VIM-encoding Inc(pSTY) plasmids and chromosome-borne integrative and mobilizable elements (IMEs) and integrative and conjugative elements (ICEs) in Pseudomonas

BACKGROUND: The carbapenem-resistance genes bla(VIM) are widely disseminated in Pseudomonas, and frequently harbored within class 1 integrons that reside within various mobile genetic elements (MGEs). However, there are few reports on detailed genetic dissection of bla(VIM)-carrying MGEs in Pseudomonas. METHODS: This study presented the complete sequences of five bla(VIM-2/-4)-carrying MGEs, including two plasmids, two chromosomal integrative and mobilizable elements (IMEs), and one chromosomal integrative and conjugative element (ICE) from five different Pseudomonas isolates. RESULTS: The two plasmids were assigned to a novel incompatibility (Inc) group Inc(pSTY), which included only seven available plasmids with determined complete sequences and could be further divided into three subgroups Inc(pSTY)-1/2/3. A detailed sequence comparison was then applied to a collection of 15 MGEs belonging to four different groups: three representative Inc(pSTY) plasmids, two Tn6916-related IMEs, two Tn6918-related IMEs, and eight Tn6417-related ICEs and ten of these 15 MGEs were first time identified. At least 22 genes involving resistance to seven different categories of antibiotics and heavy metals were identified within these 15 MGEs, and most of these resistance genes were located within the accessory modules integrated as exogenous DNA regions into these MGEs. Especially, eleven of these 15 MGEs carried the bla(VIM) genes, which were located within 11 different concise class 1 integrons. CONCLUSION: These bla(VIM)-carrying integrons were further integrated into the above plasmids, IMEs/ICEs with intercellular mobility. These MGEs could transfer between Pseudomonas isolates, which resulted in the accumulation and spread of bla(VIM) among Pseudomonas and thus was helpful for the bacteria to survival from the stress of antibiotics. Data presented here provided a deeper insight into the genetic diversification and evolution of VIM-encoding MGEs in Pseudomonas. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12941-022-00502-w.