Abstract
Pseudomonas putida is a bacterium commonly found in soils, water and plants. Although P. putida group strains are considered to have low virulence, several nosocomial isolates with carbapenem- or multidrug-resistance have recently been reported. In the present study, we developed a multilocus sequence typing (MLST) scheme for P. putida. MLST loci and primers were selected and designed using the genomic information of 86 clinical isolates sequenced in this study as well as the sequences of 20 isolates previously reported. The genomes were categorised into 68 sequence types (STs). Significant linkage disequilibrium was detected for the 68 STs, indicating that the P. putida isolates are clonal. The MLST tree was similar to the haplotype network tree based on single nucleotide morphisms, demonstrating that our MLST scheme reflects the genetic diversity of P. putida group isolated from both clinical and environmental sites.
Highlights
Pseudomonas putida, a rod-shaped gram-negative bacterium, harbours a broad spectrum of metabolic enzymes and is found in edaphic as well as in aquatic environments[1]
Based on the 16S rRNA sequence, Pseudomonas species was categorized into 5 groups; the P. aeruginosa group, the P. chlororaphis group, the P. fluorescens group, the P. pertucinogena group, and the P. putida group[22]
We found that this Multilocus sequence typing (MLST) scheme was applicable for P. putida, P. mosselii, and P. parafulva
Summary
Pseudomonas putida, a rod-shaped gram-negative bacterium, harbours a broad spectrum of metabolic enzymes and is found in edaphic as well as in aquatic environments[1]. Some P. putida strains colonises plant roots creating a mutual relationship between the plant and bacteria This bacterium represents a robust microbial platform for metabolic engineering with biocatalytic activity, thereby conferring it with a high biotechnological value[2]. Yonezuka et al conducted a phylogenetic analysis based on 16S rRNA analysis, concatenated sequences of nine housekeeping genes and average nucleotide identity (ANI)[13]. They concluded that the analysis based on the concatenated sequences as well as on ANI showed high resolution. We developed a MLST scheme using 8 housekeeping genes extracted from whole genome sequences of 86 P. putida strains recently isolated from clinical sites in Japan, in addition to the complete genome sequences accessible in the public database
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