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

Abstract

Background The carbapenem-resistance genes blaVIM 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 blaVIM-carrying MGEs in Pseudomonas. Methods This study presented the complete sequences of five blaVIM-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 IncpSTY, which included only seven available plasmids with determined complete sequences and could be further divided into three subgroups IncpSTY-1/2/3. A detailed sequence comparison was then applied to a collection of 15 MGEs belonging to four different groups: three representative IncpSTY 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 blaVIM genes, which were located within 11 different concise class 1 integrons. Conclusion These blaVIM-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 blaVIM 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.

Conjugative Plasmid pPPUT-Tik1-1 from a Permafrost Pseudomonas putida Strain and Its Present-Day Counterparts Inhabiting Environments and Clinics

“…The use of the classical approach to classify Pseudomonas plasmids by the type of their replicon proteins fails to separate two subgroups of the plasmids, containing or lacking the conjugation genes. Earlier, we found the same problem during the study of Acinetobacter plasmids [17]. The use of a complex approach in the classification of plasmids related to pPPUT-Tik1-1 made it possible to reliably determine the boundaries of the pPPUT-Tik1-1 group and separate the two subgroups of these plasmids.…”

“…To improve the plasmid classification, two main methods have been developed later, i.e., typing for the replication initiation genes and typing for the relaxation (MOB genes, encoding the conjugative complex) genes [8,[13][14][15][16][17]. While replicon typing aims at plasmid replication regions with non-degenerate primers, MOB typing classifies plasmids into relaxase subfamilies using degenerate primers.…”

“…In most cases, the criteria used for classification include the molecular structure of the backbone region (replication, partition, mobilization and conjugation modules) and the properties determined with the accessory region (resistance to heavy metals and antibiotics, ability to degrade xenobiotics and pathogenicity in relation to plants, animals and humans), as well as plasmid host range. At the same time, it is obvious that development of a satisfactory classification of plasmids is still far away [16,17].…”

Abundant diversity of accessory genetic elements and associated antimicrobial resistance genes in pseudomonas aeruginosa isolates from a single Chinese hospital

“…Our conjugal transfer experiment confirms the Inc pPA7790 plasmid pNY13932-OXA can to transfer between cells. Furthermore, the horizontal transferability of Tn6417-related ICEs and Inc p60512−IMP plasmids was demonstrated in our previous studies [42,59,60]. Of note, Inc p60512−IMP plasmids are transferred through electroporation rather than conjugation because they contain only four conjugal transfer genes (traA, traC, traD and cpl), which is insufficient for plasmid conjugation [43,61].…”

Genetic Characteristics of Novel IncpSE5381-aadB Plasmids, Integrative and Mobilizable Elements, and Integrative and Conjugative Elements in Pseudomonas aeruginosa

“…13 IMEs typically utilize conjugation mechanisms encoded by other MGEs to achieve transfer and integration 14 while ICEs mainly use tyrosine/serine recombinases or DDE transposases for chromosomal integration and excision. 15 In previous study, a number of novel MGEs were identified in P. aeruginosa in China, such as the novel Inc groups: Inc p60512−IMP and Inc pPA7790 ; 16 Tn6852-related IMEs carrying bla PER-1 and bla CARB-2 : Tn6853; 17 Tn6417-related ICEs carrying bla VIM-1 : Tn6953; 18 and Multiple Tn1403-related transposons carrying different class 1 integrons: Tn6847, Tn6849, Tn7454, Tn7484, etc. 16,17,19 Multiple types of novel MGEs are frequently identified in China, which pose unknown challenges to the containment of bacterial resistance.…”