Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen

Wheat bran supplementation improved polystyrene degradation efficiency of Zophobas atratus larvae by alleviating intestinal injury caused by polystyrene-intake

Wheat bran supplementation significantly improves the polystyrene consumption capacity of Zophobas atratus larvae. However, the underlying mechanism remains unclear, limiting further advancements in degradation efficiency. This study seeks to clarify the mechanism by analyzing intestinal morphology, gut microbiota structure, gene transcription, and targeted metabolites. Specifically, histopathology results demonstrated that wheat bran supplementation alleviated polystyrene-induced intestinal injury in larvae. From a genetic perspective, genes related to annexins and tight junction proteins were upregulated in intestinal tissues. These genetic changes positively correlated with increased levels of short-chain fatty acids, eicosanoids, and beneficial bacteria (e.g., Latilactobacillus curvatus). Moreover, wheat bran supplementation alleviated gut microbiota dysbiosis, suppressed pathogenic bacteria, reduced over upregulation of NADPH oxidase activity related genes, and up-regulated genes linked to the intestinal immune system process pathway, thereby mitigating the intestinal injury. It also upregulated genes associated with the aromatase activity pathway, promoting the degradation of polystyrene and its intermediates. In summary, wheat bran supplementation enhanced the polystyrene degradation efficiency of Z. atratus larvae by upregulating genes linked to the aromatase activity pathway and mitigating intestinal injury (through modulation of intestinal gene transcription, microbiota structure, and metabolites). Our findings offer new insights into improving the efficiency of insect-mediated plastic biodegradation.

The roles of bacteria on urolithiasis progression and associated compounds

As a common urological disease, the formation of urinary tract stones involves multiple factors, including genetics, the environment, dietary habits, and bacterial species (e.g., Proteus mirabilis and Escherichia coli). Previous studies have demonstrated that P. mirabilis primarily contributes to infectious urinary calculus formation by producing urease, an enzyme that breaks down urea into ammonia and carbon dioxide, thereby altering the urinary pH and promoting crystal formation and growth. In contrast, calcium oxalate (CaOx) stones are the main type of kidney stones, and the most common bacteria in CaOx stones are E. coli. Intriguingly, E. coli can also facilitate stone formation via flagellin and other virulence factors, which induce renal epithelial cell injury and increase crystal adhesion and aggregation. These bacteria play complex and multidimensional roles in the formation of urinary tract stones, necessitating further research to elucidate their underlying mechanisms. Here, we summarise the roles of common urinary tract bacteria, particularly P. mirabilis and E. coli, in forming urinary tract stones, aiming to enhance our understanding of urolithiasis exploration in the future.

Phage steering in the presence of a competing bacterial pathogen

The rise of antibiotic-resistant bacteria has necessitated the development of alternative therapeutic strategies, such as bacteriophage therapy, where viruses infect bacteria, reducing bacterial burden. However, rapid bacterial resistance to phage treatment remains a critical challenge, potentially leading to failure. Phage steering, which leverages the evolutionary dynamics between phage and bacteria, offers a novel solution by driving bacteria to evolve away from virulence factors or resistance mechanisms. In this study, we examined whether phage steering using bacteriophage Luz19 could function in the presence of a competing pathogen, Staphylococcus aureus (SA) (USA300), while targeting Pseudomonas aeruginosa (PAO1). Through in vitro co-evolution experiments with and without the competitor, we observed that Luz19 consistently steered P. aeruginosa away from the Type IV pilus (T4P), a key virulence factor, without interference from SA. Genomic analyses revealed mutations in T4P-associated genes, including pilR and pilZ, which conferred phage resistance. Our findings suggest that phage steering remains effective even in polymicrobial environments, providing a promising avenue for enhancing bacteriophage therapy efficacy in complex infections.IMPORTANCEPhage steering-using phages that bind essential virulence or resistance-associated structures-offers a promising solution by selecting for resistance mutations that attenuate pathogenic traits. However, it remains unclear whether this strategy remains effective in polymicrobial contexts, where interspecies interactions may alter selective pressures. Here, we demonstrate that Pseudomonas aeruginosa evolves phage resistance via loss-of-function mutations in Type IV pilus (T4P) when challenged with the T4P-binding phage Luz19 and that this evolutionary trajectory is preserved even in the presence of a competing pathogen, Staphylococcus aureus. Phage resistance was phenotypically confirmed via twitching motility assays and genotypically via whole-genome sequencing. These findings support the robustness of phage steering under interspecies competition, underscoring its translational potential for managing complex infections-such as those seen in cystic fibrosis-where microbial diversity is the norm.

Unlocking Enhanced Efficacy of Aminoglycoside Antibiotics Against Pseudomonas aeruginosa

Infectious diseases continue to be a global health burden. Among the major human pathogens is the Gram-negative bacterium Pseudomonas aeruginosa, which is particularly due to its wide range of drug resistance mechanisms. Aminoglycosides, which have long been used in treating pseudomonal infections, are increasingly undermined by resistance. This opinion article discusses the use and challenges of aminoglycosides against P. aeruginosa and highlights recent strategies that enhance aminoglycoside efficacy. These include combinational therapies, metabolic stimulants/adjuvants, silver, and more recently developed derivatives such as AGXX, many of which have been reported to potentiate the cytotoxic effects of aminoglycosides and re-sensitise aminoglycoside-resistant strains. While these findings pave the way for future therapies, the clinical relevance of many in vitro studies remains to be investigated.

The Iron Metalloproteome of Pseudomonas aeruginosa Under Oxic and Anoxic Conditions

Pseudomonas aeruginosa is a major contributor to human infections and is widely distributed in the environment. Its ability for growth under aerobic and anaerobic conditions provides adaptability to environmental changes and in confronting immune responses. We applied native 2-dimensional metalloproteomics to P. aeruginosa to examine how use of iron within the metallome responds to oxic and anoxic conditions. Analyses revealed four iron peaks comprised of metalloproteins with synergistic functions, including: 1) respiratory and metabolic enzymes, 2) oxidative stress response enzymes, 3) DNA synthesis and nitrogen assimilation enzymes, and 4) denitrification enzymes and related copper enzymes. Fe peaks were larger under anoxic conditions, consistent with increased iron demand due to anaerobic metabolism and with the denitrification peak absent under oxic conditions. Three ferritins co-eluted with the first and third iron peaks, localizing iron storage with these functions. Several enzymes were more abundant at low oxygen, including alkylhydroperoxide reductase C that deactivates organic radicals produced by denitrification, all three classes of ribonucleotide reductases (including monomers and oligomer forms), ferritin (increasing in ratio relative to bacterioferritin), and denitrification enzymes. Superoxide dismutase and homogentisate 1,2-dioxygenase were more abundant at high oxygen. Several Fe peaks contained iron metalloproteins that co-eluted earlier than their predicted size, implying additional protein-protein interactions and suggestive of cellular organization that contributes to iron prioritization in Pseudomonas with its large genome and flexible metabolism. This study characterized the iron metalloproteome of one of the more complex prokaryotic microorganisms, attributing enhanced iron use under anaerobic denitrifying metabolism to its specific metalloprotein constituents.

Transcriptional Regulatory Systems in Pseudomonas: A Comparative Analysis of Helix-Turn-Helix Domains and Two-Component Signal Transduction Networks

Bacterial communities in diverse environmental niches respond to various external stimuli for survival. A primary means of communication between bacterial cells involves one-component (OC) and two-component signal transduction systems (TCSs). These systems are key for sensing environmental changes and regulating bacterial physiology. TCSs, which are the more complex of the two, consist of a sensor histidine kinase for receiving an external input and a response regulator to convey changes in bacterial cell physiology. For numerous reasons, TCSs have emerged as significant targets for antibacterial drug design due to their role in regulating expression level, bacterial viability, growth, and virulence. Diverse studies have shown the molecular mechanisms by which TCSs regulate virulence and antibiotic resistance in pathogenic bacteria. In this study, we performed a thorough analysis of the data from multiple public databases to assemble a comprehensive catalog of the principal detection systems present in both the non-pathogenic Pseudomonas putida KT2440 and the pathogenic Pseudomonas aeruginosa PAO1 strains. Additionally, we conducted a sequence analysis of regulatory elements associated with transcriptional proteins. These were classified into regulatory families based on Helix-turn-Helix (HTH) protein domain information, a common structural motif for DNA-binding proteins. Moreover, we highlight the function of bacterial TCSs and their involvement in functions essential for bacterial survival and virulence. This comparison aims to identify novel targets that can be exploited for the development of advanced biotherapeutic strategies, potentially leading to new treatments for bacterial infections.

