Molecular identification of clinical Nocardia isolates from India

Abstract

The epidemiology of nocardiosis is evolving with increasing number of Nocardia species causing human infection. In recent years molecular techniques are used to identify Nocardia species. We have limited data available on the spectrum of Nocardia species isolated from clinical samples in India. A molecular study is employed on 30 clinical isolates maintained at our National Culture Collection to evaluate the techniques in identifying the agents. The isolates were identified by sequencing two promising genes; 16S rRNA and hsp65. Both hsp65 and 16s rDNA could reliably identify 90% of Nocardia isolates viz. N. farcinica, N. cyriacigeorgica, N. brasiliensis, N. otitidiscaviarum, N. amamiensis, and N. pneumoniae. The mean percentage dissimilarity of sequence identification was higher while using hsp65 gene (4%, range 0 to 7.9%) as compared to 16S gene (2.3%, range 0 to 8.9%). Two isolates that showed ambiguous results both in short segment of 16S rDNA and hsp65 sequences could be resolved by sequencing larger fragment (~1000bp) of 16S rDNA. Both these isolates were identified as N. beijingensis with similarity of 99.8% and 100% with the standard strain. Genotyping of N. cyriacigeorgica strains was performed using hsp65 gene sequences and compared with earlier described genotypes. Our N. cyriacigeorgica isolates belonged to genotype 1 (4 nos.) and genotype 2 (2 nos.). The present study highlights a wide spectrum of Nocardia species in India and emphasis the need of molecular techniques for identification to species level