Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans.

Nocardiaspecies, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soilNocardiastrains from Lara State, Venezuela, were studied by 16S rRNA andgyrB(subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just sevenNocardiaspecies with one or two strains each, except forNocardia cyriacigeorgicawith 29, were identified. MLSA confirmed the species assignments made by 16S rRNA andgyrBanalyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19N. cyriacigeorgicastrains found at five locations which grouped into a soil-only cluster. The soil strains ofN. cyriacigeorgicashowed fewergyrB haplotypes than the examined human strains (13 vs. 17) but did show a larger number ofgyrBSNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (p <= 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with publicN. cyriacigeorgicagenomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed nameNocardia venezuelensis).