35. Depristo M, Banks E, Poplin R, Garimella K, Maguire J et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011; 43:491–498 [View Article] [PubMed]
     [Google Scholar]
  36. Van der Auwera G, Carneiro MO, Hartl C, Poplin R, del Angel G et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinforma 2014; 43:
     [Google Scholar]
  37. Contreras-moreira B, Vinuesa P. GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article] [PubMed]
     [Google Scholar]
  38. Vinuesa P, Contreras-moreira B. Robust Identification of Orthologues and Paralogues for Microbial Pan-Genomics Using GET_HOMOLOGUES: A Case Study of pIncA/C Plasmids. In Bacterial Pangenomics 2015 pp 203–232 https://doi.org/10.1007/978-1-4939-1720-4
     [Google Scholar]
  39. Lefébure T, Stanhope MJ. Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol 2007; 8:71 [View Article]
     [Google Scholar]
  40. Tettelin H, Riley D, Cattuto C, Medini D. Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol 2008; 11:472–477 [View Article] [PubMed]
     [Google Scholar]
  41. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
     [Google Scholar]
  42. Brynildsrud O, Bohlin J, Scheffer L, Eldholm V. Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biol 2016; 17:1–9
     [Google Scholar]
  43. Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. Get_phylomarkers, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genus Stenotrophomonas. Front Microbiol 2018; 9:771 [View Article] [PubMed]
     [Google Scholar]
  44. Csűös M. Count: Evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics 2010; 26:1910–1912 [View Article] [PubMed]
     [Google Scholar]
  45. Tatusov RL, Galperin MY, Natale DA, Koonin E. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33–36 [View Article] [PubMed]
     [Google Scholar]
  46. Medini D, Donati C, Tettelin H, Mausignani V, Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev 2005; 15:589–594 [View Article] [PubMed]
     [Google Scholar]
  47. Yang T, Zhong J, Zhang J, Li C, Yu X et al. Pan-Genomic Study of Mycobacterium tuberculosis Reflecting the Primary/ Secondary Genes, Generality/ Individuality, and the Interconversion Through Copy Number Variations. Front Microbiol 2018; 9:1886 [View Article] [PubMed]
     [Google Scholar]
  48. Periwal V, Patowary A, Vellarikkal SK, Gupta A, Singh M et al. Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome. PLoS One 2015; 10:e0122979 [View Article] [PubMed]
     [Google Scholar]
  49. Zakham F, Sironen T, Vapalahti O, Kant R. Pan and Core Genome Analysis of 183 Mycobacterium tuberculosis Strains Revealed a High Inter-Species Diversity among the Human Adapted Strains. Antibiotics (Basel) 2021; 10:500 [View Article] [PubMed]
     [Google Scholar]
  50. Zakham F, Aouane O, Ussery D, Benjouad A, Ennaji M. Computational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains. Microb Inform Exp 2012; 2:7 [View Article] [PubMed]
     [Google Scholar]
  51. Trost B, Haakensen M, Pittet V, Ziola B, Kusalik A. Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera. BMC Microbiol 2010; 10:1–18 [View Article]
     [Google Scholar]
  52. Bolotin E, Hershberg R. Gene loss dominates as a source of genetic variation within clonal pathogenic bacterial species. Genome Biol Evol 2015; 7:2173–2187 [View Article] [PubMed]
     [Google Scholar]
  53. Duan J, Wainwright MS, Comeron JM, Saitou N, Sanders AR et al. n.d Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum Mol Genet 2003:205–2016
     [Google Scholar]
  54. Capon F, Allen MH, Ameen M, Burden AD, Tillman D et al. A synonymous SNP of the corneodesmosin gene leads to increased mRNA stability and demonstrates association with psoriasis across diverse ethnic groups. Hum Mol Genetics 2004; 13:2361–2368 [View Article]
     [Google Scholar]
  55. Gröschel MI, Sayes F, Simeone R, Majlessi L, Brosch R. ESX secretion systems: mycobacterial evolution to counter host immunity. Nat Rev Microbiol 2016; 14:677–691 [View Article] [PubMed]
     [Google Scholar]
  56. Bitter W, Houben ENG, Bottai D, Brodin P, Brown EJ et al. Systematic genetic nomenclature for type VII secretion systems. PLoS Pathog 2013; 5:e1000507
     [Google Scholar]
  57. Ates LS, Ummels R, Commandeur S, van der Weerd R, Sparrius M et al. Essential Role of the ESX-5 Secretion System in Outer Membrane Permeability of Pathogenic Mycobacteria. PLoS Genet 2015; 11:e1005190 [View Article] [PubMed]
