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Background    Pseudomonas putida  is a Gram-negative, non-fermenting bacterium frequently encountered in various environmental niches.  P. putida  rarely causes disease in humans, though serious infections and outbreaks have been reported from time to time. Some have suggested that  P. putida  functions as an exchange platform for antibiotic resistance genes (ARG), and thus represents a serious concern in the spread of ARGs to more pathogenic organisms within a hospital. Though poorly understood, the frequency of ARG exchange between  P. putida  and the more virulent  Pseudomonas aeruginosa  and its clinical relevance are particularly important for designing efficient infection control strategies, such as deciding whether high-risk patients colonized with a multidrug resistant but typically low pathogenic  P. putida  strain should be contact isolated or not.    Results  In this study, 21,373 screening samples (stool, rectal and throat swab) were examined to determine the presence of  P. putida  in a high-risk group of haemato-oncology patients during a 28-month period. A total of 89  P. putida  group strains were isolated from 85 patients, with 41 of 89 (46.1%) strains harbouring the metallo-beta-lactamase gene  bla   VIM . These 41 clinical isolates, plus 18  bla    VIM   positive environmental  P. putida  isolates, and 17  bla    VIM   positive  P. aeruginosa  isolates, were characterized by whole genome sequencing (WGS).  We constructed a maximum-likelihood tree to separate the 59  bla   VIM  positive  P. putida  group strains into eight distinct phylogenetic clusters.  Bla   VIM-1  was present in 6 clusters while  bla   VIM-2  was detected in 4 clusters. Five  P. putida  group strains contained both,  bla   VIM-1  and  bla   VIM-2  genes.  In contrast, all  P. aeruginosa  strains belonged to a single genetic cluster and contained the same ARGs. Apart from  bla   VIM-2  and  sul  genes, no other ARGs were shared between  P. aeruginosa  and  P. putida . Furthermore, the  bla   VIM-2  gene in  P. aeruginosa  was predicted to be only chromosomally located.    Conclusion  These data provide evidence that no exchange of comprehensive ARG harbouring mobile genetic elements had occurred between  P. aeruginosa  and  P. putida group  strains during the study period, thus eliminating the need to implement enhanced infection control measures for high-risk patients colonized with a  bla   VIM  positiv  P. putida  group strains in our clinical setting.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4216-2) contains supplementary material, which is available to authorized users.

bmc genomics

Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa