Integron-mediated gene cassette dynamics in Enterobacterales under selective antibiotic pressure

Antimicrobial resistance among Enterobacterales is an urgent global crisis, with horizontal gene transfer being one of the major driving forces behind it. The integrons play a significant role in this process. Here, we present the investigation of gene cassette dynamics of integrons among the Enterobacterales under selective antibiotic pressure.

We analysed Escherichia coli (n = 214), Klebsiella pneumoniae (n = 210), and Salmonella Typhi (n = 70) isolates for antibiotic susceptibility, and performed Sanger sequencing for the integron region of multidrug-resistant isolates. The evolution assay was carried out to determine the gene cassette rearrangement under stress. RT-qPCR was performed to investigate the gene expression on exposure to trimethoprim and streptomycin. All the E. coli and K. pneumoniae isolates were MDR, and showed the highest resistance to ampicillin (94%) and ceftazidime (95.2%), respectively. Integron screening revealed a higher abundance of class 1 integrons followed by class 2 integrons in both isolates. Sequencing revealed the presence of trimethoprim and streptomycin-resistant gene cassettes within integrons. The phenotypic assays revealed that integron-positive isolates carried more resistance to antibiotics than integron-negative isolates. The combination of 2 antibiotics (trimethoprim + streptomycin) showed gene upregulation in the isolates, depicting the synergistic activity of the antibiotics. The evolution assay revealed a change of the gene cassette arrangement from dfrA12-aadA2 to dfrA17-aadA5 after streptomycin treatment in K. pneumoniae.

The prevalence of integrons thus enhanced the antibiotic resistance, even under antibiotic pressure. These findings highlight the potential role of integrons in antimicrobial resistance among the studied clinical isolates and suggest that monitoring integron-associated resistance may be useful in clinical settings.