The RstB sensor acts on the PhoQ sensor to control expression of PhoP-regulated genes

The impact of aztreonam-clavulanic acid exposure on gene expression and mutant selection using a multidrug-resistant E. coli

Multidrug-resistant Escherichia coli poses a significant threat to the healthcare system by causing treatment failure in infected patients. The use of a beta-lactam in combination with a beta-lactamase inhibitor has been shown to be an effective strategy to solve this problem. In vitro antimicrobial susceptibility experiments have demonstrated the antimicrobial activity of aztreonam and clavulanate. In this investigation, we conducted a transcriptomic analysis to reveal the downstream differential gene expression in E. coli ymmD45 (a strain newly isolated and found to carry the New Delhi metallo-β-lactamase gene) following exposure to aztreonam and clavulanate separately, as well as their combination. Differential gene expression, pathway enrichment, and gene network analyses demonstrated the polygenic nature of the response to the combination treatment, which suppressed the expression of pivotal virulence genes, disrupted two-component regulatory systems for bacteria to resist external stress, and interfered with the formation of the cellular membrane. Results from single-step mutant selection combined with deep whole-genome sequencing also revealed the spontaneous origin of the resistance mutations and confirmed action mechanisms during the combination treatment. Our study contributes valuable insights into the impact of antibiotic exposure on gene expression, laying the groundwork for understanding antibiotic resistance development in the treatment of multi-drug resistant infections through in vitro studies.IMPORTANCEMultidrug-resistant Escherichia coli is a major challenge in treating infections effectively. Aztreonam and clavulanate combination is promising in combating these resistant bacteria. By investigating the antimicrobial activity of aztreonam and clavulanate using transcriptomic analysis and mutant selection, this research sheds light on the mechanisms underlying antibiotic resistance and the effectiveness of combination therapies. The findings highlight how this particular antibiotic combination suppresses virulence genes, disrupts bacterial regulatory systems, and interferes with cellular functions critical for resistance. Moreover, the study lays the groundwork for understanding antibiotic resistance development in the treatment of multi-drug resistant infections through in vitro studies, offering insights that could inform future strategies in clinical settings. Ultimately, our findings could guide the development of better treatment strategies for multidrug-resistant infections, improving patient outcomes and helping to manage antibiotic resistance in healthcare.

Adaptation to host-specific bacterial pathogens drive rapid evolution of novel PhoP/PhoQ regulation pathway modulating the virulence

The presence of the PhoP-PhoQ system is usually different in various bacterial groups, suggesting that PhoP can control the expression of different genes in species. However, little is known about the evolution of the PhoP-PhoQ system among bacterial pathogens. Here, we study the evolution of PhoP and PhoQ regulation in 15 species of Enterobacteriaceae family. We have determined that the regulatory objectives adopted by PhoP and PhoQ are mainly different, due to the result of horizontal gene transfer events and even the change in the genetic content between closely related species. We have compared many possibilities tests (M1 vs. M2 and M7 with M8) to determine the positive selection. Estimating parameters at M1 and M2, with positive selection in M2 of the two proteins. The proportions of positive selection sites significant with ω = 4.53076 for PhoP and ω = 4.21041 PhQ. M8 was significant for PhoP and PhQ proteins. To further confirm the positive selection results, we used the Selecton server to confer positive selection on individual sites using the Mechanistic-Empirical Combination model, and we noticed that several sites had been identified under selection pressure during the evolution. There was a strong indication for the positive selection in bacterial genes of PhoP and PhoQ showed the results. By the use of REL and IFEL, the positive selection for PhoP was detected 14 and 11 sites respectively at different codon positions. The positively selected sites of amino acids such as Arginine, Alanine, Lysine, and Leucine are more important for the production of signals. Our results suggest that the positive selection of PhoP-PhoQ genes in host adaptation during evolution raises an intriguing possibility causes subtle variations in actions of PhoP-PhoQ and also increases the opportunities that cause modification in protein structure for the evolution of increasing pathogenicity in bacterial pathogens.

