Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 28, Number 7—July 2022
Research

Novel Mycobacterium tuberculosis Complex Genotype Related to M. caprae

Joseph Shea, Carol Smith, Tanya A. Halse, Donna Kohlerschmidt, Amy K. Rourke, Kimberlee A. Musser, Vincent Escuyer, and Pascal LapierreComments to Author 
Author affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA

Main Article

Figure

Phylogenetic SNP tree of strain 20-2359 and diverse group of representative Mycobacterium caprae, M. bovis, and other species and strains gathered from publicly available databases. Phylogenetic tree was calculated from the SNP alignment using IQ-TREE 1.6.12, with automatic best model selection (TVM+F+ASC+R2 model), and with 1,000 bootstrap support calculations (18). We used 14,688 variable genomic sites for this analysis. BCG, bacillus Calmette-Guérin; SNP, single-nucleotide polymorphism.

Figure. Phylogenetic SNP tree of strain 20-2359 and diverse group of representative Mycobacterium caprae, M. bovis, and other species and strains gathered from publicly available databases. Phylogenetic tree was calculated from the SNP alignment using IQ-TREE 1.6.12, with automatic best model selection (TVM+F+ASC+R2 model), and with 1,000 bootstrap support calculations (18). We used 14,688 variable genomic sites for this analysis. BCG, bacillus Calmette-Guérin; SNP, single-nucleotide polymorphism.

Main Article

References
  1. Velayati  AA, Farnia  P. The species concept. In: Velayati AA, Farnia P, editors. Atlas of Mycobacterium tuberculosis. Boston: Academic Press; 2017. p. 1–16.
  2. Ngabonziza  JCS, Loiseau  C, Marceau  M, Jouet  A, Menardo  F, Tzfadia  O, et al. A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nat Commun. 2020;11:2917. DOIPubMedGoogle Scholar
  3. Clarke  C, Van Helden  P, Miller  M, Parsons  S. Animal-adapted members of the Mycobacterium tuberculosis complex endemic to the southern African subregion. J S Afr Vet Assoc. 2016;87:1322. DOIPubMedGoogle Scholar
  4. Coscolla  M, Lewin  A, Metzger  S, Maetz-Rennsing  K, Calvignac-Spencer  S, Nitsche  A, et al. Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee. Emerg Infect Dis. 2013;19:969–76. DOIPubMedGoogle Scholar
  5. Senghore  M, Diarra  B, Gehre  F, Otu  J, Worwui  A, Muhammad  AK, et al. Evolution of Mycobacterium tuberculosis complex lineages and their role in an emerging threat of multidrug resistant tuberculosis in Bamako, Mali. Sci Rep. 2020;10:327. DOIPubMedGoogle Scholar
  6. Cvetnic  Z, Katalinic-Jankovic  V, Sostaric  B, Spicic  S, Obrovac  M, Marjanovic  S, et al. Mycobacterium caprae in cattle and humans in Croatia. Int J Tuberc Lung Dis. 2007;11:652–8.PubMedGoogle Scholar
  7. Doran  P, Carson  J, Costello  E, More  S. An outbreak of tuberculosis affecting cattle and people on an Irish dairy farm, following the consumption of raw milk. Ir Vet J. 2009;62:390–7. DOIPubMedGoogle Scholar
  8. Halse  TA, Escuyer  VE, Musser  KA. Evaluation of a single-tube multiplex real-time PCR for differentiation of members of the Mycobacterium tuberculosis complex in clinical specimens. J Clin Microbiol. 2011;49:2562–7. DOIPubMedGoogle Scholar
  9. Halse  TA, Edwards  J, Cunningham  PL, Wolfgang  WJ, Dumas  NB, Escuyer  VE, et al. Combined real-time PCR and rpoB gene pyrosequencing for rapid identification of Mycobacterium tuberculosis and determination of rifampin resistance directly in clinical specimens. J Clin Microbiol. 2010;48:1182–8. DOIPubMedGoogle Scholar
  10. Shea  J, Halse  TA, Lapierre  P, Shudt  M, Kohlerschmidt  D, Van Roey  P, et al. Comprehensive whole-genome sequencing and reporting of drug resistance profiles on clinical cases of Mycobacterium tuberculosis in New York State. J Clin Microbiol. 2017;55:1871–82. DOIPubMedGoogle Scholar
  11. Votintseva  AA, Pankhurst  LJ, Anson  LW, Morgan  MR, Gascoyne-Binzi  D, Walker  TM, et al. Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) cultures. J Clin Microbiol. 2015;53:1137–43. DOIPubMedGoogle Scholar
  12. Smith  C, Halse  TA, Shea  J, Modestil  H, Fowler  RC, Musser  KA, et al. Assessing nanopore sequencing for clinical diagnostics: a comparison of next-generation sequencing (NGS) methods for Mycobacterium tuberculosis. J Clin Microbiol. 2020;59:e00583–20. DOIPubMedGoogle Scholar
  13. Frampton  M, Houlston  R. Generation of artificial FASTQ files to evaluate the performance of next-generation sequencing pipelines. PLoS One. 2012;7:e49110. DOIPubMedGoogle Scholar
  14. Zwyer  M, Çavusoglu  C, Ghielmetti  G, Pacciarini  ML, Scaltriti  E, Van Soolingen  D, et al. A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics. Open Res Europe. 2021;1:100. DOIGoogle Scholar
  15. Wood  DE, Salzberg  SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15:R46. DOIPubMedGoogle Scholar
  16. 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. DOIPubMedGoogle Scholar
  17. Tatusova  T, DiCuccio  M, Badretdin  A, Chetvernin  V, Nawrocki  EP, Zaslavsky  L, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44:6614–24. DOIPubMedGoogle Scholar
  18. Nguyen  L-T, Schmidt  HA, von Haeseler  A, Minh  BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74. DOIPubMedGoogle Scholar
  19. Faksri  K, Xia  E, Tan  JH, Teo  Y-Y, Ong  RT-H. In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex from sequence reads using RD-Analyzer. BMC Genomics. 2016;17:847. DOIPubMedGoogle Scholar
  20. Yoshida  S, Suga  S, Ishikawa  S, Mukai  Y, Tsuyuguchi  K, Inoue  Y, et al. Mycobacterium caprae infection in captive Borneo elephant, Japan. Emerg Infect Dis. 2018;24:1937–40. DOIPubMedGoogle Scholar
  21. Chuachan  U, Kanistanon  K, Kampa  J, Chaiprasert  A. Molecular epidemiology of bovine tuberculosis in swamp buffalos in lower northeastern Thailand using spoligotyping. Khon Kaen University Veterinary Journal. 2016;26:61–76.

Main Article

Page created: May 10, 2022
Page updated: June 18, 2022
Page reviewed: June 18, 2022
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external