Engineering an antimicrobial chimeric endolysin that targets the phytopathogen Pseudomonas syringae pv. actinidiae

Global food shortages and rising antimicrobial resistance require alternatives to antibiotics and agrichemicals for the management of agricultural bacterial pathogens. The phytopathogen Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of kiwifruit canker and is responsible for major agricultural losses. Bacteriophage enzymes present an emerging antimicrobial option. Endolysins possess the ability to cleave peptidoglycan and are effective antimicrobials against gram-positive bacteria. Delivery of endolysins to the peptidoglycan of gram-negatives is impeded by the additional outer membrane. To overcome this barrier, we used VersaTile molecular shuffling to produce Psa-targeting chimeric proteins which were tested for antimicrobial activity. These chimeras consist of endolysins linked by polypeptides to diverse phage proteins mined from Psa phage genomes. A preferential configuration for antibacterial activity was observed for enzymatic domains at the N-terminus and alternative phage proteins at the C-terminus. The lead variant possessed an N-terminal modular endolysin and a C-terminal lipase. Antibacterial activity was enhanced with the addition of the chemical permeabilizers citric acid or EDTA. Mutagenesis of the lipase active site eliminated exogenous antibacterial activity towards Psa. The endolysin-lipase chimera demonstrated specificity towards Psa, illustrating potential as a targeted biocontrol agent. Overall, we generated a chimeric endolysin with exogenous and specific activity towards Psa, the causative agent of kiwifruit canker.

A review of recently discovered mechanisms of cephalosporin resistance in Pseudomonas aeruginosa

Pseudomonas aeruginosa frequently causes respiratory tract infections in immunocompromised patients as well as bloodstream, urinary tract, skin, and soft tissue infections. The increasing prevalence of multidrug-resistant P. aeruginosa strains poses a significant clinical challenge. Cephalosporin antibiotics from the β-lactam class are commonly prescribed to treat infections owing to their broad spectrum of activity and generally low host toxicity. P. aeruginosa utilizes β-lactamase enzymes, efflux pumps, and mutations in outer membrane porins/transporters and target proteins, all of which confer resistance to cephalosporin antibiotics. This review categorizes resistance mechanisms into (i) well-characterized pathways, such as AmpC β-lactamase and Mex efflux pumps, (ii) recently described mutations linked to cephalosporin resistance (e.g., ygfB, sltB1, pbp3, galU, pmrAB, fusA1, and gyrA), and (iii) hypothetical β-lactamases and other mechanisms requiring further validation. A variety of β-lactamase inhibitors have been developed to overcome β-lactamase-mediated resistance, but resistance has already been observed toward inhibitors via the accumulation of mutations within the targeted β-lactamase enzyme or increased activity of efflux pumps. Understanding the regulation and pathways that lead to resistance is crucial in developing effective strategies to combat P. aeruginosa infections and extending the therapeutic lifespan of cephalosporin antibiotics.

Pseudomonas aeruginosa clinical isolates in Egypt: phenotypic, genotypic, and antibiofilm assessment of Pluronic F-127

BACKGROUND

Virulence factors play an important role in developing bacterial resistance leading to the increased severity of Pseudomonas aeruginosa infections. Several genes encoding for virulence factors is coordinated by the quorum sensing (QS) system. In the present study, the prevalence of virulence genes, particularly those involved in controlling biofilm formation, and their correlation with antibiotic resistance patterns was investigated. The ability of the pathogens to form biofilm and the impact of Pluronic F-127 as a potential biofilm inhibitor was assessed.

RESULTS

A total of 118 P. aeruginosa clinical isolates were collected. The highest resistance rates were observed against ceftazidime (94%), while colistin was the most effective followed by polymyxin B with sensitivity rate 72% and 59%, respectively. Out of 118 isolates: 111 (94%) were biofilm producers, 24.6% of them were strong. The QS genes; lasR and rhlR, were detected in 85% and 89% of the isolates, respectively, toxA gene in 95% and ampC gene in 69% of the isolates. Pluronic F-127 was confirmed as a biofilm inhibitor in lowest concentration used 1.25 mg/ml which inhibits 78% of strong biofilm forming isolates and has better effect on detachment of established biofilm by 90% of biofilm forming isolates.

CONCLUSION

The ability of bacteria to form biofilms contributes greatly to the development of antibiotic resistance, which leads to the occurrence of persistent and chronic bacterial illnesses. Many isolates exhibited moderate to strong biofilm forming ability, which showed a high resistance pattern. The results demonstrated that Pluronic F-127 has a promising level of biofilm inhibition and detachment in most isolates. It has a chance to serve as a substitute means for combating biofilm formation.

Antibacterial properties of silver and gold nanoparticles synthesized using Cannabis sativa waste extract against Pseudomonas aeruginosa

AIMS

The study aimed to explore the sustainable synthesis of metal nanoparticles using a green and eco-friendly resource. Specifically, it investigated the utilization of Cannabis sativa waste extract for the production of gold and silver nanoparticles, focusing on their antimicrobial activity against gram-negative bacteria, particularly Pseudomonas aeruginosa strains, which are significant in nosocomial infections.

METHODS

Cannabis sativa waste extract was employed to synthesize gold and silver nanoparticles through a green synthesis approach. The produced nanoparticles were characterized using transmission electron microscopy (TEM), atomic absorption spectrometry (AAS), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR). The antimicrobial efficacy of the synthesized nanoparticles was assessed through their minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and minimal biofilm inhibitory concentration (MBIC) against Pseudomonas aeruginosa, utilizing a microcultivation device, solid medium cultivation, and a metabolic activity assay in a polystyrene microtiter plate, respectively.

RESULTS

The TEM analysis revealed the size and morphology of the nanoparticles, while AAS confirmed their concentration. XRD provided insights into the crystalline structure, and FTIR analysis identified the molecular structure of the nanoparticle's stabilizing layer. The synthesized nanoparticles showed significant antimicrobial activity against Pseudomonas aeruginosa, with determined MIC, MBC, and MBIC values of produced silver nanoparticles, showcasing their potential as effective antimicrobial agents.

CONCLUSIONS

This study successfully demonstrated the synthesis of silver and gold nanoparticles using Cannabis sativa waste extract and highlighted their potent antimicrobial properties. It underscores the potential of utilizing plant waste extracts in sustainable nanomaterial synthesis and contributes to the fields of green nanotechnology and waste valorization within the circular economy. The findings also offer valuable insights into developing natural waste source-based antimicrobial agents.

Potential of vB_Pa_ZCPS1 phage embedded in situ gelling formulations as an ocular delivery system to attenuate Pseudomonas aeruginosa keratitis in a rabbit model

Pseudomonas aeruginosa keratitis (or pink eye) is a challenging ocular infection that causes serious complications due to the deficiency of effective antibiotic treatment. Thus, in this study we isolated and characterized a specific bacteriophage, phage vB_Pa_ZCPS1, to be used to formulate an in situ- gel loaded bacteriophage for an in vivo rabbit infection treatment model. Phage vB_Pa_ZCPS1 is a double-stranded DNA bacterial virus, of 46,135 bp encoding 75 open reading frames (ORFs) with no antibiotic resistance genes detected. Moreover, it has a podoviral morphotype from the Caudoviricetes class with a 62.4 nm capsid and a short inflexible tail of around 18.8 nm, as indicated by the transmission electron microscope (TEM). Phage vB_Pa_ZCPS1 presented good stability to the UV exposure and a wide range of pH values from 3.0 to 11.0. In addition, the phage-bacteria dynamics study showed that phage vB_Pa_ZCPS1 was effective against P. aeruginosa, especially at low multiplicities of infections (MOIs), including 0.001, 0.01, and 0.1. Respectively, it was loaded to the characterized in situ gel composed of 14 % Pluronic F-127 and 1.5 % HPMC K4M polymer. The in situ-gel has a gelling time of 30 s ± 1, and a temperature of 33 °C ± 1, where the viscosity of the gel increases 10-fold. For the in vivo trial, the infected group treated with phage presented improved clinical outcomes, where the histopathological analysis revealed normal corneal thickness and intact corneal stratified squamous epithelium. Thus, the in situ-gel loaded phage vB_Pa_ZCPS1 could be a potential candidate approach to treat P. aeruginosa keratitis.

Phenolic-Rich Wine Pomace Extracts as Antioxidant and Antipathogenic Agents Against Pseudomonas aeruginosa

Background/Objectives: Wine pomace is a rich source of bioactive phenolic compounds with potential health benefits. This study aimed to evaluate the antipathogenic and antioxidant properties of ethanol and ethyl acetate extracts from wine pomace of three grape varietals (Tannat, Bonarda, and Malbec) to explore their potential as natural alternatives for mitigating bacterial virulence in Pseudomonas aeruginosa. Methods: Successive exhaustion extractions were performed using solvents of increasing polarity (ethyl acetate and ethanol). The phenolic content was quantified, and the antioxidant activity was evaluated using standard assays. The antipathogenic activity against P. aeruginosa was assessed by measuring biofilm formation, elastase and protease activity, pyocyanin production, and swarming motility. Quorum sensing (QS) inhibition was tested using a violacein production assay in Chromobacterium violaceum. Results: Ethanol was more effective at extracting phenolic compounds, with Tannat exhibiting the highest total phenolic content (162.5 µg GAE/mg). HPLC-DAD analysis identified 16 phenolic acids, 18 flavonoids, and 3 stilbenes across the extracts. The ethanol extracts showed strong antioxidant activity (phosphomolybdenum reducing capacity 67-128 μg AAE/mg, ABTS•+ scavenging 37-71 µg/mL, Fe3+ reducing power 31-68 µg/mL) and inhibited biofilm formation (up to 61%), elastase (up to 41%), and protease (up to 46%) activities in P. aeruginosa. The extracts also reduced pyocyanin production (up to 78%) and swarming motility (up to 68%), suggesting interference with QS. Moreover, the extracts inhibited violacein production in C. violaceum, confirming QS inhibition (up to 26%). Conclusions: Among the extracts, ethanol-extracted Tannat pomace showed the most substantial antipathogenic and antioxidant activities. The results add value to wine pomace by suggesting its use as natural extracts rich in phenolic compounds, capable of controlling the bacterial virulence of Pseudomonas aeruginosa without promoting the development of resistance.

