Comparative transcriptomics of multidrug resistant Acinetobacter baumannii in response to antibiotic treatments

Multidrug resistant Acinetobacter baumannii, a major hospital-acquired pathogen, is a serious health threat and poses great challenge to healthcare providers. Although there have been many genomic studies on their evolution and antibiotic resistance, there are very limited transcriptome studies on their responses to antibiotics. We conducted a comparative transcriptomic study on twelve strains with different growth rates and antibiotic resistance profiles, including three fast-growing pan-drug resistant strains, under separate treatment of three antibiotics, namely amikacin, imipenem and meropenem. We performed deep sequencing using a strand-specific RNA-sequencing protocol, and employed de novo transcriptome assembly to analyze gene expression in the form of polycistronic transcripts. Our results indicated that genes associated with transposable elements generally showed higher levels of expression under antibiotic-treated conditions, and many of these transposon-associated genes have been attributed to drug resistance. Using co-expressed transposon genes as markers, we further identified and experimentally validated two novel genes of which overexpression confer significant increase in amikacin-resistance. To the best of our knowledge, this study described, for the first time, a comparative transcriptomic analysis of multidrug resistant A. baumannii under different antibiotic treatments, and revealed a new relationship between transposons and antibiotic resistance.