title: Molecular identification of clinical Nocardia isolates from India.
abstract: The epidemiology of nocardiosis is evolving with increasing number of Nocardia spp. causing human infection. In recent years, molecular techniques have been used to identify Nocardia spp. There are limited data available on the spectrum of Nocardia spp. isolated from clinical samples in India. Here, a molecular study was carried on 30 clinical isolates maintained in our National Culture Collection to evaluate the techniques used for identifying the agents. The isolates were identified by sequencing two promising genes: the 16S rRNA gene and hsp65. Both hsp65 and the 16S rRNA gene could reliably identify 90 % of Nocardia isolates, i.e. N. farcinica, N. cyriacigeorgica, N. brasiliensis, N. otitidiscaviarum, N. amamiensis and N. pneumoniae. The mean percentage dissimilarity of sequence identification was higher using the hsp65 gene (4 %, range 0-7.9 %) compared with the 16S rRNA gene (2.3 %, range 0-8.9 %). Two isolates that showed ambiguous results in both the short segment of the 16S rRNA gene and hsp65 sequences could be resolved by sequencing a larger fragment (∼1000 bp) of the 16S rRNA gene. Both of these isolates were identified as N. beijingensis with similarities of 99.8 and 100 % compared with the standard strain. Genotyping of N. cyriacigeorgica strains was performed using hsp65 gene sequences and compared with previously described genotypes. Our N. cyriacigeorgica isolates belonged to genotype 1 (n = 4) and genotype 2 (n = 2). The present study highlights a wide spectrum of Nocardia spp. in India and emphasizes the need for molecular techniques for identification to the species level.
authors.affiliation: Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
authors.forename: Shivaprakash M
authors.initials: SM
authors.lastname: Rudramurthy
authors.affiliation: Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
authors.forename: Prasanna
authors.initials: P
authors.lastname: Honnavar
authors.affiliation: Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
authors.forename: Harsimran
authors.initials: H
authors.lastname: Kaur
authors.affiliation: Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
authors.forename: Palash
authors.initials: P
authors.lastname: Samanta
authors.affiliation: Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
authors.forename: Pallab
authors.initials: P
authors.lastname: Ray
authors.affiliation: Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
authors.forename: Anup
authors.initials: A
authors.lastname: Ghosh
authors.affiliation: Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
authors.forename: Arunaloke
authors.initials: A
authors.lastname: Chakrabarti
mesh_terms: D000328:Adult; D044822:Biodiversity; D018834:Chaperonin 60 / Q000235:genetics; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005260:Female; D006801:Humans; D007194:India; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D009615:Nocardia / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D009617:Nocardia Infections / Q000382:microbiology*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D018834:Chaperonin 60; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S