Type IV PilD mutant stimulates the formation of persister cells in Pseudomonas aeruginosa

BACKGROUND

Pseudomonas aeruginosa clinical isolates that lack motility do not express type IV pilin, yet the biological roles of this absence in the infection process remain poorly understood.

OBJECTIVES

We asked whether the absence of motility in these bacteria is associated with increased antibiotic persistence.

METHODS

In this study, we analysed type IV PilD protein sequences in the database and conducted antibiotic-tolerant persister cell assays.

RESULTS

We found that PilD variants were common in P. aeruginosa clinical isolates. Our results revealed that inactivation of PilD resulted in a significantly higher level of surviving persister cells following ciprofloxacin treatment. This PilD-mediated persistence did not involve previously described mechanisms, such as phenazine pyocyanin, biofilm or stringent response.

CONCLUSIONS

Our findings connect the non-motility of clinical P. aeruginosa isolates with the survival of persister cells, highlighting the clinical significance for the development of strategies to eradicate P. aeruginosa infections.

Microbial diversity and interactions: Synergistic effects and potential applications of Pseudomonas and Bacillus consortia

Microbial diversity and interactions in the rhizosphere play a crucial role in plant health and ecosystem functioning. Among the myriads of rhizosphere microbes, Pseudomonas and Bacillus are prominent players known for their multifaceted functionalities and beneficial effects on plant growth. The molecular mechanism of interspecies interactions between natural isolates of Bacillus and Pseudomonas in medium conditions is well understood, but the interaction between the two in vivo remains unclear. This paper focuses on the possible synergies between Pseudomonas and Bacillus associated in practical applications (such as recruiting beneficial microbes, cross-feeding and niche complementarity), and looks forward to the application prospects of the consortium in agriculture, human health and bioremediation. Through in-depth understanding of the interactions between Pseudomonas and Bacillus as well as their application prospects in various fields, this study is expected to provide a new theoretical basis and practical guidance for promoting the research and application of rhizosphere microbes.

An anticipatory mechanism enhances the cooperative behaviors of quorum sensing mutants in Pseudomonas aeruginosa

Social interactions substantially influence the dynamics and functions of microbial communities. Cooperative behaviors serve to benefit populations, yet they are often exploited by cheating cells, thus creating a conflict between individuals in the microbial population. However, the underlying mechanisms by which cooperative behaviors are stabilized are incompletely elucidated. Here, we used quorum sensing (QS) as a model of cooperation, and functionally studied QS regulator LasR variant strains in the context of cooperative behaviors. We found that a LasR228 variant strain, bearing a non-conserved substitution in LasR, exhibited minimal LasR-dependent phenotypes. However, the function of this LasR228 variant strain was restored by inactivation of the transcriptional repressor PsdR, and the phenotypes of this variant strain were similar to the parental strain. Furthermore, we illustrate a post-transcriptional regulatory mechanism responsible for the activation of the LasR228 variant. Unlike LasR228, the PsdR-null-LasR228 strain demonstrated cooperative behaviors in competition with the LasR-null strain. Since psdR mutations precede the emergence of LasR variants in the evolution of P. aeruginosa using casein broth, this PsdR-mediated cooperative mechanism serves as an anticipatory control against potential cheating LasR variant strains. Additionally, our cell-killing assay showed that the cooperative PsdR-null-LasR228 strain was associated with increased bacterial pathogenicity to eukaryotic host cells. In conclusion, our study reveals the functional plasticity of LasR variants, which can be modulated by secondary mutations, affecting cooperation and conflict within populations. Our identification of a novel cooperative molecular mechanism offers insight into the maintenance of cooperation within microbial communities.

Co-regulation of cooperative and private traits by PsdR in Pseudomonas aeruginosa

Social interactions profoundly shape the dynamics and functionality of microbial populations. However, mechanisms governing the regulation of cooperative or individual traits have remained elusive. Here, we investigated the regulatory mechanisms of social behaviors by characterizing the fitness of transcriptional regulator PsdR mutants in cooperating Pseudomonas aeruginosa populations. In a canonical model described previously, PsdR was shown to solely have a nonsocial role in adaptation of these populations by controlling the intracellular uptake and processing of dipeptides. In addition to these known private traits, we found that PsdR mutants also enhanced cooperation by increasing the production of quorum sensing (QS)-regulated public goods. Although private dipeptide utilization promotes individual absolute fitness, it only partially accounts for the growth advantage of PsdR mutants. The absence of the QS master regulator LasR delayed the appearance of PsdR variants in an evolution experiment. We also demonstrated that the growth fitness of PsdR mutants is determined by a combination of the QS-mediated cooperative trait and the dipeptide metabolism-related private trait. This dual trait is co-regulated by PsdR, leading to the rapid spread of PsdR variants throughout the population. In conclusion, we identified a new social model of co-regulating cooperative and private traits in PsdR variants, uncovering the social and nonsocial roles of this transcriptional regulator in cooperating bacterial populations. Our findings advance the fundamental understanding of bacterial social interactions and provide insights into population evolution, pathogen infection control and synthetic biotechnology.

Structure and activity of a phosphinothricin N-acetyltransferase (PSPTO_3321) from Pseudomonas syringae pv. tomato DC3000

Phosphinothricin inhibits plant glutamine synthetase and is used as a herbicide. Streptomyces hygroscopicus and Streptomyces viridochromogenes, which produce phosphinothricin naturally, encode acetyltransferases that confer phosphinothricin resistance. In the Pseudomonas genome database, a number of proteins have been annotated as phosphinothricin acetyltransferases and putative phosphinothricin acetyltransferases. One such protein is PSPTO_3321 from P. syringae, a strain that causes tomato speck. Here, we reveal that PSPTO_3321 from P. syringae, termed syr_pat, is a phosphinothricin acetyltransferase, and also retains a lower level of activity against the structurally similar substrate methionine sulfoximine. We solved a 1.6 Å resolution crystal structure of syr_pat alone and a 2.5 Å resolution structure for a complex with L-phosphinothricin. We also characterised active site mutants, providing insights into substrate specificity. Our work now provides a basis for further study of the reaction mechanism.

Haemophilus influenzae remains the predominant otitis media pathogen in Australian children undergoing ventilation tube insertion in the PCV13 era

INTRODUCTION

Understanding patterns of bacterial carriage and otitis media (OM) microbiology is crucial for assessing vaccine impact and informing policy. The microbiology of OM can vary with geography, time, and interventions like pneumococcal conjugate vaccines (PCVs). We evaluated the microbiology of nasopharyngeal and middle ear effusions in children living in Western Australia, 11 years following the introduction of PCV13.

METHODS

Children undergoing surgery for recurrent acute OM and/or chronic OM with effusion (cases), and children undergoing surgery for non-infectious reasons (controls), were recruited. Nasopharyngeal swabs and middle ear effusions (MEE - cases only) were collected, and quantitative PCR applied for detection of Haemophilus influenzae, Moraxella catarrhalis, Streptococcus pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus pyogenes. S. pneumoniae-positive MEE were serotyped by culture.

RESULTS

Nasopharyngeal swabs from 166 children under 5 years of age (123 cases, 43 controls) and MEE from 103 cases (93 with bilateral effusion - 196 MEE samples) were collected between September 2022 to December 2023. Nasopharyngeal carriage of H. influenzae was more common and density 10 times higher in cases compared to controls (84.2% H. influenzae carriage-positive cases versus 48.9% of controls, p=0.024; mean DNA concentration of 1.8 pg/µL versus 0.13 pg/µL, p=0.037). S. pneumoniae was more commonly carried in cases (not significant), and carriage density was higher in cases compared to controls (mean pneumococcal DNA concentration of 0.4 pg/µL versus 0.09 pg/µL, p=0.049). M. catarrhalis carriage and carriage density were similar between cases and controls (82.1% versus 76.7%). Carriage of 2 or more otopathogen species was common (80% of swabs). In the MEE, H. influenzae predominated (53% PCR-positive) followed by M. catarrhalis (31%), S. pneumoniae (22%), S. aureus (6%), S. pyogenes (2%) and P. aeruginosa (2%). Polymicrobial infection was identified in 26% of effusions. Of the S. pneumoniae PCR-positive MEE, 14 specimens from 11 children were culturable and all serotypes were non-PCV13 types.

CONCLUSION

The aetiology of recurrent and/or chronic OM in children continues to be primarily associated with H. influenzae. These data highlight the need for a concerted effort to develop effective preventative strategies for H. influenzae, most notably, nontypeable (NTHi). Higher valency PCVs may impact on pneumococcal OM.

