Multidrug-resistant clinical strains identified as Pseudomonas putida group cluster independently of P. putida and Pseudomonas monteilii type strains in a phylogenetic analysis using eight concatenated hypervariable housekeeping sequences

Abstract

Phylogenetic analysis was performed by using a concatenation of eight full-length polymorphic genes encoding large hypervariable proteins (designated C8HKP) selected from among 121 housekeeping proteins shared and conserved in Pseudomonas aeruginosa strain PAO1, Pseudomonas fluorescens strain A506, Pseudomonas putida NBRC 14164, Pseudomonas stutzeri ATCC 17588, and Pseudomonas syringae pv. phaseolicola strain 1448A, which were selected from phylogenetically different groups. The results were compared with those of a previously reported phylogenetic analysis that used a multilocus sequence analysis (MLSA) incorporating four housekeeping genes (16S rRNA, gyrB, rpoB, and rpoD; designated 4MLSA). Comparison of the substitution rates between C8HKP and 4MLSA revealed that C8HKP was strongly correlated (R²=0.897) with 4MLSA and had twice the resolving power of 4MLSA. Furthermore, the phylogenetic positions of the genus Pseudomonas were almost identical between the two methods. These results indicate that C8HKP is suitable for phylogenetic analysis of Pseudomonas species. Additionally, C8HKP phylogenetic analysis was performed on draft genome sequences for 33 clinical isolates identified as P. putida group by 16S rRNA gene analysis. The results revealed that several strains belonged to three independent clusters in the P. putida group. Classification of novel species in the P. putida group will therefore be required.