## 5 Materials and Methods
### Transcriptomic Study  
The strain ST258-KPC3, ST258-KPC3 CA, ST846-OXA48, and ST846-OXA48 CA were cultured on solid LB plates, with or without CHLX according to the requirement of the strains and incubated at 37 \({}^{\circ}\)C for 24 h. One colony was removed and inoculated in liquid LB medium, with (1/16 \(\times\) MIC) CHLX for the CA strain and incubated overnight at 37 \({}^{\circ}\)C with shaking (180 rpm). The inoculum was diluted (1:100) in LB media with (1/4 \(\times\) MIC) CHLX for CA strains and without CHLX for wild-type strains. Then, when the culture reached a logarithmic growth phase (OD\({}_{600\;\mathrm{nm}}\): 0.6), the RNA was extracted using the High Pure RNA Isolation kit (Roche, Mannheim, Germany), following the kit instructions, and the extract was treated with DNase (Roche, Mannheim, Germany). The RNA was subsequently quantified in a Nanodrop ND-100 spectrophotometer (NanoDrop Technologies, Waltham, MA, USA) and was analyzed with an Agilent 2100 Bioanalyzer with RNA 6000 Nano reagents and RNA Nano Chips (Agilent Technologies, Santa Clara, CA, USA) to determine the quality and the integrity of the samples. All extractions were carried out for quadruple. After RNA extraction of the four replicates of each strain, rRNA and tRNA were removed using the Ribo-Zero rRNA removal kits (bacteria) (Illumina, San diego, CA, USA). The rRNA depletion was checked using Agilent RNA ScreenTape Assay (TapeStation 4200 Agilent, Santa Clara, CA, USA) and the RNA was quantified by Qubit TM RNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA). Then, the transcriptomic libraries  
\begin{table}
\begin{tabular}{c c c} \hline \hline ST846-OXA48 & _K. pneumoniae_ low-risk clone carrying \(\beta\)-lactamase OXA48 & This study \\ \hline ST846-OXA48 CA & _K. pneumoniae_ low-risk clone carrying \(\beta\)-lactamase OXA48 adapted to CHLX & This study \\ \hline ST846-OXA48 CA & _K. pneumoniae_ low-risk clone carrying \(\beta\)-lactamase OXA48 adapted to CHLX and cured plasmid strain & This study \\ \hline pCA24N & Expression plasmid Cm\({}^{R}\), LacIq & [45] \\ \hline pCA24N (_pemIK_) & Expression plasmid pCA24N with the TA systems _pemIK_ & This study \\ \hline pCA24N (_pemK_) & Expression plasmid pCA24N with the TA systems _pemIK_ & This study \\ \hline \hline \end{tabular}
\end{table}
Table 3: _Cont._were performed using the Ion RNAseq Kit v2 in combination with the Ion Xpress TM RNA-Seq Barcode 01-16 Kit. Sequencing was carried out by emulsion PCR with Ion Sphere Particles (IPs). The enrichment of the library carrying IPs and the subsequent loading of the chip was developed in the Ion Chef automated system using the Ion PI Hi-Q Chef kit (Thermo Fisher Scientific, Waltham, MA, USA) and Ion PI chips v3 (Thermo Fisher Scientific, Waltham, MA, USA). Chip analysis was carried out on the Ion Proton sequencer (Thermo Fisher Scientific, Waltham, MA, USA). The generated data was analyzed using the specific software of the Torrent Suite 5.6.2 platform (Thermo Fisher Scientific, Waltham, MA, USA). The resulting readings (approx. 60 million) were exported in a FASTQ file using the FileExporter 4.6.0.0 (Thermo Fisher Scientific, Waltham, MA, USA) plugin. The alignment of the sequences against their respective controls was performed with the STAR software. Subsequently, the aligned readings were counted using the htseq-count software (HTSeq 0.6.1.p2). All data was normalized using DESeq2.