Phylogenomic analyses and reclassification of species within the genus Tsukamurella: Insights to species definition in the post-genomic era

Frontiers in Microbiology

Volumn 7, Issue JUL, 2016, Pages

  Teng, Jade L L ^a,b   Tang, Ying ^a   Huang, Yi ^a   Guo, Feng Biao ^c   Wei, Wen ^d   Chen, Jonathan H K ^a   Wong, Samson S Y ^a,b   Lau, Susanna K P ^a,b   Woo, Patrick C Y ^a,b  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b THE UNIVERSITY OF HONG KONG   (Hong Kong)

^c UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

^d CHONGQING UNIVERSITY   (China)

Author keywords

Genomics; Phylogenomic; Reclassification; Species; Tsukamurella

Indexed keywords

ARTICLE; BACTERIUM; CLASSIFICATION; DNA DNA HYBRIDIZATION; GENE SEQUENCE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR GENETICS; NONHUMAN; PHENOTYPE; PHYLOGENOMICS; SEQUENCE ANALYSIS; TSUKAMURELLA; TSUKAMURELLA CARBOXY DIVORANS; TSUKAMURELLA PSEUDOSPUMAE; TSUKAMURELLA PULMONIS; TSUKAMURELLA SPONGIAE; TSUKAMURELLA SUNCHONENSIS; TSUKAMURELLA TYROSINOSOLVENS;

EID: 84983050302     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2016.01137     Document Type: Article

References (50)

