Genomic Virulence Features of Two Novel Species Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., Isolated from Patients with Chronic Pulmonary Diseases

Abstract

Strains 335427^T and 234509^T, isolated from two 76-year-old patients with chronic pulmonary diseases, were the subject of polyphasic taxonomic studies and comparative genomic analyses for virulence factors. The 16 rRNA gene sequence similarity between strains 335427^T and 234509^T and their closest phylogenetic neighbors Nocardia asiatica NBRC 100129^T and Nocardia abscessus NBRC 100374^T were 99.5% and 100%, respectively. Digital DNA-DNA hybridization values between the aforementioned studied strains were well below the 70% threshold for assigning prokaryotic strains to a novel species. Strains 335427^T and 234509^T have genome sizes of 8.49 Mpb and 8.07 Mpb, respectively, with G + C content of 68.5%. Isolate 335427^T has C_16:0, C_18:1 ω₉c, C_18:0 and C_18:0 10 methyl as major fatty acids (>15%) and mycolic acids formed of 52-54 carbon atoms. However, only C_18:1 ω₉c was detected for isolate 234509^T, which had mycolic acids with 44-56 carbon. Based on phenotypic and genetic data, strains 335427^T (DSM 109819^T = CECT 9924^T) and 234509^T (DSM 111366^T = CECT 30129^T) merit recognition as novel species, which are named Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., respectively. All the strains studied had homologous VF-associated genes to those described in M. tuberculosis, including experimentally verified virulence genes in humans related to tuberculosis. The narGHIJ (nitrate reduction pathway) and gvpAFGOJLMK (gas vesicles) genetic maps of strains 335427^T, 234509^T, NBRC 100129^T and NBRC 100374^T showed the same syntenic block and raise the question of whether their functions are interlinked during the infection of the human host. However, further research is required to decipher the role of the gas vesicle in the pathogenicity mechanism of Nocardia spp.

Keywords: actinobacteria; infection; phylogenomics; polyphasic taxonomy.

Figure 1

Phylogenetic trees based on 16S rRNA gene (A) and genome sequences (B) showing the phylogenetic position of isolates 335427^T and 234509^T within the evolutionary radiation of the genus Nocardia and their relationship with one another and with their closest phylogenetic relatives.

Figure 2

Comparative genomic map of the pathogenicity genes of isolates 335427^T and 234509^T genomes and their closest type strains. The circadian maps represent a BLASTN comparison of the genomes of isolates 335427^T and 234509^T (black inner rings) and its GC content (black frequency ring) with the genomes N. asiatica NBRC 100129^T (red ring) and N. abscessus NBRC 100374^T (blue ring). The pathogenicity genes are annotated with black labelled arrows and labels in red. The legends show the percentages of identity of genome alignment.

Figure 3

Synteny of the nar and gvp gene clusters sub-region in isolates 335427^T and 234509^T and their closest relatives. All the genes present on these clusters showed identity values over 72% between isolates 3355612^T and 234509^T and the closest neighbors.