Identification of Aeromonas hydrophila Genes Preferentially Expressed after Phagocytosis by Tetrahymena and Involvement of Methionine Sulfoxide Reductases

Free-living protozoa affect the survival and virulence evolution of pathogens in the environment. In this study, we explored the fate of Aeromonas hydrophila when co-cultured with the bacteriovorous ciliate Tetrahymena thermophila and investigated bacterial gene expression associated with the co-culture. Virulent A. hydrophila strains were found to have ability to evade digestion in the vacuoles of this protozoan. In A. hydrophila, a total of 116 genes were identified as up-regulated following co-culture with T. thermophila by selective capture of transcribed sequences (SCOTS) and comparative dot-blot analysis. A large proportion of these genes (42/116) play a role in metabolism, and some of the genes have previously been characterized as required for bacterial survival and replication within macrophages. Then, we inactivated the genes encoding methionine sulfoxide reductases, msrA, and msrB, in A. hydrophila. Compared to the wild-type, the mutants ΔmsrA and ΔmsrAB displayed significantly reduced resistance to predation by T. thermophila, and 50% lethal dose (LD₅₀) determinations in zebrafish demonstrated that both mutants were highly attenuated. This study forms a solid foundation for the study of mechanisms and implications of bacterial defenses.

A comparative proteomic analysis of Salmonella typhimurium under the regulation of the RstA/RstB and PhoP/PhoQ systems

In pathogenic bacteria, the two-component regulatory systems (TCSs) play important roles in signal transduction and regulation of their pathogenesis. Here, we used quantitative proteomic methods to comparatively analyze functional networks under the control of the RstA/RstB system versus the PhoP/PhoQ system in Salmonella typhimurium. By comparing the proteomic profile from a wild-type strain to that from a ΔrstB strain or a ΔphoPQ strain under a condition known to activate these TCSs, we found that the levels of 159 proteins representing 6.92% of the 2297 proteins identified from the ΔrstB strain and 341 proteins representing 14.9% of the 2288 proteins identified from the ΔphoPQ strain were significantly changed, respectively. Bioinformatics analysis revealed that the RstA/RstB system and the PhoP/PhoQ system coordinated with regard to the regulation of specific proteins as well as metabolic processes. Our observations suggested that the regulatory networks controlled by the PhoP/PhoQ system were much more extensive than those by the RstA/RstB system, whereas the RstA/RstB system specifically regulated expression of the constituents participating in pyrimidine metabolism and iron acquisition. Additional results also suggested that the RstA/RstB system was required for regulation of Salmonella motility and invasion.

Modulation of virulence genes by the two-component system PhoP-PhoQ in avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) infections are a very important problem in the poultry industry. PhoP-PhoQ is a two-component system that regulates virulence genes in APEC. In this study, we constructed strains that lacked the PhoP or PhoQ genes to assess regulation of APEC pathogenicity by the PhoP-PhoQ two-component system. The PhoP mutant strain AE18, PhoQ mutant strain AE19, and PhoP/PhoQ mutant strain AE20 were constructed by the Red homologous recombination method. Swim plates were used to evaluate the motility of the APEC strains, viable bacteria counting was used to assess adhesion and invasion of chick embryo fibroblasts, and Real-Time PCR was used to measure mRNA expression of virulence genes. We first confirmed that AE18, AE19, and AE20 were successfully constructed from the wild-type AE17 strain. AE18, AE19, and AE20 showed significant decreases in motility of 70.97%, 83.87%, and 37.1%, respectively, in comparison with AE17. Moreover, in comparison with AE17, AE18, AE19, and AE20 showed significant decreases of 63.11%, 65.42%, and 30.26%, respectively, in CEF cell adhesion, and significant decreases of 59.83%, 57.82%, and 37.90%, respectively, in CEF cell invasion. In comparison with AE17, transcript levels of sodA, polA, and iss were significantly decreased in AE18, while transcript levels of fimC and iss were significantly decreased in AE19. Our results demonstrate that deletion of PhoP or PhoQ inhibits invasion and adhesion of APEC to CEF cells and significantly reduces APEC virulence by regulating transcription of virulence genes.