Carbapenem-Resistant Pseudomonas aeruginosa's Resistome: Pan-Genomic Plasticity, the Impact of Transposable Elements and Jumping Genes

Pseudomonas aeruginosa, a Gram-negative, motile bacterium, may cause significant infections in both community and hospital settings, leading to substantial morbidity and mortality. This opportunistic pathogen can thrive in various environments, making it a public health concern worldwide. P. aeruginosa's genomic pool is highly dynamic and diverse, with a pan-genome size ranging from 5.5 to 7.76 Mbp. This versatility arises from its ability to acquire genes through horizontal gene transfer (HGT) via different genetic elements (GEs), such as mobile genetic elements (MGEs). These MGEs, collectively known as the mobilome, facilitate the spread of genes encoding resistance to antimicrobials (ARGs), resistance to heavy metals (HMRGs), virulence (VGs), and metabolic functions (MGs). Of particular concern are the acquired carbapenemase genes (ACGs) and other β-lactamase genes, such as classes A, B [metallo-β-lactamases (MBLs)], and D carbapenemases, which can lead to increased antimicrobial resistance. This review emphasizes the importance of the mobilome in understanding antimicrobial resistance in P. aeruginosa.

Antibiotic Resistance and Virulence Determinants of Pseudomonas aeruginosa Isolates Cultured from Hydrocarbon-Contaminated Environmental Samples

Crude oil and its derivates are among the most important environmental pollutants, where P. aeruginosa strains producing AlkB1 and AlkB2 alkane hydroxylases are often involved in their biodegradation. The aim of this study was to analyze antibiotic resistance and virulence determinants of a P. aeruginosa isolate cultured from a hydrocarbon-contaminated soil sample from Ogoniland, Nigeria, and to compare its characteristics with P. aeruginosa isolates cultured worldwide from hydrocarbon-contaminated environments or from clinical samples. Using the ResFinder reference database, a catB7 chloramphenicol acetyltransferase gene, an ampC-type PDC β-lactamase gene, and an OXA-50 type β-lactamase gene were identified in all P. aeruginosa strains analyzed in this study. In some of these P. aeruginosa strains, loss-of-function mutations were detected in the regulatory genes mexR, nalC, or nalD, predicting an efflux-mediated acquired antibiotic-resistance mechanism. Several P. aeruginosa sequence types that were associated with oil-contaminated environments have also been cultured from human clinical samples worldwide, including sequence types ST532, ST267, ST244, and ST1503. Our findings also indicate that environmental P. aeruginosa may serve as the source of human infections, warranting further studies from a One Health perspective about the application of P. aeruginosa for the in situ bioremediation of hydrocarbon-contaminated sites.

Modulation of the Pseudomonas aeruginosa quorum sensing cascade by MexT-regulated factors

Pseudomonas aeruginosa (Pa) uses quorum sensing (QS), a cell-cell communication system that enables it to sense cell density and to alter gene expression. Pa has three complete QS circuits controlled by the regulators LasR, RhlR, and PqsR, that together activate hundreds of genes. In the well-studied strain PAO1, QS is organized hierarchically, with PqsR and RhlR activity dependent on LasR. This hierarchy depends on the non-QS transcription factor MexT; deletion of mexT allows for RhlR activity in the absence of LasR. We aimed to identify how MexT modulates the Pa QS architecture. We compared the transcriptome of PAO1 to that of PAO1ΔmexT and determined a MexT regulon. We identified two MexT-regulated operons that may affect the QS hierarchy: the efflux pump genes mexEF-oprN and the Pseudomonas quinolone signal (PQS) synthesis genes pqsABCDE. We tested whether the products of these genes affected the QS hierarchy. A mexEF knockout mutant, like a mexT deletion mutant, exhibited RhlR activity earlier, and to a higher magnitude, than wild-type PAO1. MexEF-OprN is known to export quinolones, and we found that exogenous addition of PQS, through PqsE, also resulted in earlier and higher magnitude of RhlR activity compared to wild-type PAO1. We also discovered alternate QS architectures in clinical isolates, where RhlR activity is not fully dependent on LasR. In these isolates, surprisingly, MexT does not influence the relationship between LasR and RhlR. Our work reveals a new suite of factors that regulate QS in Pa, with implications for bacterial behaviors in environmental and clinical settings.

Genomic Characterization of Extremely Antibiotic-Resistant Strains of Pseudomonas aeruginosa Isolated from Patients of a Clinic in Sincelejo, Colombia

Pseudomonas aeruginosa is an opportunistic pathogen classified as a priority and a great public health concern; therefore, this research focuses on the genomic characterization of extremely resistant strains of P. aeruginosa isolated from patients in a clinic in Sincelejo, Colombia. Seven strains were analyzed by whole genome sequencing using the Illumina NovaSeq platform, with a focus on the identification of resistance genes and virulence factors through the CARD and VFDB databases. An ANI (Average Nucleotide Identity) analysis was carried out to determine the genetic relationship between the strains, complemented by a phylogenomic analysis to place the strains in different evolutionary clades. The results revealed that six of the strains are of Colombian origin, while one strain (547256) belongs to the high-risk clone ST773, previously unidentified in Colombia. Genome size ranged from 6 to 7.4 Mbp, indicating differences in genetic content among strains. Phylogenomic analysis confirmed that five strains belong to a multidrug-resistant (MDR) group, while one strain (572897) showed high alignment with a laboratory strain, and strain 547256 was not associated with any specific clade. Clinically, 100% of strains showed carbapenem resistance, resistance genes, and virulence factors that make them difficult to treat. This study provides key insights into the genetic diversity and resistance patterns of P. aeruginosa in this region, underscoring the need to monitor high-risk clones and optimize therapeutic strategies.

Genetic Diversity in Antimicrobial Resistance Determinants Among Pathogenic Pseudomonas aeruginosa in India

The drastic rise in antibiotic resistance has become a global challenge, including India, due to high morbidity. The delayed identification and lack of treatment are the major causes of death. However, there is a shortage of precise information on the specific resistance pattern and sequence types of Pseudomonas aeruginosa from India that can help in diagnostics and therapy. A total of 16 clinical isolates were collected from the western region of India, along with 181 P. aeruginosa genomes of India from public database were retrieved and thoroughly analysed for antibiotics resistance determinants for associated sequence types and O-serotypes using different bioinformatics tools. Of all collected isolates (n = 16), 9 were extensively drug-resistant (XDR), 6 were multidrug-resistant (MDR), and only 1 isolate was susceptible to selected antibiotics. ST357 (n = 23; 11.6%) was the most frequent, followed by ST308, and ST1203. In serotyping, O11 (n = 85; 43%) was most prevalent. A novel ST4937 was reported and submitted to PubMLST. blaNDM-1 carbapenemase was found in (n = 45; 22.8%) isolates, whereas class D blaOXA-488 was present in (n = 38; 19.2%) isolates, further, several variants were found for class C blaPDC genes, where blaPDC-3 and blaPDC-19a were found to be predominant. We discovered that the amounts of carbapenemases and extended spectrum beta-lactamases (ESBL) genes were lower in India. This can be a relief sometimes, but a rise in high-risk clones could lead to longer hospital stays and more deaths. Therefore, ongoing surveillance of these strains is essential for effective infection management and containment of their spread.

Spatial transcriptomics identifies novel Pseudomonas aeruginosa virulence factors

To examine host-pathogen interactions, we leveraged a dual spatial transcriptomics approach that simultaneously captures the expression of Pseudomonas aeruginosa genes alongside the entire host transcriptome using a murine model of ocular infection. This method revealed differential pathogen- and host-specific gene expression patterns in infected corneas, which generated a unified transcriptional map of infection. By integrating these data, we developed a predictive ridge regression model trained on images from infected tissues. The model achieved an R2 score of 0.923 in predicting bacterial burden distributions and identifying novel biomarkers associated with disease severity. Among iron acquisition pathogen-specific gene transcripts that showed significant enrichment at the host-pathogen interface, we discovered the novel virulence mediator PA2590, which was required for bacterial virulence. This study therefore highlights the power of combining bacterial and host spatial transcriptomics to uncover complex host-pathogen interactions and identify potentially druggable targets.

Establishment and characterization of persistent Pseudomonas aeruginosa infections in air-liquid interface cultures of human airway epithelial cells

Bacteria exhibit distinct behaviors in laboratory settings compared to infection environments. The presence of host cells induces changes in bacterial activity, while pathogens trigger immune responses that shape the microenvironment. Studying infection dynamics by microscopy, cytokine screening, and dual RNA sequencing in an air-liquid interface model, we found that prolonged Pseudomonas aeruginosa colonization of airway epithelium led to a pro-inflammatory response, consistent across P. aeruginosa strains, despite differences in the dynamics of this response. Concurrently, P. aeruginosa formed non-attached aggregates on the apical side of the cell layer and upregulated genes involved in biofilm formation and virulence. Notably, there was remarkable resemblance between the P. aeruginosa transcriptional profile in our model and that previously reported upon host cell contact. Developing a platform that replicates host microenvironments is vital not only for gaining deeper insights into the interplay between host and pathogen but also for evaluating therapeutic strategies in conditions that closely mirror clinical environments.

