Antibacterial-resistant Pseudomonas aeruginosa: clinical impact and complex regulation of chromosomally encoded resistance mechanisms

Chlorination-induced spread of antibiotic resistance genes in drinking water systems

Chlorine, the most widely utilized disinfectant for drinking water globally, has recently been implicated in facilitating the spread of antibiotic resistance genes (ARGs), raising concerns about its underestimated environmental and ecological risks. However, given the current fragmented research focus and results, a comprehensive understanding of the potential mechanisms and influencing factors behind chlorination-promoted ARGs transmission in drinking water systems is crucial. This work is the first to systematically review the variations in abundance, transmission mechanisms, influencing factors, and mitigation strategies related to ARGs during the chlorination process. The results indicated that chlorination could induce genetic mutations and promote horizontal gene transfer through multiple pathways, including increased reactive oxygen species, enhanced membrane permeability, stimulation of the SOS response, and activation of efflux pumps. In addition, this work delves into significant discoveries regarding the factors affecting ARG transmission in drinking water, such as chlorine concentration, reaction time, disinfection byproducts, pipe materials, biofilms, and the water matrix. A series of effective strategies from water source to point-of-use were proposed aimed at mitigating ARGs transmission risks in the drinking water system. Finally, we address existing challenges and outline future research directions to overcome these bottlenecks. Overall, this review aims to advance our understanding of the role of chlorination in the dissemination of ARGs and to inspire innovative research ideas for optimizing disinfection techniques, minimizing the risks of antibiotic resistance transmission, and enhancing the safety of drinking water.

Outer membrane permeability of Pseudomonas aeruginosa through β-lactams: new evidence on the role of OprD and OpdP porins in antibiotic resistance

Gram-negative bacteria are a major concern for public health, particularly due to the continuous rise of antibiotic resistance. A major factor that helps the development of resistance is the outer membrane that is essential since it acts as a strong permeability barrier to many antibiotics that are effective against other bacteria. In this study, we determine the specific permeability coefficients for various antibiotics in Pseudomonas aeruginosa strains, which differ from each other for their porin expressions. We showed that OprD and OpdP porins contribute both to internalize meropenem and biapenem. Using qRT-PCR, we demonstrated that their expression is dependent of the various phases of cellular growth. We were able to show how the OpdP porin is less expressed in exponential growth phases, while it tends to be produced when the bacterial culture enters into the latent phase, in an inversely proportional way compared to the OprD porin. The deletion of the OpdP porin, in the presence of meropenem at concentrations equivalent to the MIC values, contributes to the selection of carbapenem-resistant strains. Therefore, the presence of mutations/deletions of the OpdP porin should receive greater consideration from a clinical point of view as the use of meropenem at nonoptimal concentrations could lead to the appearance of resistance phenotypes.IMPORTANCECarbapenem-resistant strains of Pseudomonas aeruginosa are among the major threats to public health. The permeability of the outer membrane for the β-lactam antibiotics is one of the major factors that reduce the activity of the antibiotics. In this study, we measure the low permeability coefficient of the P. aeruginosa outer membrane to β-lactams. The methodology we develop to determine the permeability can be applied to other antibiotic families and/or pathogens.

Current innovations in mRNA vaccines for targeting multidrug-resistant ESKAPE pathogens

The prevalence of multidrug-resistant (MDR) ESKAPE pathogens, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa, represents a critical global public health challenge. In response, mRNA vaccines offer an adaptable and scalable platform for immunotherapy against ESKAPE pathogens by encoding specific antigens that stimulate B-cell-driven antibody production and CD8+ T-cell-mediated cytotoxicity, effectively neutralizing these pathogens and combating resistance. This review examines recent advancements and ongoing challenges in the development of mRNA vaccines targeting MDR ESKAPE pathogens. We explore antigen selection, the nuances of mRNA vaccine technology, and the complex interactions between bacterial infections and antibiotic resistance. By assessing the potential efficacy of mRNA vaccines and addressing key barriers to their paraclinical implementation, this review highlights the promising function of mRNA-based immunization in combating MDR ESKAPE pathogens.

Pharmacodynamic interaction of apotransferrin and anti-pseudomonal antibiotics against extensively drug-resistant Pseudomonas aeruginosa in a dynamic PK/PD model

The rise of antibiotic resistance in clinical settings poses a major challenge. Apotransferrin has emerged as a potential non-traditional therapy for combating infections, potentially preventing resistance development while enhancing bactericidal effects. This study evaluated the efficacy of apotransferrin combined with antipseudomonal antibiotics against extensively drug-resistant (XDR) Pseudomonas aeruginosa isolates. Twenty XDR P. aeruginosa clinical isolates were evaluated. Different apotransferrin concentrations were tested to determine the optimal in vitro concentration. Time-kill assays assessed the combined effects of apotransferrin with meropenem or ceftolozane/tazobactam (C/T). A chemostat model using four selected isolates validated the most effective combinations and monitored resistance emergence. Apotransferrin monotherapy did not reduce bacterial load, but its combination with antipseudomonal antibiotics enhanced efficacy. Meropenem activity improved in 10/20 isolates, and C/T activity in 13/20 compared to antibiotic monotherapy. The chemostat model confirmed synergistic interactions between apotransferrin and C/T in two isolates, with additive effects in two others. This combination outperformed the most effective monotherapy in all isolates, with no emergence of new C/T-resistant strains. In conclusion, the combination of apotransferrin with C/T demonstrated superior in vitro efficacy against XDR P. aeruginosa isolates compared to either treatment alone. These findings suggest that apotransferrin could be a valuable adjunctive therapy, enhancing the antimicrobial effects of existing antibiotics and potentially extending their clinical utility.

