Large-scale plasmidome and carbapenem mobilome analysis reveals a mechanistic duality: high-power specialists and...

Carbapenem resistance represents a critical global public health threat, with the rapid dissemination of carbapenemase genes largely mediated by plasmids. Although mobile genetic elements (MGEs), including transposons (Tn), insertion sequences (IS), and integrons (In), are known to drive this process, the mechanistic interplay between different MGE classes and the carbapenem resistome remains insufficiently characterized at a global scale.

We performed a large-scale, systematic analysis of 6,017 plasmids carrying carbapenemase genes extracted from 72,556 complete plasmid sequences. Antimicrobial resistance genes were identified using AMRFinderPlus, and MGEs were detected through an integrative workflow combining TnCentral, INTEGRALL, ISFinder, ABRicate, and ISEScan. Functional associations between carbapenemase genes and MGEs were defined using a conservative genomic proximity threshold (≤5 kb). Statistical association analyses, network topology metrics, and a Mobilization-Resistance Score were applied to characterize mobilization strength and replicon-level dissemination potential.

Our analysis revealed a dual mechanistic architecture governing carbapenem resistance dissemination. Integrons and transposons acted as high-fidelity specialists, showing the strongest associations with carbapenemase genes (median ORs: 107.2 and 92.7, respectively). In contrast, insertion sequences exhibited lower individual association strength (median OR: 17.3) but structured the global mobilome network. IS6_292 emerged as the apex generalist, displaying the highest betweenness centrality (3,815.87) and forming significant associations with 13 distinct carbapenemase genes. At the replicon level, dissemination potential quantified by the Mobilization-Resistance Score identified IncFIB(pQil) and IncR as the most potent supervector platforms, despite the higher frequency of IncX3 and IncL plasmids. These replicons combine high MGE diversity with multiple carbapenemase genes, forming high-risk vectors for resistance acquisition and spread.

These findings demonstrate that carbapenemase dissemination is driven by complementary mobilization strategies: structurally specialized, high-strength transmission mediated by integrons and transposons, and structurally central, generalist dissemination mediated by insertion sequences. This duality reshapes the understanding of carbapenem resistome evolution and highlights structurally critical MGEs and high-scoring plasmid replicons as strategic surveillance targets. Focusing genomic monitoring on these elements may support the development of precision-based containment strategies to mitigate the global spread of carbapenem resistance.