Conway, T. | Search bioRxiv

bioRxiv2017

The primary transcriptome, small RNAs, and regulation of antimicrobial resistance in Acinetobacter baumannii

AO_SCPCAPBSTRACTC_SCPCAPWe present the first high-resolution determination of transcriptome architecture in the priority pathogen Acinetobacter baumannii. Pooled RNA from 16 laboratory conditions was used for differential RNA-seq (dRNA-seq) to identify 3731 transcriptional start sites (TSS) and 110 small RNAs, including the first identification in A. baumannii of sRNAs encoded at the 3 end of coding genes. Most sRNAs were conserved among sequenced A. baumannii genomes, but were only weakly conserved or absent in other Acinetobacter species. Single nucleotide mapping of TSS enabled prediction of -10 and -35 RNA polymerase binding sites and revealed an unprecedented base preference at position +2 that hints at an unrecognized transcriptional regulatory mechanism. To apply functional genomics to the problem of antimicrobial resistance, we dissected the transcriptional regulation of the drug efflux pump responsible for chloramphenicol resistance, craA. The two craA promoters were both down-regulated >1000-fold when cells were shifted to nutrient limited medium. This conditional down-regulation of craA expression renders cells sensitive to chloramphenicol, a highly effective antibiotic for the treatment of multidrug resistant infections. An online interface that facilitates open data access and visualization is provided as \"AcinetoCom\" (http://bioinf.gen.tcd.ie/acinetocom/).

microbiology↗

bioRxiv2017

Collateral sensitivity to β-lactam drugs in drug-resistant tuberculosis is driven by the transcriptional wiring of BlaI operon genes

BackgroundThe evolution and spread of antimicrobial resistance is a major global public health threat. In some cases the evolution of resistance to one antimicrobial seemingly results in enhanced sensitivity to another (known as collateral sensitivity). This largely underexplored phenomenon represents a fascinating evolutionary paradigm that opens new therapeutic possibilities for patients infected with pathogens unresponsive to classical treatments. Intrinsic resistance to {beta}-lactams in Mycobacterium tuberculosis (Mtb, the causative agent of tuberculosis) has traditionally curtailed the use of these low-cost and easy-to-administer drugs for tuberculosis treatment. Recently, {beta}-lactam sensitivity has been reported in strains resistant to classical tuberculosis drug therapy, leading to a resurgence of interest in using {beta}-lactams in the clinic. Unfortunately though, there remains a limited understanding of the mechanisms driving {beta}-lactam sensitivity.\n\nMethodsWe used a novel combination of systems biology and computational approaches to characterize the molecular underpinnings of {beta}-lactam sensitivity in Mtb. We performed differential gene expression and coexpression analyses of genes previously associated with {beta}-lactam sensitivity and genes associated with resistance to classical tuberculosis drugs. Protein-protein interaction and gene regulatory network analyses were used to validate regulatory interactions between these genes, and random walks through the networks identified key mediators of these interactions. Further validation was obtained using functional in silico knockout of gene pairs.\n\nResultsOur results reveal up regulation of the key regulatory inhibitor of {beta}-lactamase production, blal, following treatment with classical drugs. Co-expression and network analyses showed direct co-regulation between genes associated with {beta}-lactam sensitivity and those associated with resistance to classical tuberculosis treatment. blal and its downstream genes (sigC and atpH) were found to be key mediators of these interactions.\n\nConclusionsOur results support the hypothesis that Mtb {beta}-lactam sensitivity is a collateral consequence of the evolution of resistance to classical tuberculosis drugs, mediated through changes to transcriptional regulation. These findings support continued exploration of {beta}-lactams for the treatment of tuberculosis, particularly for patients infected with strains resistant to classical therapies that are otherwise difficult to treat. Importantly, this work also highlights the potential of systems-level and network biology approaches to improve our understanding of collateral drug sensitivity.

microbiology↗