Large-Scale Plasmidome and Carbapenem Mobilome Analysis Reveals a Mechanistic Duality: High-Power Specialists and Structural Generalists Mobile Genetic Elements

Hannay Crystynah Almeida De Souza¹Anamaria Dos Santos²Arlen Carvalho de Oliveira Almeida³Ana Beatriz Portes⁴Carlos Adam Conte-Junior⁵Pedro Panzenhagen^6*

• ¹Graduate Program in Biochemistry (PPGBq), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
• ²Graduate Program in Veterinary Hygiene (PGHIGVET), Universidade Federal Fluminense, Niterói, Brazil
• ³Graduate Program in Food Science, Institute of Chemistry, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
• ⁴Department of General Microbiology,, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
• ⁵Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
• ⁶Graduate Program in Biochemistry (PPGBq), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil

Carbapenem resistance is a significant global public health threat, with the rapid dissemination of carbapenemases often mediated by plasmids. Although Mobile Genetic Elements (MGEs), including transposons (Tn), insertion sequences (IS), and integrons (In) play central roles in this process, the mechanistic interplay between different MGE classes and the carbapenem resistome remains underexplored. Here, we performed a large-scale, systematic characterization of the co-evolution between the plasmid mobilome and the carbapenem resistome by analyzing 6,017 resistant plasmids. Our findings reveal a dual mechanistic architecture governing the dissemination of resistance. Specialized MGEs, represented by integrons and transposons, showed the strongest associations with carbapenemase genes (median ORs: 107.2 and 92.7), functioning as high-fidelity carriers. In contrast, Generalist MGEs, dominated by insertion sequences, exhibited weaker individual associations (median OR, 17.3), but they shaped the overall network structure. IS6_292 emerged as the "apex generalist," presenting the highest betweenness centrality (3,815.87) and linking to 13 carbapenemase genes. At the replicon level, the dissemination potential, quantified by the Mobilization-Resistance Score, highlighted IncFIB(pQil) and IncR as the most potent supervector platforms, despite the higher frequency of IncX3, IncL, and IncR. These replicons combine extensive MGE diversity with multiple carbapenemases, thereby forming high-risk vectors for the acquisition and spread of resistance. In conclusion, this work not only maps the transmission routes of carbapenem resistance but also provides an analytical schema that elucidates the functional and structural contributions of different MGE classes. Focusing surveillance on structurally critical MGEs contributes to the design of precise targets to mitigate the global dissemination of carbapenem resistance.