Isolation, purification, and genomic analysis of the virulent phage vB_Ncarnea_KYD1 from Nocardia spp.

Abstract:

[Background] Nocardia belongs to aerobic actinomycete. Being widely distributed, Nocardia can cause local or disseminated infection in human, especially in those with low immune function. The Nocardia infection is difficult to be clinically identified, and novel Nocardia strains are constantly being discovered. Different types of Nocardia from different regions have different prevalences and antibiotic sensitivities, which hinders the treatment. The treatment of Nocardia infection by the phage isolated from the host bacteria at the lesion has attracted great attention in recent years. [Objective] To isolate the virulent phage against Nocardia from the environment that can be used in clinic and explore the genomic characteristics. [Methods] The target phage was isolated by the double-layer plate method, and the plaque morphology was observed. The phage was purified, and the characteristics were observed through the transmission electron microscope. The DNA of the phage was extracted, and the whole genome was sequenced, annotated, and compared with the known phage genomes in the database. The phylogenetic tree was constructed for genetic evolution analysis. [Results] The virulent phage vB_Ncarnea_KYD1 with Nocardia carnea as the host, isolated from the environmental samples, formed transparent and uniform plaques with a diameter <2 mm on the double-layer plate. Genome analysis showed that the DNA of vB_Ncarnea_KYD1 was circular with a size of 66 621 bp. A total of 102 proteins and 1 tRNA-Ser were found in coding sequences (CDS). According to the transmission electron microscope observation and phylogenetic tree analysis, vB_Ncarnea_KYD1 was a new phage in the Siphophages, which experienced complex gene recombination in the evolution. vB_Ncarnea_KYD1 had practical value, and no virulence factor-related genes or antibiotic-resistance genes were found. [Conclusion] The novel virulent phage vB_Ncarnea_KYD1 of N. carnea was isolated from the environmental water sample. The transmission electron microscope observation and genome analysis showed that vB_Ncarnea_KYD1 belonged to the Siphophages. Since no relevant genes unfavorable to clinical application were found in the genome, vB_Ncarnea_KYD1 was a relatively safe virulent phage of Nocardia The findings of this study provided references for the follow-up treatment of Nocardia infection, and enriched the domestic phage resources.