The problem of bacterial resistance due to the massive and unregulated use of antibiotics is one of the most important public health issues the world facing today (Laxminarayan et al., 2013). β-lactams, the drugs of choice for clinical plasmapheresis against infections, are now being used with progressively decreasing efficacy (Bush and Bradford, 2020). Under the pressure of antibiotic selection, bacteria continue to evolve to meet the demands of their survival environment, resulting in the proliferation of β-lactam-resistant strains. Bacteria often produce β-lactamases to counteract the bactericidal effects of β-lactams.

Currently, clinically important β-lactamases include carbapenem hydrolases, plasmid-mediated AmpC enzymes, and extended-spectrum beta-lactamases (ESBLs). ESBLs, mostly including TEM-, SHV- and CTX-M-type ESBLs, can hydrolyze penicillins, cephalosporins, and have a broad resistance spectrum. The widespread use of third-generation cephalosporins has fueled the growth of the CTX-M-type ESBLs, which has succeeded in displacing the TEM- and SHV-types of ESBLs and become the dominant (Cantón and Coque, 2006, Cantón et al., 2012).

Most CTX-Ms consist of 291 amino acids (Delmas et al., 2010). In recent years, compensatory mutations in genes and the cumulative effect of mutations in response to drug selection pressure have led to an explosion in the number of genetic variants of blaCTX-Ms (Cantón et al., 2012, D'Andrea et al., 2013). Until Oct 2023, there are 288 genotypes of CTX-Ms have been discovered (http://bldb.eu/Enzymes.php). The CTX-M-type enzymes may be phylogenetically separated into six different clusters (CTX-M-1, CTX-M-2, CTX-M-8, CTX-M-9, CTX-M-25, KLUC), each of which has members that share around 94% amino acid sequences identity (Bonnet, 2004, D'Andrea et al., 2013). The genus Kluyvera is the most important reservoir of CTX-Ms (Decousser et al., 2001, Humeniuk et al., 2002, Olson et al., 2005, Poirel et al., 2002, Rodríguez et al., 2010).

The production of CTX-M-type ESBLs is an important mechanism by which bacteria develop resistance to cephalosporins, posing a major difficulty in clinical treatment. This situation was frequently found in most European countries as well as in Asia and South America (Cantón and Coque, 2006). Acquired drug resistance mediated by mobile genetic elements (MGEs) is an important reason for the existence of a large number of multi-drug resistant bacteria and pan-drug resistant bacteria. Plasmid, as an important vector of CTX-Ms transmission, plays an essential role in CTX-Ms’ evolution and transmission (Cantón et al., 2003). With the advent of the post-genome era, a growing number of plasmid sequences are now publicly available. However, there have been no systematic studies on exploring the molecular genetic signatures of plasmid-mediated CTX-Ms acquisition and elucidating the types, characteristics, and multiple resistance gene carriages of plasmids that currently harbour the CTX-Ms. In this study, complete plasmid sequences containing CTX-Ms were comprehensively collected, and comparative analyses were performed from a holistic perspective, incorporating the approaches of population genomics. Simultaneously, we further explored the coexistence of CTX-Ms with other resistance genes and the horizontal transport mechanism of CTX-Ms. Our study provides support for a more effective response to the risks associated with the evolution of CTX-Ms-bearing plasmids, and for more precise prevention and control of the spread of plasmids and the spread of bacterial resistance, which are of important public health implications.