     [Google Scholar]
  58. Bottai D, di Luca M, Majlessi L, Frigui W, Simeone R et al. Disruption of the ESX-5 system of Mycobacterium tuberculosis causes loss of PPE protein secretion, reduction of cell wall integrity and strong attenuation. Mol Microbiol 2012; 83:1195–1209 [View Article] [PubMed]
     [Google Scholar]
  59. Bukka A, Price CTD, Kernodle DS, Graham JE. Mycobacterium tuberculosis RNA expression patterns in sputum bacteria indicate secreted Esx factors contributing to growth are highly expressed in active disease. Front Microbiol 2012; 2:266 [View Article] [PubMed]
     [Google Scholar]
  60. Ohol YM, Goetz DH, Chan K, Shiloh MU, Craik CS et al. Mycobacterium tuberculosis MycP1 Protease Plays a Dual Role in Regulation of ESX-1 Secretion and Virulence. Cell Host Microbe 2010; 7:210–220 [View Article] [PubMed]
     [Google Scholar]
  61. Conrad WH, Osman MM, Shanahan JK, Chu F, Takaki KK et al. Mycobacterial ESX-1 secretion system mediates host cell lysis through bacterium contact-dependent gross membrane disruptions. Proc Natl Acad Sci U S A 2017; 114:1371–1376 [View Article] [PubMed]
     [Google Scholar]
  62. Ballesteros C, Garrido JM, Vicente J, Romero B, Galindo RC et al. First data on eurasian wild boar response to oral immunization with BCG and challenge with a mycobacterium bovis field strain. Vaccine 2009; 27:6662–6668 [View Article] [PubMed]
     [Google Scholar]
  63. Nugent G, Yockney IJ, Whitford EJ, Cross ML, Aldwell E et al. Field Trial of an Aerially-Distributed Tuberculosis Vaccine in a Low-Density Wildlife Population of Brushtail Possums (Trichosurus vulpecula. PLoS One 2016; 11:e0167144 [View Article] [PubMed]
     [Google Scholar]
  64. Gormley E, Bhuachalla DN, Keeffe JO, Murphy D, Aldwell FE et al. Oral Vaccination of Free-Living Badgers (Meles meles) with Bacille Calmette Guérin (BCG) Vaccine Confers Protection against Tuberculosis. PLoS One 2017; 12:e0168851 [View Article] [PubMed]
     [Google Scholar]
  65. Reis AC, Salvador LCM, Robbe-Austerman S, Tenreiro R, Botelho A et al. Phylogenomics sheds light on the population structure of mycobacterium bovis from a multi-host tuberculosis system. bioRxiv 2021
     [Google Scholar]
  66. Otchere ID, van Tonder AJ, Asante-Poku A, Sánchez-Busó L, Coscollá M et al. Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana. PLoS One 2019; 14:e0209395 [View Article]
     [Google Scholar]
  67. Branger M, Hauer A, Michelet L, Karoui C, Cochard T et al. Draft Genome Sequence of Mycobacterium bovis Strain D-10-02315 Isolated from Wild Boar. Genome Announc 2016; 4:16e01268 [View Article]
     [Google Scholar]
  68. Orloski K, Robbe-Austerman S, Stuber T, Hench B, Schoenbaum M. Whole genome sequencing of Mycobacterium bovis isolated from livestock in the United States, 1989-2018. Front Vet Sci 2018; 5:253 [View Article] [PubMed]
     [Google Scholar]
  69. Guimarães AMS, Zimpel CK, Ikuta CY, do Nascimento NC, dos Santos AP et al. Draft genome sequence of Mycobacterium bovis strain SP38, a pathogenic bacterium isolated from a bovine in Brazil. Genome Announc 2015; 3:
     [Google Scholar]
  70. Kim N, Jang Y, Kim JK, Ryoo S, Kwon KH et al. Complete genome sequence of Mycobacterium bovis clinical strain 1595, isolated from the laryngopharyngeal lymph node of South Korean cattle. Genome Announc 2015; 3:15e01124
     [Google Scholar]
  71. Zhu L, Zhong J, Jia X, Liu G, Kang Y et al. Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology. Nucleic Acids Res 2016; 44:730–743 [View Article] [PubMed]
     [Google Scholar]
  72. Wanzala SI, Nakavuma J, Travis DA, Kia P, Ogwang S et al. Draft genome sequences of Mycobacterium bovis BZ 31150 and Mycobacterium bovis B2 7505, pathogenic bacteria isolated from archived captive animal bronchial washes and human sputum samples in Uganda. Genome Announc 2015; 3:11 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000664
Loading
The open pan-genome architecture and virulence landscape of Mycobacterium bovis
M Gen 7, 000664 (2021); https://doi.org/10.1099/mgen.0.000664
/content/journal/mgen/10.1099/mgen.0.000664
/content/journal/mgen/10.1099/mgen.0.000664
Loading

Data & Media loading...

Supplements

Loading data from figshare Loading data from figshare

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error