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

Gema Carrasco,María J Medina-Pascual,Sylvia Valdezate,Sara Monzón,Isabel Cuesta,María San Segundo,Enrique García,Pilar Villalón,Ana Ramírez,Pilar Jiménez,Noelia Garrido

doi:10.3390/microorganisms8060900

Gema Carrasco, María J Medina-Pascual + Show 9 more

Open Access

https://doi.org/10.3390/microorganisms8060900

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Abstract

Nocardia species, 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 soil Nocardia strains from Lara State, Venezuela, were studied by 16S rRNA and gyrB (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 seven Nocardia species with one or two strains each, except for Nocardia cyriacigeorgica with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and gyrB analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 N. cyriacigeorgica strains found at five locations which grouped into a soil-only cluster. The soil strains of N. cyriacigeorgica showed fewer gyrB haplotypes than the examined human strains (13 vs. 17) but did show a larger number of gyrB SNPs (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 public N. cyriacigeorgica genomes. 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 name Nocardia venezuelensis).

Highlights

Nocardia spp. species are found everywhere from sludge and soil to contaminated soil water, deep-sea sediments [1], and desert habitats [2]
Our findings suggest that some of the soil N. cyriacigeorgica strains detected may, belong to a new subspecies or even a new species
After growth on Columbia agar supplemented with 5% (v/v) sheep s blood and buffered charcoal–yeast extract agar (BCYE) for 48–72 h at 37 ◦C under aerobic conditions, their chromosomal DNA was extracted by the boiling method

Summary

Introduction

Nocardia spp. species are found everywhere from sludge and soil to contaminated soil water, deep-sea sediments [1], and desert habitats [2]. [8,9], a result of the physiological and biochemical pressures imposed by the environmental conditions under which they live [10]. Their activity in the degradation of polycyclic aromatic hydrocarbon [11,12] focused on them as potential xenobiotic bioremediators. They cause a number of severe invasive diseases [3,13], the members of Nocardia spp. are mainly opportunistic pathogens in humans, usually affecting the lungs, central nervous system, and skin [14,15].

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