Genetic and phenotypic analysis of the virulence plasmid of a non-Shigatoxigenic enteroaggregative Escherichia coli O104:H4 outbreak strain

Enteroaggregative Escherichia coli O104:H4 is best known for causing a worldwide outbreak in 2011 due to the acquisition of a Shiga-like toxin alongside traditional enteroaggregative virulence traits; however, whilst the 2011 outbreak strain has been well studied, the virulence plasmid of O104:H4 has been subjected to far less experimental analysis. In this paper, we analyse the genetic and phenotypic contribution of the pAA virulence plasmid to a non-Shigatoxigenic O104:H4 strain (1070/13) that was nonetheless implicated in a substantial UK outbreak in 2013. We find that pAA1070 is 99.95% identical across 88% of the plasmid sequence to pTY2 from the 2011 outbreak strain and has a copy number of ~2-3 plasmid molecules per chromosome. We demonstrate that pAA1070 carries a functional CcdAB plasmid addiction system that only marginally impacts its stability under the conditions tested. None of the other toxin-antitoxin systems encoded by the plasmid appear to be functional, though we note a surprisingly high stability of the plasmid in vitro regardless. We demonstrate the expected contribution of pAA1070 to intestinal cell adhesion but find that it does not contribute to biofilm formation. When assessing the impact of pAA1070 on motility, we discovered a region of the O104:H4 chromosome that can be excised, abolishing motility via truncation of the fliR gene. Ultimately, this work demonstrates the importance of mobile genetic elements to enteroaggregative E. coli as a pathovar in its own right and highlights the complexity but necessity of experimentally characterizing genuine outbreak strains rather than laboratory strains in order to understand virulence phenotypes.

In-depth genome and comparative genome analysis of a metal-resistant environmental isolate Pseudomonas aeruginosa S-8

The present study aimed to identify the mechanisms underlying the survival of an environmental bacterium originally isolated from the waste-contaminated soil of Jhiri, Ranchi, India. Based on 16S rRNA, ANI (average nucleotide identity), and BLAST Ring Image Generator (BRIG) analysis, the isolated strain was identified as Pseudomonas aeruginosa. The present study extends the characterization of this bacterium through genomic and comparative genomic analysis to understand the genomic features pertaining to survival in stressed environments. The sequencing of the bacterium at Illumina HiSeq platform revealed that it possessed a 6.8 Mb circular chromosome with 65.9% GC content and 63 RNAs sequence. The genome also harbored several genes associated to plant growth promotion i.e. phytohormone and siderophore production, phosphate solubilization, motility, and biofilm formation, etc. The genomic analysis with online tools unraveled the various genes belonging to the bacterial secretion system, antibiotic resistance, virulence, and efflux pumps, etc. The presence of biosynthetic gene clusters (BCGs) indicated that large numbers of genes were associated to non-ribosomal synthesized peptide synthetase, polyketide synthetase, and other secondary metabolite production. Additionally, its genomes encode various CAZymes such as glycoside hydrolases and other genes associated with lignocellulose breakdown, suggesting that strain S-8 have strong biomass degradation potential. Furthermore, pan-genome analysis based on a comparison of whole genomes showed that core genome represented the largest part of the gene pools. Therefore, genome and comparative genome analysis of Pseudomonas strains is valuable for understanding the mechanism of resistance to metal stress, genome evolution, HGT events, and therefore, opens a new perspective to exploit a newly isolated bacterium for biotechnological applications.

Pseudomonads coordinate innate defense against viruses and bacteria with a single regulatory system

Bacterial cells live under the constant existential threats imposed by other bacteria and viruses. Their mechanisms for contending with these threats are well documented; however, the regulation of these diverse defense elements remains poorly understood. Here we show that bacteria can mount a genome-wide, coordinated, and highly effective immune response against bacterial and viral threats using a single regulatory pathway. Bioinformatic analyses revealed that Pseudomonas species broadly possess a specialized form of the Gac/Rsm regulatory pathway (GRP), which our prior work in Pseudomonas aeruginosa implicated in activating interbacterial antagonism defense mechanisms in response to neighbor cell death. Proteomic studies comparing GRP-activated and -inactivated strains derived from diverse Pseudomonas species showed that the pathway regulates a large and variable suite of factors implicated in defense against both bacterial and phage threats. Focusing on P. protegens, we identify profound phenotypic consequences of these factors against multiple forms of bacterial antagonism and several phage. Together, our results reveal that bacteria, like more complex organisms, couple danger sensing to the activation of an immune system with antibacterial and antiviral arms.

Multifunctional Thick Films Obtained by Electrodeposition of 1,8-Dihydroxynaphtalene, an Allomelanin Precursor

The deposition of conformal films from redox-active biological molecules, such as catechols, catecholamines, and other polyphenols, has demonstrated great versatility in terms of the substrate used. Precursors of allomelanins, mainly found in plants and fungi, have been largely overlooked as precursors for the design of conformal and robust coatings. Moreover, their potential application for the electrodeposition of films on conductive substrates has not yet been investigated. Here, the electrodeposition by cyclic voltammetry and chronoamperometry of 1,8-dihydroxynaphthalene (1,8-DHN), a precursor of allomelanin, onto gold electrodes and onto Co-Cr alloys from aqueous solution-ethanol mixtures yields films with potential sweep rate tunable thickness and swelling. The resulting films are antioxidants, and the reservoir of antioxidant moieties is not limited to their surface but also extends into the bulk of the film. In addition, the films produced after a limited energy supply (in the potential window -1 to +1 V vs Ag/AgCl) are strongly antimicrobial against two strains of Pseudomonas aeruginosa without further post-deposition treatment. In addition, their mechanical properties allow them to be detached from their substrates as free-standing films, opening avenues for diverse applications in biomedicine, energy storage, catalysis, sensing, and optoelectronics.

Quantification of Pseudomonas aeruginosa biofilms using electrochemical methods

Currently, 2.29% of deaths worldwide are caused by antimicrobial resistance (AMR), compared to 1.16% from malaria and 1.55% from human immunodeficiency virus and acquired immunodeficiency syndrome. Furthermore, deaths resulting from AMR are projected to increase to more than 10 million per annum by 2050. Biofilms are common in hospital settings, such as medical implants, and pose a particular problem as they have shown resistance to antibiotics up to 1000-fold higher than planktonic cells because of dormant states and reduced growth rates. This is compounded by the fact that many antibiotics target mechanisms of active metabolism and are therefore less effective. The work presented here aimed to develop a method for biofilm quantification, which could be translated into the clinical setting, as well as used in the screening of antibiofilm agents. This was carried out alongside crystal violet staining, as a published point of reference. This work builds upon work previously presented by Dunphy et al., in which the authors attempted to quantify the biofilm formation of Pseudomonas aeruginosa strain using hyperspectral imaging. Here, using electrochemical impedance spectroscopy and square wave voltammetry, the biofilm formation of two P. aeruginosa strains was detected within an hour after seeding P. aeruginosa on the sensor. A 40% decrease in impedance modulus was shown when P. aeruginosa biofilm had formed, compared to the media-only control. As such, this work offers a starting point for the development of real-time biofilm sensing technologies, which can be translated into implantable materials.

Regulation of antibiotic persistence and pathogenesis in Acinetobacter baumannii by glutamate and histidine metabolic pathways

BACKGROUND

Metabolite production is essential for the proliferation and environmental adaptation of all living organisms. In pathogenic bacteria, metabolite exchange during host infection can regulate their physiology and virulence. However, there is still much unknown about which specific metabolic pathways in pathogenic bacteria respond to changes in the environment during infections. This study examines how pathogenic bacterium Acinetobacter baumannii uses particular metabolic pathways to regulate its ability to antibiotic persistence and pathogenesis.

RESULTS

To determine specific metabolic pathways in pathogenic antibiotic resistance bacteria, metabolite profiles of bacteria were constructed using ultraperformance liquid chromatography/quadrupole time-of-flight mass spectrometry and multivariate statistical analysis. A. baumannii generates amino acid derivative metabolites, which are precursors for fatty acid production. Comparative genomic analysis identified specific genes regulating the production of these metabolites and fatty acids in A. baumannii. Inactivation of genes involved in glutamate metabolism, gdhA, aspB, murI1, and racD, impairs antibiotic persistence, while inactivation of the hisC gene, encoding histidinol - phosphate aminotransferase enzyme in histidine metabolic pathway, increases bacterial survival inside macrophages during infections.

CONCLUSIONS

This study reports that A. baumannii regulates antibiotic persistence and pathogenesis through glutamate and histidine metabolic pathways, respectively. These findings suggest that specific metabolic pathways regulate bacterial pathogenesis and antibiotic persistence during infections, providing potential therapeutic targets for pathogenic bacteria.