1. Abràmoff, M. D., Magalhaes, P. J., and Ram, S. J. (2004). Image processing with ImageJ. Biophotonics Int. 11, 36-42.
2. Almehmi, A., Pfister, A. K., McCowan, R., and Matulis, S. (2004). Implantable cardioverter-defibrillator infection caused by Tsukamurella. W. V. Med. J. 100, 185-186.
3. Auch, A. F., Klenk, H. P., and Göker, M. (2010). Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand. Genomic Sci. 2, 142-148. doi: 10.4056/sigs.541628
4. Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., et al. (2008). The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75
5. Bouza, E., Pérez-Parra, A., Rosal, M., Martín-Rabadán, P., Rodríguez-Créixems, M., and Marín, M. (2009). Tsukamurella: a cause of catheter-related bloodstream infections. Eur. J. Clin. Microbiol. Infect. Dis. 28, 203-210. doi: 10.1007/s10096-008-0607-2
6. Collins, M. D., Goodfellow, M., and Minnikin, D. E. (1982). A survey of the structures of mycolic acids in Corynebacterium and related taxa. J. Gen. Microbiol. 128, 129-149. doi: 10.1099/00221287-128-1-129
7. Collins, M. D., and Jones, D. (1982). Lipid composition of Corynebacterium paurometabolum (Steinhaus). FEMS Microbiol. Lett. 13, 13-16. doi: 10.1111/j.1574-6968.1982.tb08217.x
8. Collins, M. D., Smida, J., Dorsch, M., and Stackebrandt, E. (1988). Tsukamurella gen. nov., harboring Corynebacterium paurometabolum and Rhodococcus aurantiacus. Int. J. Syst. Bacteriol. 38, 385-391. doi: 10.1099/00207713-38-4-385
9. Conville, P. S., and Witebsky, F. G. (2007). "Nocardia, Rhodococcus, Gordonia, Actinomadura, Streptomyces, and other aerobic actinomycetes," in Manual of Clinical Microbiology, 9th Edn, eds P. R. Murray, E. J. Baron, J. H. Jorgensen, M. R. Louise, and M. A. Pfaller (Washington, DC: American Society for Microbiology), 515-542.
10. Delcher, A. L., Bratke, K. A., Powers, E. C., and Salzberg, S. L. (2007). Identifying bacterialgenes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673-679. doi: 10.1093/bioinformatics/btm009
11. Euzéby, J. (2008). Validation List 123. Int. J. Syst. Evol. Microbiol. 58, 1993-1994.
12. Fox, G. E., Magrum, L. J., Balch, W. E., Wolfe, R. S., and Woese, C. R. (1977). Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proc. Natl. Acad. Sci. U.S.A. 74, 4537-4541. doi: 10.1073/pnas.74.10.4537
13. Goodfellow, M., and Kumar, Y. (2012). "Genus I. Tsukamurella Collins, Smida, Dorsch and Stackebrandt 1988, 387," in Bergey's Mannual of Systematic Bacteriology, 2nd Edn, eds M. Goodfellow, P. Kämpfer, H.-J. Busse, M. E. Trujillo, K.-I. Suzuki, W. Ludwig et al. (New York, NY: Springer), 500-509.
14. Goris, J., Konstantinidis, K. T., Klappenbach, J. A., Coenye, T., Vandamme, P., and Tiedje, J. M. (2007). DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57, 81-91. doi: 10.1099/ijs.0.64483-0
15. Gupta, R., Lanter, J. M., and Woese, C. R. (1983). Sequence of the 16S ribosomal RNA from Halobacterium volcanii, an archaebacterium. Science 221, 656-659. doi: 10.1126/science.221.4611.656
16. Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95-98.
17. Jiang, Y., Chen, X., Han, L., Li, Q., Huang, X., Qiu, S. M., et al. (2013). Diversity of cultivable actinomycetes in 6 species of herbivore feces. Int. J. Microbiol. Res. 1, 76-84.
18. Kattar, M. M., Cookson, B. T., Carlson, L. D., Stiglich, S. K., Schwartz, M. A., Nguyen, T. T., et al. (2001). Tsukamurella strandjordae sp. nov., a proposed new species causing sepsis. J. Clin. Microbiol. 39, 1467-1476. doi: 10.1128/JCM.39.4.1467-1476.2001
19. Ketterlinus, R., Hsieh, S. Y., Teng, S. H., Lee, H., and Pusch, W. (2005). Fishing for biomarkers: analyzing mass spectrometry data with the new ClinProTools software. Biotechniques 38(Suppl. 6), 37-40. doi: 10.2144/05386SU07
20. Konstantinidis, K. T., and Tiedje, J. M. (2005). Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. U.S.A. 102, 2567-2572. doi: 10.1073/pnas.0409727102
21. Lapage, S. P., Sneath, P. H. A., Lessel, E. F., Skerman, V. B. D., Seeliger, H. P. R., and Clark, W. A. (eds) (1992). International Code of Nomenclature of Bacteria (1990 Revision). Bacteriological Code. Washington, DC: American Society for Microbiology.
22. Larkin, J. A., Lit, L., Sinnott, J., Wills, T., and Szentivanyi, A. (1999). Infection of aknee prosthesis with Tsukamurella species. South. Med. J. 92, 831-832. doi: 10.1097/00007611-199908000-00019
23. Lau, S. K., Tang, B. S., Teng, J. L., Chan, T. M., Curreem, S. O., Fan, R. Y., et al. (2014). Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for identification of clinically significant bacteria that are difficult to identify in clinical laboratories. J. Clin. Pathol. 67, 361-366. doi: 10.1136/jclinpath-2013-201818
24. Liu, C. Y., Lai, C. C., Lee, M. R., Lee, Y. C., Huang, Y. T., Liao, C. H., et al. (2011). Clinical characteristics of infections caused by Tsukamurella spp. and antimicrobial susceptibilities of the isolates. Int. J. Antimicrob. Agents 38, 534-537. doi: 10.1016/j.ijantimicag.2011.07.018
25. Maeda, Y., Stanley, T., Stirling, J., Griffiths, M., Calvert, A., Stuart Elborn, J., et al. (2010). No evidence of transmission of bacteria between reptiles and a CF patient-a case report of a young adult CF patient and reptiles. Zoonoses Public Health 57:e47-e53. doi: 10.1111/j.1863-2378.2009.01293.x
