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ORIGINAL RESEARCH

A Complete Genome of Nocardia terpenica NC_YFY_NT001 and Pan-Genomic Analysis Based on Different Sources of Nocardia spp. Isolates Reveal Possibly Host-Related Virulence Factors

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Pages 7259-7270 | Received 16 Aug 2022, Accepted 29 Nov 2022, Published online: 13 Dec 2022

References

  • Goodfellow M, Cross T. The Biology of the Actinomycetes. Academic Press; 1985:541.
  • Vera-Cabrera L, Ortiz-Lopez R, Elizondo-Gonzalez R, Ocampo-Candiani J, Gordon SV. Complete genome sequence analysis of Nocardia brasiliensis HUJEG-1 reveals a saprobic lifestyle and the genes needed for human pathogenesis. PLoS One. 2013;8(6):e65425. doi:10.1371/journal.pone.0065425
  • Wilson JW. Nocardiosis: updates and clinical overview. Mayo Clin Proc. 2012;87(4):403–407. doi:10.1016/j.mayocp.2011.11.016
  • Kurup PV, Randhawa HS, Sandhu RS. A survey of Nocardia asteroides, N. caviae and N. brasiliensis occuring in soil in India. Sabouraudia. 1968;6(3):260–266. doi:10.1080/00362176885190491
  • Han HJ, Kwak MJ, Ha SM, et al. Genomic characterization of Nocardia seriolae strains isolated from diseased fish. Microbiologyopen. 2019;8(3):e00656. doi:10.1002/mbo3.656
  • Nishiuchi Y, Baba T, Hotta HH, Yano I. Mycolic acid analysis in Nocardia species. The mycolic acid compositions of Nocardia asteroides, N. farcinica, and N. nova. J Microbiol Methods. 1999;37(2):111–122. doi:10.1016/s0167-7012(99)00055-x
  • Nocard E. Note sur la maladie des boeufs de la Guadeloupe connue sous le nom de farcin. Ann de l’Institut Pasteur. 1888;2:293–302.
  • Long PF. A retrospective study of Nocardia infections associated with the acquired immune deficiency syndrome (AIDS). Infection. 1994;22(5):362–364. doi:10.1007/BF01715551
  • Ali T, Chakraburtty A, Mahmood S, Bronze MS. Risk of nocardial infections with anti-tumor necrosis factor therapy. Am J Med Sci. 2013;346(2):166–168. doi:10.1097/MAJ.0b013e3182883708
  • Wadhwa T, Baveja U, Kumar N, Govil D, Sengupta S. Clinical manifestations of nocardiosis: study of risk factors and outcomes in a tertiary care hospital. J Lab Physicians. 2017;9(4):288–295. doi:10.4103/JLP.JLP_111_16
  • Brown-Elliott BA, Brown JM, Conville PS, Wallace RJ. Clinical and laboratory features of the Nocardia spp. based on current molecular taxonomy. Clin Microbiol Rev. 2006;19(2):259–282. doi:10.1128/CMR.19.2.259-282.2006
  • Minero MV, Marin M, Cercenado E, Rabadan PM, Bouza E, Munoz P. Nocardiosis at the turn of the century. Medicine. 2009;88(4):250–261. doi:10.1097/MD.0b013e3181afa1c8
  • Eisenblatter M, Disko U, Stoltenburg-Didinger G, et al. Isolation of Nocardia paucivorans from the cerebrospinal fluid of a patient with relapse of cerebral nocardiosis. J Clin Microbiol. 2002;40(9):3532–3534. doi:10.1128/jcm.40.9.3532-3534.2002
  • Jeong JH, Moon SM, Park PW, et al. Multiple brain abscesses caused by nocardia asiatica in a patient with systemic lupus erythematosus: the first case report and literature review. Ann Lab Med. 2017;37(5):459–461. doi:10.3343/alm.2017.37.5.459
  • Kennedy KJ, Chung KH, Bowden FJ, et al. A cluster of nocardial brain abscesses. Surg Neurol. 2007;68(1):43–9; discussion 49. doi:10.1016/j.surneu.2006.08.067
  • Bradsher RW, Monson TP, Steele RW. Brain abscess due to Nocardia caviae. Report of a fatal outcome associated with abnormal phagocyte function. Am J Clin Pathol. 1982;78(1):124–127. doi:10.1093/ajcp/78.1.124
  • Piau C, Kerjouan M, Le Mouel M, et al. First case of disseminated infection with Nocardia cerradoensis in a human. J Clin Microbiol. 2015;53(3):1034–1037. doi:10.1128/JCM.02979-14
  • Igbaseimokumo U, El Shafie S, Al Khal AL. First human infection of nocardia crassostreae in an immunocompetent patient. Chin Med J. 2016;129(1):114–115. doi:10.4103/0366-6999.172609
  • Barnaud G, Deschamps C, Manceron V, et al. Brain abscess caused by Nocardia cyriacigeorgica in a patient with human immunodeficiency virus infection. J Clin Microbiol. 2005;43(9):4895–4897. doi:10.1128/JCM.43.9.4895-4897.2005
  • Yamamoto F, Yamashita S, Kawano H, et al. Meningitis and ventriculitis due to Nocardia araoensis infection. Intern Med. 2017;56(7):853–859. doi:10.2169/internalmedicine.56.7332
  • Majeed A, Mushtaq A, Zangeneh T, et al. Intractable cerebral Nocardia mexicana in a GvHD patient successfully treated with linezolid. Bone Marrow Transplant. 2017;52(10):1476–1478. doi:10.1038/bmt.2017.167
  • Gezici AR, Daglioglu E, Ergungor F, Okay O, Polat O. Cerebral abscess caused by Nocardia nova. Neurol Neurochir Pol. 2008;42(2):153–156.