In vitro potentiation of tetracyclines in Pseudomonas aeruginosa by RW01, a new cyclic peptide

The pipeline for new drugs against multidrug-resistant Pseudomonas aeruginosa remains limited, highlighting the urgent need for innovative treatments. New strategies, such as membrane-targeting molecules acting as adjuvants, aim to enhance antibiotic effectiveness and combat resistance. RW01, a cyclic peptide with low antimicrobial activity, was selected as an adjuvant to enhance drug efficacy through membrane permeabilization. RW01's activity was evaluated via antimicrobial susceptibility testing in combination with existing antibiotics on 10 P. aeruginosa strains and analog synthesis. Synergy was assessed using checkerboard assays, and one-step mutants were generated to identify altered pathways through whole-genome sequencing and variant analysis. Permeabilizing activity was studied using flow cytometry and real-time fluorescence measurement. In vivo toxicity was assessed in female C57BL/6J mice, and possible interaction with mouse serum was also evaluated. Susceptibility testing revealed specific synergy with tetracyclines, with up to a 16-fold reduction in minimum inhibitory concentrations. Sequencing revealed that resistance to the RW01-minocycline combination involved mutations in the pmrB gene, affecting outer membrane lipopolysaccharide composition. This was further confirmed by the identification of cross-resistance to colistin in these mutants. RW01 reduced the mutant prevention concentration of minocycline from 64 to 8 mg/L. RW01 was demonstrated to enhance membrane permeabilization and therefore minocycline uptake with statistical significance. Synthetic derivatives of RW01 showed a complete loss of activity, highlighting the importance of RW01's D-proline(NH2) residue. No acute or cumulative in vivo toxicity was observed in mice. These findings suggest that RW01 could revitalize obsolete antimicrobials and potentially expand therapeutic options against multidrug-resistant P. aeruginosa.

Anaerobiosis and Mutations Can Reduce Susceptibility of Pseudomonas aeruginosa to Tobramycin Without Reducing the Cellular Concentration of the Antibiotic

Chronic infections of Pseudomonas aeruginosa are commonly treated with tobramycin. During infections, the bacteria can exist under conditions of oxygen deprivation that render them less susceptible to this antibiotic. The aims of this research were to investigate the genetic basis of tobramycin resistance under anaerobic conditions, and to investigate the effects of anaerobiosis and mutations on the cellular concentration of tobramycin. Ten mutants with lowered susceptibility to tobramycin than wild-type bacteria were evolved from a laboratory reference strain under anaerobic conditions. Mutations were identified by genome sequencing. Mutations had arisen most frequently in the fusA1 gene that encodes elongation factor EF-G1A and in genes involved in twitching motility. Cellular concentrations of tobramycin were then measured. Mutations in fusA1 or absence of the MexXY efflux pump that is associated with tobramycin resistance did not alter the cellular tobramycin concentration under either anaerobic or aerobic conditions. Anaerobic growth reduced the cellular concentration of tobramycin, relative to aerobically grown bacteria, in some but not all of five tested P. aeruginosa isolates. Overall, our findings indicate that anaerobiosis and mutations that reduce aminoglycoside effectiveness do not lower the cellular concentration of antibiotic but instead reduce susceptibility through other mechanisms.

Chronic wounds and adaptive Pseudomonas aeruginosa: A phenotypic and genotypic characterization

Phenotypic and genetic diversity is found in varying prevalence in clinical populations where beneficial adaptations enable the bacteria to avoid recognition and eradication by the host immune system. This study aimed to investigate the presence of Pseudomonas aeruginosa in chronic venous leg ulcers wounds over an 8-week time course. This was performed using genomic and phenotypic approaches to understand the survival and persistence of Pseudomonas strains. The findings of this study show that the two patients were colonized with a recurring P. aeruginosa genotype with only minor phenotypic differences and few SNP differences, suggesting that the Pseudomonas isolates present in the wound can survive and proliferate in the host's hostile environment. The results provided from this study will allow us to understand P. aeruginosa colonization during a 8 week time period.

Molecular Markers Specific for the Pseudomonadaceae Genera Provide Novel and Reliable Means for the Identification of Other Pseudomonas Strains/spp. Related to These Genera

Background/Objectives: Taxon-specific conserved signature indels (CSIs) exhibit a strong predictive ability of being found in other members of specific taxa/genera. Recently, multiple exclusively shared CSIs were identified for several newly described Pseudomonadaceae genera (viz. Aquipseudomonas, Atopomonas, Caenipseudomonas, Chryseomonas Ectopseudomonas, Geopseudomonas, Halopseudomonas, Metapseudomonas, Phytopseudomonas, Serpens, Stutzerimonas, Thiopseudomonas, and Zestomonas). This study examines the potential applications of these CSIs for identifying other Pseudomonas spp. (strains) related to these genera. Methods: This work utilized the AppIndels.com server, which uses information regarding the presence of known taxon-specific CSIs in a genome for predicting its taxonomic affiliation. For this purpose, sequence information for different CSIs specific for the Pseudomonadaceae species/genera were added to the server's database. Results: The AppIndels server was used to predict the taxonomic affiliation of 1972 genomes of unclassified Pseudomonas spp. (strains/isolates). Based upon finding a significant number of CSIs matching a specific taxon, the AppIndels server made positive predictions regarding the taxonomic affiliation of 299 examined genomes into the following clades/genera: Pseudomonas sensu stricto clade (46), Pseudomonas aeruginosa (64), Ectopseudomonas (46), Chryseomonas (32), Stutzerimonas (31), Metapseudomonas (22), Aquipseudomonas (21), Phytopseudomonas (17), Halopseudomonas (9), Geopseudomonas (4), Thiopseudomonas (3), Serpens (2), and Caenipseudomonas and Zestomonas (1 each). Phylogenetic studies confirmed that the taxonomic predictions by the server were 100% accurate. Conclusions: Our results demonstrate that the CSIs specific for Pseudomonadaceae species/genera, in conjunction with the AppIndels server, provides a novel and useful tool for identifying other species/strains affiliated with these species/genera. Phylogenetic studies suggest that many examined Pseudomonas strains constitute novel species in the indicated genera.

Impairing protein-protein interactions in an essential tRNA modification complex: An innovative antimicrobial strategy against Pseudomonas aeruginosa

Protein-protein interactions (PPIs) have been recognized as a promising target for the development of new drugs, as proved by the growing number of PPI modulators reaching clinical trials. In this context, peptides represent a valid alternative to small molecules, owing to their unique ability to mimic the target protein structure and interact with wider surface areas. Among the possible fields of interest, bacterial PPIs represent an attractive target to face the urgent necessity to fight antibiotic resistance. Growing attention has been paid to the YgjD/YeaZ/YjeE complex responsible for the essential t6A37 tRNA modification in bacteria. We previously identified an α-helix on the surface of Pseudomonas aeruginosa YeaZ, crucial for the YeaZ-YeaZ homodimer formation and the conserved YeaZ-YgjD interactions. Herein, we present our studies for impairing the PPIs involved in the formation of the YeaZ dimers through synthetic peptide derivatives of this helical moiety, both in vitro with purified components and on P. aeruginosa cells. Our results proved the possibility of targeting those PPIs which are usually essential for protein functioning and thus are refractory to mutational changes and antibiotic resistance development.

Digital insights into Pseudomonas aeruginosa PBH03: in-silico analysis for genomic toolbox and unraveling cues for heavy metal bioremediation

BACKGROUND

The genomes of publicly available electroactive Pseudomonas aeruginosa strains are currently limited to in-silico analyses. This study analyzed the electroactive Pseudomonas aeruginosa PBH03 genome using comparative in-silico studies for biotechnological applications.

OBJECTIVE

Comparative in-silico and experimental analyses were conducted to identify the novel traits of P. aeruginosa PBH03 by genome sequencing.

METHODS

The publicly available genomes of Pseudomonas aeruginosa strains (PA01, PA14, and KRP1) were used for a comparative in-silico study with PBH03. Genome assembly, annotation, phylogenetic analysis, metabolic reconstruction, and comparative functional genes analysis were conducted using bioinformatics tools. The experimental analyses were conducted to validate the heavy metal resistance (Hg and Cu), salinity tolerance levels of PBH03, and acetate assimilation under microaerobic conditions.

RESULTS

Computational analysis showed that the PBH03 genome had a size of 6.8 Mb base pairs with a GC content of 65.7%. Whole genome annotation identified the unique genes absent in the previously sequenced Pseudomonas aeruginosa genomes. These genes were associated with resistance to heavy metals, such as Cu, Hg, As, and a Co-Zn-Cd efflux system. In addition, clustered, regularly interspaced short palindromic repeats, transposable elements, and conjugative transfer proteins were observed in the clustering-based systems. The strain exhibited resistance to Hg (150 mg/L) and Cu (500 mg/L) and showed growth at salinity levels of 40 g/L (typical sea/ocean levels). PBH03 could consume acetate up to 110 mM.

CONCLUSION

Integrating in-silico and experimental data highlights the intriguing adaptive genomic qualities of PBH03, making it a promising candidate for various biotechnological applications.