26. Nam, S. W., Kim, W., Chun, J., and Goodfellow, M. (2004). Tsukamurella pseudospumae sp. nov., a novel actinomycete isolated from activated sludge foam. Int. J. Syst. Evol. Microbiol. 54, 1209-1212. doi: 10.1099/ijs.0.02939-0
27. Olson, J. B., Harmody, D. K., Bej, A. K., and McCarthy, P. J. (2007). Tsukamurella spongiae sp. nov., a novel actinomycete isolated from a deep-water marine sponge. Int. J. Syst. Evol. Microbiol. 57, 1478-1481. doi: 10.1099/ijs.0.64837-0
28. Palys, T., Nakamura, L. K., and Cohan, F. M. (1997). Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int. J. Syst. Bacteriol. 47, 1145-1156. doi: 10.1099/00207713-47-4-1145
29. Park, S. W., Kim, S. M., Park, S. T., and Kim, Y. M. (2009). Tsukamurella carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete. Int. J. Syst. Evol. Microbiol. 59, 1541-1544. doi: 10.1099/ijs.0.005959-0
30. Richter, M., and Rosselló-Móra, R. (2009). Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U.S.A. 106, 19126-19131. doi: 10.1073/pnas.0906412106
31. Sasser, M. (1990). "Identification of bacteria through fatty acid analysis," in Methods in Phytobacteriology, eds Z. Klement, K. Rudolph and D. C. Sands (Budapest: Akademiai Kiado), 199-204.
32. Schwartz, M. A., Tabet, S. R., Collier, A. C., Wallis, C. K., Carlson, L. C., Nguyen, T. T., et al. (2002). Central venous catheter-related bacteremia due to Tsukamurella species in the immunocompromised host: a case series and review of the literature. Clin. Infect. Dis. 35:e72-e77. doi: 10.1099/ijs.0.005959-0
33. Seong, C. N., Kim, Y. S., Baik, K. S., Goodfellow, M., et al. (2003). Tsukamurella sunchonensis sp. nov., a bacterium associated with foam in activated sludge. J. Microbiol. 41, 83-88.
34. Shaer, A. J., and Gadegbeku, C. A. (2001). Tsukamurella peritonitis associated with continuous ambulatory peritoneal dialysis. Clin. Nephrol. 56, 241-246.
35. Stackebrandt, E., and Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44, 846-849. doi: 10.1099/00207713-44-4-846
36. Steinhaus, E. A. (1941). A study of the bacteria associated with thirty species of insects. J. Bacteriol. 42, 757-790.
37. Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30, 2725-2729. doi: 10.1093/molbev/mst197
38. Teng, J. L., Huang, Y., Tse, H., Chen, J. H., Tang, Y., Lau, S. K., et al. (2014). Phylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus. Genome Biol. Evol. 6, 2930-2943. doi: 10.1093/gbe/evu232
39. Teng, J. L., Tang, Y., Wong, S. S., Ngan, A. H., Huang, Y., Tsang, C. C., et al. (2015). Tsukamurella hongkongensis sp. nov. and Tsukamurella sinensis sp. nov. isolated from patients with keratitis, catheter-related bacteraemia and conjunctivitis in Hong Kong. Int. J. Syst. Bacteriol. 66, 391-397. doi: 10.1099/ijsem.0.000733
40. Tse, H., Tsoi, H. W., Leung, S. P., Lau, S. K., Woo, P. C., and Yuen, K. Y. (2010). Complete genome sequence of Staphylococcus lugdunensis strain HKU09-01. J. Bacteriol. 192, 1471-1472. doi: 10.1128/JB.01627-09
41. Verroken, A., Janssens, M., Berhin, C., Bogaerts, P., Huang, T. D., Wauters, G., et al. (2010). Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of Nocardia species. J. Clin. Microbiol. 48, 4015-4021. doi: 10.1128/JCM.01234-10
42. Wayne, L. G. (1988). International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Zentralbl. Bakteriol. Mikrobiol. Hyg. A 268, 433-434. doi: 10.1016/S0176-6724(88)80120-2
43. Wei, W., Gao, F., Du, M. Z., Hua, H. L., Wang, J., and Guo, F. B. (2016). Zisland Explorer: detect genomic islands by combining homogeneity and heterogeneity properties. Brief. Bioinform. doi: 10.1093/bib/bbw019 [Epub ahead of print].
44. Wei, W., and Guo, F. B. (2011). Prediction of genomic islands in seven human pathogens using the Z-Island method. Genet. Mol. Res. 10, 2307-2315. doi: 10.4238/2011.October.5.1
45. Woo, P. C., Lau, S. K., Teng, J. L., Tse, H., and Yuen, K. Y. (2008). Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Eur. J. Clin. Microbiol. Infect. Dis. 14, 908-934. doi: 10.1111/j.1469-0691.2008.02070.x
46. Woo, P. C., Lau, S. K., Tse, H., Teng, J. L., Curreem, S. O., Tsang, A. K., et al. (2009). The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLoS. Genet. 5:e1000416. doi: 10.1371/journal.pgen.1000416
47. Woo, P. C., Ngan, A. H., Lau, S. K., and Yuen, K. Y. (2003). Tsukamurella conjunctivitis: a novel clinical syndrome. J. Clin. Microbiol. 41, 3368-3371. doi: 10.1128/JCM.41.7.3368-3371.2003
48. Woo, P. C., Wu, A. K., Tsang, C. C., Leung, K. W., Ngan, A. H., Curreem, S. O., et al. (2014). Streptobacillus hongkongensis sp. nov., isolated from patients with quinsy and septic arthritis, and emended descriptions of the genus Streptobacillus and Streptobacillus moniliformis. Int. J. Syst. Bacteriol. 64, 3034-3039. doi: 10.1099/ijs.0.061242-0
49. Yassin, A. F., Rainey, F. A., Brzezinka, H., Burghardt, J., Rifai, M., Seifert, P., et al. (1996). Tsukamurella pulmonis sp. nov. Int. J. Syst. Bacteriol. 46, 429-436. doi: 10.1099/00207713-46-2-429
50. Yassin, A. F., Rainey, F. A., Burghardt, J., Brzezinka, H., Schmitt, S., Seifert, P., et al. (1997). Tsukamurella tyrosinosolvens sp. nov. Int. J. Syst. Bacteriol. 47, 607-614. doi: 10.1099/00207713-47-3-607