Phylogenetic Tree Based on 16S rRNA Sequences
Since microorganisms are more prone to gene mutation or gene drift under radiation [11], the soil contaminated by radiation likes a natural domestication site for “super bacteria”. In this study, a new strain with multi-antibiotic resistance was isolated from the radiation-polluted soil from Xinjiang Uyghur Autonomous Region, China. According to the result of 16S DNA sequencing, it was identified as D. acidovorans and named as Delftia acidovorans B804 (Fig. 1).
Multidrug resistance phenotype of D. acidovorans B804
The antibiotic resistance test was performed according to the Kirby-Bauer disk diffusion method and evaluated by the standards of the Clinical and Laboratory Standards Institute guidelines [12]. As shown in Fig. 2, D. acidovorans B804 exhibited strong resistances to furadantin, streptomycin, lincomycin, linezolid, fosfomycin, ampicillin, rifampicin and erythromycin, and intermediate resistance to tetracycline and chloramphenicol. This result indicated that D. acidovorans showed a multidrug resistance phenotype, which was consistent with previous reports [4].
Since the D. acidovorans infections increased remarkably [13–15], analyzing the pathogenic genes and antibiotic resistance genes in D. acidovorans B804 by the whole genome sequencing will be meaningful. Here, we further sequenced the whole genome of D. acidovorans B804 to reveal its potential pathogenic genes and antibiotic resistance genes.
Genome Properties
The total size of D. acidovorans B804 genome was 6,661,314 bp, with a GC content of 66.73% (Fig. 3), and no plasmid was detected. 6579 candidate protein coding sequences (CDS) were predicted with a total gene length of 5,963,265 bp, accounting for 89.52% of the genome. 79 tRNAs genes (encoding 21 types of tRNAs) and 15 rRNAs gene (five 5S rRNA, five 16S rRNA, and five 23S rRNA gene) were predicted in this genome.
Gene Function Annotation
Annotated by GO database (Fig. 4), 4760 functional genes were predicted, including 2272 cellular component related genes (mainly related to integral component of membrane, cytoplasm and plasma membrane), 3728 molecular function related genes (mainly involved in DNA binding, ATP binding and transcription factor activity, sequence-specific DNA binding), 3507 biological process related genes (mainly related to oxidation-reduction process, regulation of transcription and DNA-templated and transport). Annotated by COG database (Fig. 5), 5432 functional genes were predicted, belonging to 4 categories (metabolism, information storage and processing, poorly characterized and cellular processes and signaling), which can be subdivided into 22 types (in which, 554 are related to transcription, 473 are related to amino acid transport and metabolism, 416 are related to organic ion transport and metabolism, 368 are related to energy production and conversion, and 296 are related to signal transduction mechanisms). Annotated by KEGG database (Fig. 6), 2987 functional genes were predicted and divided into 6 categories (384 for cellular processes, 2397 for metabolism, 159 for human diseases, 230 for genetic information processing, 76 for organismal systems and 503 for environmental information processing). Based on the comparison with CAZy database (Fig. 7), 22 carbohydrate-activity enzyme genes were annotated, which belong to 5 protein families: glycosyl transferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases and carbohydrate-binding modules. These enzymes have the functions of degrading, modifying and generating glycosidic bonds. In-depth research on CAZyme is of great significance for revealing the metabolic mechanism of microbial carbohydrates.
Antibiotic resistance-related genes and pathogenic genes in D. acidovorans B804
403 antibiotic resistance-related genes were predicted in the genome of D. acidovorans B804, such as linezolid (clbB), fosfomycin (murA), rifampicin (rpoB, iri, pps), tetracycline (otrC, adeN, adeS, adeR, adeB, adeF, oqxA, oqxB), fluoroquinolone (gyrB, mexD), bacitracin (bacA, bcrA), cephalosporin (smeS, SRT-2, nmcR, OXA-114a, ADC-2), glycopeptide ( vanHB, vanHD, vanSN), diaminopyrimidine (dfrC, dfrE), chloramphenicol (cmlv, floR), penam (mtrA, mtrD, mtrC) and phenicol (golS, mexT, oprN, acrR, triA, kasA, inhA, opmH) (Table S1). In addition, some multidrug resistance genes, such as mdtN, msbA, nalD, mdtP, were also predicted. Meanwhile, 89 pathogenic genes with potential virulence or lethal phenotypes were predicted in the genome of D. acidovorans B804. According to the results of pathogen host interactions analysis, 12 possible hosts were predicted, for example, Triticum, Oryza sativa, Tenebrio molitor, Caenorhabditis elegans, Rattus, Mus musculus and Homo sapiens (Table S2). Notably, 17 of these genes were closely associated with some human diseases like infections and salmonellosis.