RhlR-mediated cooperation in cystic fibrosis-adapted isolates of Pseudomonas aeruginosa

Pseudomonas aeruginosa uses quorum sensing (QS) to regulate the expression of dozens of genes, many of which encode shared products, called "public goods." P. aeruginosa possesses two complete acyl-homoserine lactone (AHL) QS circuits: the LasR-I and RhlR-I systems. Canonically, these systems are hierarchically organized: RhlR-I activity depends on LasR-I activation. However, in contrast to laboratory strains, isolates from people with cystic fibrosis can engage in AHL QS using only the transcription factor RhlR. In these isolates, RhlR regulates AHL QS and the production of secreted public goods, such as the exoprotease elastase, which are accessible to both producing and non-producing cells. When P. aeruginosa strains that use LasR to regulate elastase production are grown on casein as the sole carbon and energy source, LasR-null mutant "cheaters" commonly arise in populations due to a selective growth advantage. We asked if these social dynamics might differ in "RhlR cooperators": populations that use RhlR, not LasR, to regulate public goods. We passaged RhlR cooperators from several genetic backgrounds in casein broth. We found that cheaters emerged among most RhlR cooperators. However, in one isolate background, E90, RhlR-null mutants were dramatically outcompeted by RhlR cooperators. In this background, the mechanism by which RhlR mutants are outcompeted by RhlR cooperators is AHL-dependent and occurs in stationary phase but is not the same as previously described "policing" mechanisms. Our data suggest that cheating, or the lack thereof, does not explain the lack of RhlR mutants observed in most infection environments.IMPORTANCEQuorum sensing (QS) mutants arise in a variety of populations of bacteria, but mutants of the gene encoding the transcription factor RhlR in Pseudomonas aeruginosa appear to be infrequent. Our work provides insight on the mechanisms through which RhlR-mediated cooperation is maintained in a LasR-null population of P. aeruginosa. Characterizing the selective pressure(s) that disfavor mutations from occurring in RhlR may enhance our understanding of P. aeruginosa evolution in chronic infections and potentially guide the development of therapeutics targeting the RhlR-I QS circuit.

Proteomic profiling of zinc homeostasis mechanisms in Pseudomonas aeruginosa through data-dependent and data-independent acquisition mass spectrometry

Zinc is central to the function of many proteins, yet the mechanisms of zinc homeostasis and their interplay with other cellular systems remain underexplored. In this study, we employ data-dependent acquisition (DDA) and data-independent acquisition (DIA) mass spectrometry to investigate proteome changes in Pseudomonas aeruginosa under conditions of different zinc availability. Using these methods, we detected 2143 unique proteins, 1578 of which were identified by both DDA and DIA. We demonstrated that most of the previously described Zn homeostasis systems exhibit proteomic responses that follow similar trends to those seen in transcriptomics studies. However, some proteins that are considered instrumental in Zn homeostasis, notably those in Zn transporter ZnuABC, were not detected by our methods, although other proteins of other uptake systems were abundant. Furthermore, changes in abundance of multiple Zn-metalloproteins and Zn-independent homologs were clearly observable, with respective increases and decreases when Zn was provided, though the magnitude of these changes varied. Most of the Zn-metalloproteins observed were located in one of two Zur-regulated operons between PA5534 and PA5541. This study provides a view of Zn homeostasis mechanisms that is complementary to existing transcriptomics investigations: as gene transcripts are not strictly proportional to the actual distribution of proteins within a cell, analysis of the proteome offers another way to assess the relative use and importance of similar or ostensibly redundant systems in different conditions and can highlight shifts in metal prioritization between metalloproteins.

Complete genome sequence of Pseudomonas aeruginosa YK01, a sequence type 16 isolated from a patient with keratitis

OBJECTIVES

Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, is frequently associated with multidrug resistance and global epidemic outbreaks, contributing significantly to morbidity and mortality in hospitalized patients. However, P. aeruginosa belonging to the sequence type (ST) 16 was rarely reported. Here, this report presents the complete genome sequence of YK01, a ST16 P. aeruginosa isolate from a patient with keratitis. The complete reference genome of P. aeruginosa YK01 is expected to provide valuable data for investigating its genomic population, enhancing understanding of genetic basis of P. aeruginosa species complex.

DATA DESCRIPTION

A complete genome of 6.3 Mb was obtained for P. aeruginosa YK01 by combining Illumina 150-bp short reads and Nanopore long reads. The assembly is fully complete with chromosomal genome size of 6,183,266 bp, presenting a GC content of 66.7%, and a plasmid with the size of 46,067 bp, presenting GC content of 59.0%. Predicted chromosomal genomic features include 5,709 CDS, 12 rRNAs, 63 tRNAs, 4 ncRNAs, and 5,788 genes. To our knowledge, this genome data represents the first complete genome of P. aeruginosa ST16, providing crucial information for further comparative genome analysis.

Bisubstrate Analog Inhibitors of DXP Synthase Show Species Specificity

1-Deoxy-d-xylulose 5-phosphate synthase (DXPS) is a unique thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the formation of DXP, a branchpoint metabolite required for the biosynthesis of vitamins and isoprenoids in bacterial pathogens. DXPS has relaxed substrate specificity and utilizes a gated mechanism, equipping DXPS to sense and respond to diverse substrates. We speculate that pathogens utilize this distinct gated mechanism in different ways to support metabolic adaptation during infection. DXPS is susceptible to time-dependent inhibition by bisubstrate analogs. We suggest that potential differences in the ligand-gated mechanism that may accompany alternative activities of DXPS homologues may enable the development of species-specific bisubstrate analog inhibitors. Here, we evaluate known bisubstrate analog inhibitors of Escherichia coli DXPS (EcDXPS) against DXPS from Pseudomonas aeruginosa (PaDXPS), a Gram-negative pathogen with a remarkable capacity to adapt to diverse environments. Our results indicate that these inhibitors are significantly less potent against PaDXPS compared to EcDXPS. Acceptor site residues that stabilize the phosphonolactyl-ThDP adduct (PLThDP) of bisubstrate analog d-PheTrAP on EcDXPS are not as critical for stabilization of this PLThDP adduct on PaDXPS. Substitution of EcR99 or the analogous PaR106 reduces the potency of both d-PheTrAP and the simpler BAP scaffold, suggesting a common role of these arginine residues in stabilizing PLThDP adducts. However, although EcR99 is required for potent, time-dependent inhibition of EcDXPS by d-PheTrAP, PaR106 does not appear to govern slow-onset inhibition. This work demonstrates that species-specific targeting of DXPS by bisubstrate analogs is possible and highlights mechanistic differences that should be considered in the design of homologue-specific inhibitors, toward narrow-spectrum approaches targeting DXPS.

Prophages are Infrequently Associated With Antibiotic Resistance in Pseudomonas aeruginosa Clinical Isolates

Lysogenic bacteriophages can integrate their genome into the bacterial chromosome in the form of a prophage and can promote genetic transfer between bacterial strains in vitro . However, the contribution of lysogenic phages to the incidence of antimicrobial resistance (AMR) in clinical settings is poorly understood. Here, in a set of 186 clinical isolates of Pseudomonas aeruginosa collected from respiratory cultures from 82 patients with cystic fibrosis (CF), we evaluate the links between prophage counts and both genomic and phenotypic resistance to six anti-pseudomonal antibiotics: tobramycin, colistin, ciprofloxacin, meropenem, aztreonam, and piperacillin-tazobactam. We identified 239 different prophages in total. We find that P. aeruginosa isolates contain on average 3.06 +/- 1.84 (SD) predicted prophages. We find no significant association between the number of prophages per isolate and the minimum inhibitory concentration (MIC) for any of these antibiotics. We then investigate the relationship between particular prophages and AMR. We identify a single lysogenic phage associated with phenotypic resistance to the antibiotic tobramycin and, consistent with this association, we observe that AMR genes associated with resistance to tobramycin are more likely to be found when this prophage is present. However we find that they are not encoded directly on prophage sequences. Additionally, we identify a single prophage statistically associated with ciprofloxacin resistance but do not identify any genes associated with ciprofloxacin phenotypic resistance. These findings suggest that prophages are only infrequently associated with the AMR genes in clinical isolates of P. aeruginosa .

Importance

Antibiotic-resistant infections of Pseudomonas aeruginosa , a leading pathogen in patients with Cystic Fibrosis (CF) are a global health threat. While lysogenic bacteriophages are known to facilitate horizontal gene transfer, their role in promoting antibiotic resistance in clinical settings remains poorly understood. In our analysis of 186 clinical isolates of P. aeruginosa from CF patients, we find that prophage abundance does not predict phenotypic resistance to key antibiotics but that specific prophages are infrequently associated with tobramycin resistance genes. In addition, we do not find antimicrobial resistance (AMR) genes encoded directly on prophages. These results highlight that while phages can be associated with AMR, phage-mediated AMR transfer may be rare in clinical isolates and difficult to identify. This work is important for future efforts on mitigating AMR in Cystic Fibrosis and other vulnerable populations affected by Pseudomonas aeruginosa infections and advances our understanding of bacterial-phage dynamics in clinical infections.

