The Molecular Basis of Acinetobacter baumannii Cadmium Toxicity and Resistance

DksA is a conserved master regulator of stress response in Acinetobacter baumannii

Coordination of bacterial stress response mechanisms is critical for long-term survival in harsh environments for successful host infection. The general and specific stress responses of well-studied Gram-negative pathogens like Escherichia coli are controlled by alternative sigma factors, archetypically RpoS. The deadly hospital pathogen Acinetobacter baumannii is notoriously resistant to environmental stresses, yet it lacks RpoS, and the molecular mechanisms driving this incredible stress tolerance remain poorly defined. Here, using functional genomics, we identified the transcriptional regulator DksA as a master regulator for broad stress protection and virulence in A. baumannii. Transcriptomics, phenomics and in vivo animal studies revealed that DksA controls ribosomal protein expression, metabolism, mutation rates, desiccation, antibiotic resistance, and host colonization in a niche-specific manner. Phylogenetically, DksA was highly conserved and well-distributed across Gammaproteobacteria, with 96.6% containing DksA, spanning 88 families. This study lays the groundwork for understanding DksA as a major regulator of general stress response and virulence in this important pathogen.

Biotin pathway in novel Fodinibius salsisoli sp. nov., isolated from hypersaline soils and reclassification of the genus Aliifodinibius as Fodinibius

Hypersaline soils are extreme environments that have received little attention until the last few years. Their halophilic prokaryotic population seems to be more diverse than those of well-known aquatic systems. Among those inhabitants, representatives of the family Balneolaceae (phylum Balneolota) have been described to be abundant, but very few members have been isolated and characterized to date. This family comprises the genera Aliifodinibius and Fodinibius along with four others. A novel strain, designated 1BSP15-2V2^T, has been isolated from hypersaline soils located in the Odiel Saltmarshes Natural Area (Southwest Spain), which appears to represent a new species related to the genus Aliifodinibius. However, comparative genomic analyses of members of the family Balneolaceae have revealed that the genera Aliifodinibius and Fodinibius belong to a single genus, hence we propose the reclassification of the species of the genus Aliifodinibius into the genus Fodinibius, which was first described. The novel strain is thus described as Fodinibius salsisoli sp. nov., with 1BSP15-2V2^T (=CCM 9117^T = CECT 30246^T) as the designated type strain. This species and other closely related ones show abundant genomic recruitment within 80-90% identity range when searched against several hypersaline soil metagenomic databases investigated. This might suggest that there are still uncultured, yet abundant closely related representatives to this family present in these environments. In-depth in-silico analysis of the metabolism of Fodinibius showed that the biotin biosynthesis pathway was present in the genomes of strain 1BSP15-2V2^T and other species of the family Balneolaceae, which could entail major implications in their community role providing this vitamin to other organisms that depend on an exogenous source of this nutrient.

Breaching the Barrier: Genome-Wide Investigation into the Role of a Primary Amine in Promoting E. coli Outer-Membrane Passage and Growth Inhibition by Ampicillin

Gram-negative bacteria are problematic for antibiotic development due to the low permeability of their cell envelopes. To rationally design new antibiotics capable of breaching this barrier, more information is required about the specific components of the cell envelope that prevent the passage of compounds with different physiochemical properties. Ampicillin and benzylpenicillin are β-lactam antibiotics with identical chemical structures except for a clever synthetic addition of a primary amine group in ampicillin, which promotes its accumulation in Gram-negatives. Previous work showed that ampicillin is better able to pass through the outer membrane porin OmpF in Escherichia coli compared to benzylpenicillin. It is not known, however, how the primary amine may affect interaction with other cell envelope components. This study applied TraDIS to identify genes that affect E. coli fitness in the presence of equivalent subinhibitory concentrations of ampicillin and benzylpenicillin, with a focus on the cell envelope. Insertions that compromised the outer membrane, particularly the lipopolysaccharide layer, were found to decrease fitness under benzylpenicillin exposure, but had less effect on fitness under ampicillin treatment. These results align with expectations if benzylpenicillin is poorly able to pass through porins. Disruption of genes encoding the AcrAB-TolC efflux system were detrimental to survival under both antibiotics, but particularly ampicillin. Indeed, insertions in these genes and regulators of acrAB-tolC expression were differentially selected under ampicillin treatment to a greater extent than insertions in ompF. These results suggest that maintaining ampicillin efflux may be more significant to E. coli survival than full inhibition of OmpF-mediated uptake. IMPORTANCE Due to the growing antibiotic resistance crisis, there is a critical need to develop new antibiotics, particularly compounds capable of targeting high-priority antibiotic-resistant Gram-negative pathogens. In order to develop new compounds capable of overcoming resistance a greater understanding of how Gram-negative bacteria are able to prevent the uptake and accumulation of many antibiotics is required. This study used a novel genome wide approach to investigate the significance of a primary amine group as a chemical feature that promotes the uptake and accumulation of compounds in the Gram-negative model organism Escherichia coli. The results support previous biochemical observations that the primary amine promotes passage through the outer membrane porin OmpF, but also highlight active efflux as a major resistance factor.