secA1 gene sequence polymorphisms for species identification of Nocardia species and recognition of intraspecies genetic diversity.
Sequence analysis of the Nocardia essential secretory protein SecA1 gene (secA1) for species identification of 120 American Type Culture Collection (ATCC) and clinical isolates of Nocardia (16 species) was studied in comparison with 5'-end 606-bp 16S rRNA gene sequencing. Species determination by both methods was concordant for all 10 ATCC strains. secA1 gene sequencing provided the same species identification as 16S rRNA gene analysis for 94/110 (85.5%) clinical isolates. However, 40 (42.6%) isolates had sequences with <99.0% similarity to archived secA1 sequences for the species, including 29 Nocardia cyriacigeorgica (96.6 to 98.9% similarity) and 4 Nocardia veterana (91.5 to 98.9% similarity) strains. Discrepant species identification was obtained for 16 (14.5%) clinical isolates, including 13/23 Nocardia nova strains (identified as various Nocardia species by secA1 sequencing) and 1 isolate each of Nocardia abscessus (identified as Nocardia asiatica), Nocardia elegans (Nocardia africana), and Nocardia transvalensis (Nocardia blacklockiae); both secA1 gene sequence analysis and deduced amino acid sequence analysis determined the species to be different from those assigned by 16S rRNA gene sequencing. The secA1 locus showed high sequence diversity (66 sequence or genetic types versus 40 16S rRNA gene sequence types), which was highest for N. nova (14 secA1 sequence types), followed by Nocardia farcinica and N. veterana (n = 7 each); there was only a single sequence type among eight Nocardia paucivorans strains. The secA1 locus has potential for species identification as an adjunct to 16S rRNA gene sequencing but requires additional deduced amino acid sequence analysis. It may be a suitable marker for phylogenetic/subtyping studies.
Kong
Fanrong
F
Centre for Infectious Diseases and Microbiology, University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia.
Wang
Huiping
H
Zhang
Erqing
E
Sintchenko
Vitali
V
Xiao
Meng
M
Sorrell
Tania C
TC
Chen
Xiaoyou
X
Chen
Sharon C-A
SC
D000251:Adenosine Triphosphatases / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D006801:Humans; D026901:Membrane Transport Proteins / Q000235:genetics*; D008969:Molecular Sequence Data; D009615:Nocardia / Q000145:classification* / Q000235:genetics*; D009617:Nocardia Infections / Q000382:microbiology; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D000069816:SEC Translocation Channels; D000081416:SecA Proteins; D017422:Sequence Analysis, DNA
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D026901:Membrane Transport Proteins; D012336:RNA, Ribosomal, 16S; D000069816:SEC Translocation Channels; D000251:Adenosine Triphosphatases; D000081416:SecA Proteins
Open Microbiol J. 2009 Jun 23;3:97-105
19639036
BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S15
19534740
J Clin Microbiol. 2005 Jun;43(6):2881-5
15956412
J Clin Microbiol. 2008 Jan;46(1):265-73
18003809
Clin Microbiol Rev. 2006 Apr;19(2):259-82
16614249
J Clin Microbiol. 2006 Feb;44(2):536-46
16455910
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
PLoS One. 2008 Jul 30;3(7):e2802
18665273
J Med Microbiol. 2010 May;59(Pt 5):548-555
20110385
J Clin Microbiol. 2006 Aug;44(8):2760-6
16891489
J Clin Microbiol. 2010 Feb;48(2):503-11
19955277
J Clin Microbiol. 2007 Sep;45(9):2761-4
17626177
J Clin Microbiol. 2007 Apr;45(4):1146-51
17301281
Mycopathologia. 2009 Feb;167(2):95-105
18781396
Clin Microbiol Rev. 2004 Oct;17(4):840-62, table of contents
15489351
J Clin Microbiol. 2004 Nov;42(11):5139-45
15528707
Int J Syst Evol Microbiol. 2009 Oct;59(Pt 10):2408-14
19622667
Biol Direct. 2009 Sep 29;4:35
19788732
J Clin Microbiol. 2000 Jan;38(1):158-64
10618080
J Clin Microbiol. 2003 Feb;41(2):851-6
12574299
J Med Microbiol. 2010 Feb;59(Pt 2):165-171
19833784
Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12794-7
19666622
Clin Microbiol Rev. 1994 Jul;7(3):357-417
7923055
J Clin Microbiol. 2004 Feb;42(2):578-84
14766819