Structural insights into the mosaic and modular organization of fourteen co-occurring resistance genes in multidrug resistant Enterobacteriaceae

Up to 14 co-occurring antimicrobial resistance genes (ARG) were previously detected in multiple outbreaks in the Netherlands involving various Enterobacteriaceae species, clones and plasmids, but similar multidrug resistance regions (MRR). This study aimed to map the reported occurrence, mosaic and modular genetic context of the involved ARG. Google Scholar and PubMed Central were queried for articles describing long-read assemblies with ≥ 6 co-occurring ARG. Plasmid (n = 119) and chromosomal (n = 8) sequences of 9 bacterial taxa originating from North America (n = 39), Europe (n = 34), Africa (n = 16), Asia (n = 14), Oceania (n = 13) and South America (n = 7) were extracted from NCBI. Based on colocalized insertions sequences, transposons and integrons, the ARGs could be divided into nine distinct resistance elements. These elements presented a total of 118 mosaic structural variants (SV): qnrB1 (SV = 27; n = 102), blaCTX‑M‑15 (SV = 23; n = 137), tet(A) (SV = 18; n = 93), dfrA14 (SV = 14; n = 115), sul2-strA-strB (SV = 13; n = 120), blaTEM‑1b (SV = 12; n = 119), aac(6')‑Ib‑cr-blaOXA‑1-catB3 (SV = 7; n = 137), aac(3)‑IIe (SV = 2; n = 92), and aadA1-catA1 SV = 2; n = 12). The MRR showed high modularity with no clear ARG order. Still, three frequent sub-configurations were found. Firstly, blaTEM‑1b was flanked by sul2-strA-strB downstream (92.6%) and blaCTX‑M‑15 upstream (84.0%). Secondly, qnrB1 was flanked by tet(A) upstream (62.4%) and dfrA14 (63.4%) downstream. Thirdly, aac(3)‑IIe was flanked by aac(6')‑Ib‑cr-blaOXA‑1-catB3 upstream (80.4%). In conclusion, the 14 ARG co-occur globally in similar MRR that are complex to interpret due to modularity and mosaicism. Still, the preservation of these clinically relevant resistance elements infers a potential means of transfer between distinct Enterobacteriaceae isolates.