  • Brown BA, Lopes JO, Wilson RW, et al. Disseminated Nocardia pseudobrasiliensis infection in a patient with AIDS in Brazil. Clin Infect Dis. 1999;28(1):144–145. doi:10.1086/517180
  • Arends JE, Stemerding AM, Vorst SP, de Neeling AJ, Weersink AJ. First report of a brain abscess caused by Nocardia veterana. J Clin Microbiol. 2011;49(12):4364–4365. doi:10.1128/JCM.01062-11
  • Hu N, Zou W, Cai Q, et al. The first report of cerebral nocardiosis caused by nocardia terpenica together with exiguobacterium profundum bacteremia. Case report. Jundishapur J Microbiol. 2018;11(10):e69604. doi:10.5812/jjm.69604
  • Hoshino Y, Watanabe K, Iida S, et al. Nocardia terpenica sp. nov., isolated from Japanese patients with nocardiosis. Int J Syst Evol Microbiol. 2007;57(Pt7):1456–1460. doi:10.1099/ijs.0.64695-0
  • Gonzalez-Carrillo C, Millan-Sauceda C, Lozano-Garza HG, et al. Genomic changes associated with the loss of nocardia brasiliensis virulence in mice after 200 in vitro passages. Infect Immun. 2016;84(9):2595–2606. doi:10.1128/IAI.00329-16
  • Beaman BL, Black CM, Doughty F, Beaman L. Role of superoxide dismutase and catalase as determinants of pathogenicity of Nocardia asteroides: importance in resistance to microbicidal activities of human polymorphonuclear neutrophils. Infect Immun. 1985;47(1):135–141. doi:10.1128/iai.47.1.135-141.1985
  • Mannle D, McKinnie SMK, Mantri SS, et al. Comparative genomics and metabolomics in the genus nocardia. mSystems. 2020;5(3). doi:10.1128/mSystems.00125-20
  • Nouioui I, Cortes-Albayay C, Neumann-Schaal M, et al. Genomic virulence features of two novel species Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., isolated from patients with chronic pulmonary diseases. Microorganisms. 2020;8(10):1517. doi:10.3390/microorganisms8101517
  • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359. doi:10.1038/nmeth.1923
  • Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27(21):2987–2993. doi:10.1093/bioinformatics/btr509
  • Arndt D, Grant JR, Marcu A, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44(W1):W16–W21. doi:10.1093/nar/gkw387
  • Page AJ, Cummins CA, Hunt M, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31(22):3691–3693. doi:10.1093/bioinformatics/btv421
  • Liu B, Zheng D, Jin Q, Chen L, Yang J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res. 2019;47(D1):D687–D692. doi:10.1093/nar/gky1080
  • Margalit I, Muhsen K, Ben Ari Y, et al. Nocardia colonization in contrast to nocardiosis: a comparison of patients’ clinical characteristics. Eur J Clin Microbiol Infect Dis. 2020;39(4):759–763. doi:10.1007/s10096-019-03796-5
  • Martinez Tomas R, Menendez Villanueva R, Reyes Calzada S, et al. Pulmonary nocardiosis: risk factors and outcomes. Respirology. 2007;12(3):394–400. doi:10.1111/j.1440-1843.2007.01078.x
  • Takiguchi Y, Ishizaki S, Kobayashi T, et al. Pulmonary nocardiosis: a clinical analysis of 30 cases. Intern Med. 2017;56(12):1485–1490. doi:10.2169/internalmedicine.56.8163
  • Komaki H, Ichikawa N, Hosoyama A, et al. Genome based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in seven strains of five representative Nocardia species. BMC Genomics. 2014;15:323. doi:10.1186/1471-2164-15-323
  • Nouioui I, Ha SM, Baek I, Chun J, Goodfellow M. Genome insights into the pharmaceutical and plant growth promoting features of the novel species Nocardia alni sp. nov. BMC Genomics. 2022;23(1):70. doi:10.1186/s12864-021-08257-y
  • Patra P, Mondal N, Patra BC, Bhattacharya M. Epitope-based vaccine designing of nocardia asteroides targeting the virulence factor mce-family protein by immunoinformatics approach. Int J Pept Res Ther. 2020;26(2):1165–1176. doi:10.1007/s10989-019-09921-4
  • Xu S, Wei M, Li G, et al. Comprehensive analysis of the nocardia cyriacigeorgica complex reveals five species-level clades with different evolutionary and pathogenicity characteristics. mSystems. 2022;7(3):e0140621. doi:10.1128/msystems.01406-21
  • Fatahi-Bafghi M. Nocardiosis from 1888 to 2017. Microb Pathog. 2018;114:369–384. doi:10.1016/j.micpath.2017.11.012
  • Parish T, Hatfull GF, Jacobs WR. Two-component regulatory systems of mycobacteria. Microbiol Spectr. 2014;2(1). doi:10.1128/microbiolspec.MGM2-0010-2013
  • Rifat D, Bishai WR, Karakousis PC. Phosphate depletion: a novel trigger for Mycobacterium tuberculosis persistence. J Infect Dis. 2009;200(7):1126–1135. doi:10.1086/605700
  • Parish T, Smith DA, Roberts G, Betts J, Stoker NG. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology. 2003;149(Pt 6):1423–1435. doi:10.1099/mic.0.26245-0