Dual RNA sequencing of a co-culture model of Pseudomonas aeruginosa and human 2D upper airway organoids

Pseudomonas aeruginosa is a Gram-negative bacterium that is notorious for airway infections in cystic fibrosis (CF) subjects. Bacterial quorum sensing (QS) coordinates virulence factor expression and biofilm formation at population level. Better understanding of QS in the bacterium-host interaction is required. Here, we set up a new P. aeruginosa infection model, using 2D upper airway nasal organoids that were derived from 3D organoids. Using dual RNA-sequencing, we dissected the interaction between organoid epithelial cells and WT or QS-mutant P. aeruginosa strains. Since only a single healthy individual and a single CF subject were used as donors for the organoids, conclusions about CF-specific effects could not be deduced. However, P. aeruginosa induced epithelial inflammation, whereas QS signaling did not affect the epithelial airway cells. Conversely, the epithelium influenced infection-related processes of P. aeruginosa, including QS-mediated regulation. Comparison of our model with samples from the airways of CF subjects indicated that our model recapitulates important aspects of infection in vivo. Hence, the 2D airway organoid infection model is relevant and may help to reduce the future burden of P. aeruginosa infections in CF.

Inovirus-Encoded Peptides Induce Specific Toxicity in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a common opportunistic pathogen associated with nosocomial infections. The primary treatment for infections typically involves antibiotics, which can lead to the emergence of multidrug-resistant strains. Therefore, there is a pressing need for safe and effective alternative methods. Phage therapy stands out as a promising approach. However, filamentous prophages (Pfs) commonly found in P. aeruginosa encode genes with phage defense activity, thereby reducing the efficacy of phage therapy. Through a genomic analysis of the Pf4 prophage, we identified a 102 bp gene co-transcribed with the upstream gene responsible for phage release (zot gene), giving rise to a 33-amino-acid polypeptide that we have named Pf4-encoded toxic polypeptide (PftP4). The overexpression of PftP4 demonstrated cellular toxicity in P. aeruginosa, with subcellular localization indicating its presence in the cell membrane and a subsequent increase in membrane permeability. Notably, PftP4 homologues are found in multiple Pf phages and exhibit specificity in their toxicity towards P. aeruginosa among the tested bacterial strains. Our study reveals that the novel Pf-encoded polypeptide PftP4 has the potential to selectively target and eradicate P. aeruginosa, offering valuable insights for combating P. aeruginosa infections.

Pseudomonas aeruginosa as a model bacterium in antiphage defense research

Bacteriophages, or phages, depend on their bacterial hosts for proliferation, leading to a coevolutionary relationship characterized by on-going arms races, where bacteria evolve diverse antiphage defense systems. The development of in silico methods and high-throughput screening techniques has dramatically expanded our understanding of bacterial antiphage defense systems, enormously increasing the known repertoire of the distinct mechanisms across various bacterial species. These advances have revealed that bacterial antiphage defense systems exhibit a remarkable level of complexity, ranging from highly conserved to specialized mechanisms, underscoring the intricate nature of bacterial antiphage defense systems. In this review, we provide a concise snapshot of antiphage defense research highlighting two preponderantly commandeered approaches and classification of the known antiphage defense systems. A special focus is placed on the model bacterial pathogen, Pseudomonas aeruginosa in antiphage defense research. We explore the complexity and adaptability of these systems, which play crucial roles in genome evolution and adaptation of P. aeruginosa in response to an arsenal of diverse phage strains, emphasizing the importance of this organism as a key emerging model bacterium in recent antiphage defense research.

Hypermutability bypasses genetic constraints in SCV phenotypic switching in Pseudomonas aeruginosa biofilms

Biofilms are critical in the persistence of Pseudomonas aeruginosa infections, particularly in cystic fibrosis patients. This study explores the adaptive mechanisms behind the phenotypic switching between Small Colony Variants (SCVs) and revertant states in P. aeruginosa biofilms, emphasizing hypermutability due to Mismatch Repair System (MRS) deficiencies. Through experimental evolution and whole-genome sequencing, we show that both wild-type and mutator strains undergo parallel evolution by accumulating compensatory mutations in factors regulating intracellular c-di-GMP levels, particularly in the Wsp and Yfi systems. While wild-type strains face genetic constraints, mutator strains bypass these by accessing alternative genetic pathways regulating c-di-GMP and biofilm formation. This increased genetic accessibility, driven by higher mutation rates and specific mutational biases, supports sustained cycles of SCV conversion and reversion. Our findings underscore the crucial role of hypermutability in P. aeruginosa adaptation, with significant implications for managing persistent infections in clinical settings.

Anti-Biofilm Agents to Overcome Pseudomonas aeruginosa Antibiotic Resistance

Pseudomonas aeruginosa is one of world's most threatening bacteria. In addition to the emerging prevalence of multi-drug resistant (MDR) strains, the bacterium also possesses a wide variety of virulence traits that worsen the course of the infections. Particularly, its ability to form biofilms that protect colonies from antimicrobial agents is a major cause of chronic and hard-to-treat infections in immune-compromised patients. This protective barrier also ensures cell growth on abiotic surfaces and thus enables bacterial survival on medical devices. Hence, as the WHO alerted to the need to develop new treatments, the use of anti-biofilm agents (ABAs) appeared as a promising approach. Given the selection pressure imposed by conventional antibiotics, a new therapeutic strategy has emerged that aims at reducing bacterial virulence without inhibiting cell growth. So-called anti-virulence agents (AVAs) would then restore the efficacy of conventional antibiotics (ATBs) or potentiate the effectiveness of the immune system. The last decade has seen the development of ABAs as AVAs against P. aeruginosa. This review aims to highlight the design strategy and critical features of these molecules to pave the way for further discoveries of highly potent compounds.

Whole-Genome Sequencing of Resistance, Virulence and Regulation Genes in Extremely Resistant Strains of Pseudomonas aeruginosa

BACKGROUND/OBJECTIVES

Pseudomonas aeruginosa is a clinically significant opportunistic pathogen, renowned for its ability to acquire and develop diverse mechanisms of antibiotic resistance. This study examines the resistance, virulence, and regulatory mechanisms in extensively drug-resistant clinical strains of P. aeruginosa.

METHODS

Antibiotic susceptibility was assessed using the Minimum Inhibitory Concentration (MIC) method, and whole-genome sequencing (WGS) was performed on the Illumina NovaSeq platform.

RESULTS

The analysis demonstrated a higher prevalence of virulence genes compared to resistance and regulatory genes. Key virulence factors identified included secretion systems, motility, adhesion, and biofilm formation. Resistance mechanisms observed comprised efflux pumps and beta-lactamases, while regulatory systems involved two-component systems, transcriptional regulators, and sigma factors. Additionally, phenotypic profiles were found to correlate with resistance genes identified through genotypic analysis.

CONCLUSIONS

This study underscores the significant resistance and virulence of the clinical P. aeruginosa strains analyzed, highlighting the urgent need for alternative strategies to address infections caused by extensively drug-resistant bacteria.

Microbial chemotaxis in degradation of xenobiotics: Current trends and opportunities

Chemotaxis, the directed movement of microbes in response to chemical gradients, plays a crucial role in the biodegradation of xenobiotics, such as pesticides, industrial chemicals, and pharmaceuticals, which pose significant environmental and health risks. Emerging trends in genomics, proteomics, and synthetic biology have advanced our understanding and control of these processes, thereby enabling the development of engineered microorganisms with tailored chemotactic responses and degradation capabilities. This process plays an essential physiological role in processes, such as surface sensing, biofilm formation, quorum detection, pathogenicity, colonization, symbiotic interactions with the host system, and plant growth promotion. Field applications have demonstrated the potential of bioremediation for cleaning contaminated environments. Therefore, it helps to increase the bioavailability of pollutants and enables bacteria to access distantly located pollutants. Despite considerable breakthroughs in decoding the regulatory mechanisms of bacterial chemotaxis, there are still gaps in knowledge that need to be resolved to harness its potential for sensing and degrading pollutants in the environment. This review covers the role of bacterial chemotaxis in the degradation of xenobiotics present in the environment, focusing on chemotaxis-based bacterial and microfluidic biosensors for environmental monitoring. Finally, we highlight the current challenges and future perspectives for developing more effective and sustainable strategies to mitigate the environmental impact of xenobiotics.

Point Mutation Analysis of the Drug Efflux Pump MexB in Clinical Isolates of Pseudomonas aeruginosa

The rapid emergence of drug-resistant microbes has recently become a major concern in the medical field. In Pseudomonas aeruginosa, one of the most important mechanisms underlying antibiotic resistance is MexAB-OprM system, increases in this efflux system result in greater resistance to a wide range of drugs, and genetic mutations have been identified as a contributing factor. Thus, this study characterized point mutations in the mexB gene that are common to 39 clinical P. aeruginosa isolates obtained from The Pseudomonas Genome Database. Basic Local Alignment Search Tool (BLAST) was used to compare the mexB gene sequences of those 39 strains with PAO1. The majority of these point mutations were silent mutations without amino acid mutations. Mutations 2730, 495, and 2280, which were abundant in the strains examined, were characterized by greater codon usage after the mutation. A positive correlation has been reported between tRNA levels and codon usage in Escherichia coli, and the same relationship may be present in P. aeruginosa. In this study, the silent mutations observed in many strains mainly involved the substitution of C or G, which resulted in a higher codon usage and stronger binding power after than before the mutation. This change is considered advantageous for survival in the human body by increasing the translation efficiency of the MexB protein. Thus, combining the silent mutation identified in this study with information on the expression level of mexB is expected to be used as an indicator to identify multidrug-resistant P. aeruginosa.