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Sequence analysis of theNocardia essential secretory protein SecA1 gene (secA1 ) for species identification of 120 American Type Culture Collection (ATCC) and clinical isolates ofNocardia (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 &lt;99.0% similarity to archivedsecA1 sequences for the species, including 29Nocardia cyriacigeorgica (96.6 to 98.9% similarity) and 4Nocardia veterana (91.5 to 98.9% similarity) strains. Discrepant species identification was obtained for 16 (14.5%) clinical isolates, including 13/23Nocardia nova strains (identified as variousNocardia species bysecA1 sequencing) and 1 isolate each ofNocardia abscessus (identified asNocardia asiatica ),Nocardia elegans (Nocardia africana ), andNocardia transvalensis (Nocardia blacklockiae ); bothsecA1 gene sequence analysis and deduced amino acid sequence analysis determined the species to be different from those assigned by 16S rRNA gene sequencing. ThesecA1 locus showed high sequence diversity (66 sequence or genetic types versus 40 16S rRNA gene sequence types), which was highest forN. nova (14secA1 sequence types), followed byNocardia farcinica andN. veterana (n = 7 each); there was only a single sequence type among eightNocardia paucivorans strains. ThesecA1 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.

secA1 Gene Sequence Polymorphisms for Species Identification of Nocardia Species and Recognition of Intraspecies Genetic Diversity