The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets

Abstract

BackgroundThe emergence of multidrug-resistant Klebsiella pneumoniae is a major public health concern. Many K. pneumoniae infections can only be treated when resorting to last-line drugs such as polymyxin B (PB). However, resistance to this antibiotic is also observed, although insufficient information is described on its mode of action as well as the mechanisms used by resistant bacteria to evade its effects. We aimed to study PB resistance and the influence of abiotic stresses in a clinical K. pneumoniae strain using whole transcriptome profiling.ResultsWe sequenced 12 cDNA libraries of K. pneumoniae Kp13 bacteria, from two biological replicates of the original strain Kp13 (Kp13) and five derivative strains: induced high-level PB resistance in acidic pH (Kp13pH), magnesium deprivation (Kp13Mg), high concentrations of calcium (Kp13Ca) and iron (Kp13Fe), and a control condition with PB (Kp13PolB). Our results show the involvement of multiple regulatory loci that differentially respond to each condition as well as a shared gene expression response elicited by PB treatment, and indicate the participation of two-regulatory components such as ArcA-ArcB, which could be involved in re-routing the K. pneumoniae metabolism following PB treatment. Modules of co-expressed genes could be determined, which correlated to growth in acid stress and PB exposure. We hypothesize that polymyxin B induces metabolic shifts in K. pneumoniae that could relate to surviving against the action of this antibiotic.ConclusionsWe obtained whole transcriptome data for K. pneumoniae under different environmental conditions and PB treatment. Our results supports the notion that the K. pneumoniae response to PB exposure goes beyond damaged membrane reconstruction and involves recruitment of multiple gene modules and intracellular targets.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3070-y) contains supplementary material, which is available to authorized users.

Metallohelices that kill Gram-negative pathogens using intracellular antimicrobial peptide pathways

“…It is interesting that a link between transcriptional acid stress response and resistance to various membrane active environmental stresses, including polymyxin B have been observed in other bacteria suggesting a mechanistic relationship. 60,61 Indeed, an upregulated gene we observed, involved in both acid response and LPS synthesis is lpxT. LpxT is an enzyme, which is induced under acidic-aerobic conditions, that catalyses the phosphorylation of lipid A.…”

Detection of Colistin-Resistant MCR-1-Positive Escherichia coli by Use of Assays Based on Inhibition by EDTA and Zeta Potential

“…Insertion sequences were confirmed by ISfinder (https://www-is.biotoul.fr). For those isolates that did not show any mutation, a reverse transcription-quantitative PCR (qRT-PCR) assay was performed to quantify the relative expression of the above-mentioned genes (35,36). Additionally, a colistin-resistant mutant E. coli strain (Δ806) was developed under selective colistin pressure, as previously described (37).…”

Network-Based Metabolism-Centered Screening of Potential Drug Targets in Klebsiella pneumoniae at Genome Scale

“…They are responsible for the biosynthesis of the bacterial cell wall components as described before (Figure 4). Of these five targets, LpxA and LpxC were also suggested as putative drug targets by Ramos et al (2016Ramos et al ( , 2018 confirming the involvement of these enzymes in polymyxin B resistance. The LpxA exhibits no significant structural or sequence homology with mammalian enzymes (Barb and Zhou, 2008;Joo, 2015).…”