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

Abstract

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.Nocardia spp. are Gram-positive saprophytic bacteria capable of causing suppurative infections, including pulmonary, cutaneous, central nervous system, and disseminated diseases. To date, approximately 90 species have been described (NCBI taxonomy for Nocardia [http://www.ncbi.nlm.nih.gov/Taxonomy /

Sulfonamide Resistance in Isolates of Nocardia spp. from a U.S. Multicenter Survey

“…Five of the six laboratories identified Nocardia isolates to the species or complex level by 16S rRNA or secA gene sequencing, PCR restriction fragment enzyme analysis (PRA), and/or drug susceptibility patterns (2,8). One laboratory (Arizona) identified isolates to the species/complex level using a combination of biochemicals, growth characteristics, and antimicrobial susceptibility patterns (2,3,6,7,12,16).…”

First case of Nocardia nova spinal abscess in an immunocompetent patient

“…16 Meanwhile, because 16S rRNA gene sequencing alone is sometimes insufficient for the identification of Nocardia species, the sequencing of other conserved regions, such as hsp65 and secA1, can serve as adjuncts to 16S rRNA sequencing. 17,18 In this case, the 16S rRNA gene sequence of CBU 09/875 showed complete identity with N. nova and strong similarity (> 99%) with two other Nocardia species, which have not yet been reported to be responsible for human infections. To improve the differentiation, hsp65 and secA1 were sequenced, and showed the greatest similarity with N. nova, N. veterana and N. africana among the species pathogenic to humans.…”

A PCR-Based Intergenic Spacer Region-Capillary Gel Electrophoresis Typing Method for Identification and Subtyping of Nocardia Species

“…DNA extracts of 145 Nocardia isolates, previously characterized by standard phenotypic methods (1) and identified to the species level by 16S rRNA gene sequencing (7,8,18,19), were studied (Table 1). Extracts were retrieved from Ϫ80°C storage.…”