Genomic and transcriptomic analyses of colistin-resistant clinical isolates of Klebsiella pneumoniae reveal multiple pathways of resistance

The emergence of multidrug-resistant (MDR) Klebsiella pneumoniae has resulted in a more frequent reliance on treatment using colistin. However, resistance to colistin (Col(r)) is increasingly reported from clinical settings. The genetic mechanisms that lead to Col(r) in K. pneumoniae are not fully characterized. Using a combination of genome sequencing and transcriptional profiling by RNA sequencing (RNA-Seq) analysis, distinct genetic mechanisms were found among nine Col(r) clinical isolates. Col(r) was related to mutations in three different genes in K. pneumoniae strains, with distinct impacts on gene expression. Upregulation of the pmrH operon encoding 4-amino-4-deoxy-L-arabinose (Ara4N) modification of lipid A was found in all Col(r) strains. Alteration of the mgrB gene was observed in six strains. One strain had a mutation in phoQ. Common among these seven strains was elevated expression of phoPQ and unaltered expression of pmrCAB, which is involved in phosphoethanolamine addition to lipopolysaccharide (LPS). In two strains, separate mutations were found in a previously uncharacterized histidine kinase gene that is part of a two-component regulatory system (TCRS) now designated crrAB. In these strains, expression of pmrCAB, crrAB, and an adjacent glycosyltransferase gene, but not that of phoPQ, was elevated. Complementation with the wild-type allele restored colistin susceptibility in both strains. The crrAB genes are present in most K. pneumoniae genomes, but not in Escherichia coli. Additional upregulated genes in all strains include those involved in cation transport and maintenance of membrane integrity. Because the crrAB genes are present in only some strains, Col(r) mechanisms may be dependent on the genetic background.

RstA is required for the virulence of an avian pathogenic Escherichia coli O2 strain E058

Certain strains of avian pathogenic Escherichia coli (APEC) cause severe extraintestinal infections in poultry, including acute fatal septicemia, subacute pericarditis, and airsacculitis. These bacteria contain an RstA/RstB regulatory system, a two-component system that may help APEC strains adapt to the extra-intestinal environment and survive under stressful conditions. Whether RstA correlates with APEC pathogenesis or acts as an APEC virulence factor has not been established. Here we provide the first evidence for an important role of rstA in APEC virulence. We generated an rstA-deficient mutant from the highly virulent APEC strain E058. Virulence of the mutant strain was evaluated in vivo and in vitro through bird infection assays, a cytotoxicity assay on chicken macrophage cell line HD-11, and a bactericidal assay to serum complement. Based on lethality assays in 1-day-old birds, rstA deletion from APEC E058 reduced the bacterial virulence in birds. The deletion also deeply impaired the capacity of APEC E058 to colonize deeper tissues of 5-week-old specific pathogen free chickens. No obvious gross or histopathological lesions were observed in the visceral organs of chickens challenged with the rstA-deficient strain. Also, rstA inactivation reduced the survival of APEC E058 within chicken macrophages. However, no significant differences were observed between the mutant and the wild-type strain in resistance to serum. Our data collectively show that the rstA gene functions in the pathogenesis of diseases caused by avian pathogenic E. coli.

(1)H, (13)C and (15)N resonance assignments of the C-terminal DNA-binding domain of RstA protein from Klebsiella pneumoniae

Bacterial cells often use two-component signal transduction systems to regulate genes in response to environmental stimuli. The RstA/RstB system is a two-component regulatory system consisting of the membrane sensor, RstB, and its cognate response regulator RstA. The RstA of Klebsiella pneumoniae consists of a N-terminal receiver domain (NRD, residues 1-119) and a C-terminal DNA-binding domain (DBD, residues 130-236). Phosphorylation of the response regulator induces a conformational change in the regulatory domain of RstA, which results in activation of the effector domain to regulate the downstream genes, including the ferrous iron transport system (Feo), at low-pH condition. Here we report the (1)H, (13)C and (15)N resonance assignments and secondary structure identification of the DBD of RstA from K. pneumoniae as a first step for unraveling the structural and functional relationship of the RstA/RstB two component system.