Carrasco Gema, Monzón Sara, San Segundo María, García Enrique, Garrido Noelia, Medina-Pascual María J, Villalón Pilar, Ramírez Ana, Jiménez Pilar, Cuesta Isabel, Valdezate Sylvia
Reference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain.
Bionformatics Unit, Applied Services, Training and Research, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain.
Microorganisms. 2020 Jun 15;8(6):900. doi: 10.3390/microorganisms8060900.
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 strains from Lara State, Venezuela, were studied by 16S rRNA and (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 species with one or two strains each, except for with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 strains found at five locations which grouped into a soil-only cluster. The soil strains of showed fewer B haplotypes than the examined human strains (13 vs. 17) but did show a larger number of 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 ( ≤ 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 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 ).
[放线菌属]是土壤微生物群中最主要的放线菌之一，可在创伤接种或吸入后导致人类感染。通过16S rRNA和[拓扑异构酶II亚基B]基因、多位点序列分析（MLSA）、全基因组测序（WGS）和微量稀释法，对来自委内瑞拉拉腊州的38株土壤菌株的鉴定、分型、系统发育关系和抗菌药敏性进行了研究。将结果与人类菌株的结果进行了比较。除了[某一菌株有]29株外，仅鉴定出7个[放线菌属]物种，每个物种有1或2株。MLSA证实了16S rRNA和[相关基因]分析所确定的物种归属（分别为89.5%和71.0%），并将每个土壤菌株与其相应的参考菌株和临床菌株归为一组，但在五个地点发现的19株菌株聚为一个仅含土壤菌株的簇。[该菌属]的土壤菌株显示出比所检测的人类菌株更少的B单倍型（分别为13个和17个），但确实显示出更多的单核苷酸多态性（分别为212个和77个）。除了β-内酰胺类、氟喹诺酮类、米诺环素和克拉霉素外，它们对其他抗菌药物的药敏性相似，土壤菌株对前三种药物更敏感（P≤0.05）。对属于仅含土壤菌株簇的4株菌株和该簇外的两株菌株进行了WGS，并将结果与公共[该菌属]基因组进行了比较。平均核苷酸/氨基酸同一性、计算机模拟的基因组与基因组杂交相似性以及基因组GC含量的差异表明，仅含土壤菌株簇的一些菌株可能属于一个新亚种甚至一个新物种（提议名称[具体名称]） 。