The virulence trait and genotype distribution amongst the Pseudomonas aeruginosa clinical strains

BACKGROUND

Pseudomonas aeruginosa is notorious for its complex virulence system and rapid adaptive drug resistance. This study aimed to compare the prevalence and genotype distribution of virulence genes in multidrug-sensitive and multidrug-resistant clinical strains of Pseudomonas aeruginosa. It is possible to better understand the genetic characteristics of Pseudomonas aeruginosa and carry out effective treatment and prevention measures.

METHODS

The genes phzS, aprA, plcH, toxA, pilA and exoU were detected amongst 184 clinical strains, whose cytotoxicity and biofilm formation ability were evaluated as well. Phenotypic screening for drug susceptibility was conducted by standard antimicrobial susceptibility test and interpreted according to standards established by CLSI.

RESULTS

A total of 94 multidrug-sensitive and 90 multidrug-resistant isolates were included in this study. Statistically significant relationship was observed in the frequency of the toxA (p = 0.002) and plcH (p = 0.001) genes between multidrug-resistant and multidrug-sensitive strains. Moreover, thirteen genotypes were observed in multidrug-sensitive strains, and seven of them were included in multidrug-resistant groups. There was statistically significant correlation found between the presence of genotype IV (p = 0.001) and genotype VII (p = 0.001) in two subgroups. Additionally, It was found that genotype III isolates exhibited most obvious cytotoxicity, and multidrug-resistant isolates of genotype III showed the most significant cytotoxicity. Moreover, the strains of strong biofilm-formation accounted for a relatively high proportion in genotype III and VI groups.

CONCLUSION

These virulence genes could form abundant genotype varieties, whose overall number is greater in multi-sensitive strains. In addition, particular genotypes were characteristically distributed and exhibited different cytotoxicity and biofilm-formation abilities.

The Interactive Dynamics of Pseudomonas aeruginosa in Global Ecology

Pseudomonas aeruginosa is an opportunistic bacterium widely distributed in both natural and urban environments, playing a crucial role in global microbial ecology. This article reviews the interactive dynamics of P. aeruginosa across different ecosystems, highlighting its capacity for adaptation and resistance in response to environmental and therapeutic pressures. We analyze the mechanisms of antibiotic resistance, including the presence of resistance genes and efflux systems, which contribute to its persistence in both clinical and nonclinical settings. The interconnection between human, animal, and environmental health, within the context of the One Health concept, is discussed, emphasizing the importance of monitoring and sustainable management practices to mitigate the spread of resistance. Through a holistic approach, this work offers insights into the influence of P. aeruginosa on public health and biodiversity.

Impact of Antimicrobial Resistance of Pseudomonas aeruginosa in Urine of Small Companion Animals in Global Context: Comprehensive Analysis

The isolation of multidrug-resistant (MDR) bacteria from the urinary tracts of pets is increasingly common, particularly in animals with concurrent health conditions. Pseudomonas aeruginosa (PA) is one of the most significant antimicrobial-resistant bacteria affecting cats and dogs within the European Union (EU). This study aims to review the prevalence and antimicrobial resistance patterns of PA isolated from urine samples of small animals globally. This pathogen is known for its opportunistic infections and is a significant concern in veterinary medicine due to its inherent resistance to multiple antibiotics and its ability to acquire additional resistance mechanisms. This review seeks to enhance educational initiatives regarding the management of emerging MDR bacteria.

Pseudomonas aeruginosa: One Health approach to deciphering hidden relationships in Northern Portugal

AIMS

Antimicrobial resistance in Pseudomonas aeruginosa represents a major global challenge in public and veterinary health, particularly from a One Health perspective. This study aimed to investigate antimicrobial resistance, the presence of virulence genes, and the genetic diversity of P. aeruginosa isolates from diverse sources.

METHODS AND RESULTS

The study utilized antimicrobial susceptibility testing, genomic analysis for resistance and virulence genes, and multilocus sequence typing to characterize a total of 737 P. aeruginosa isolates that were collected from humans, domestic animals, and aquatic environments in Northern Portugal. Antimicrobial resistance profiles were analyzed, and genomic approaches were employed to detect resistance and virulence genes. The study found a high prevalence of multidrug-resistant isolates, including high-risk clones such as ST244 and ST446, particularly in hospital sources and wastewater treatment plants. Key genes associated with resistance and virulence, including efflux pumps (e.g. MexA and MexB) and secretion systems (T3SS and T6SS), were identified.

CONCLUSIONS

This work highlights the intricate dynamics of multidrug-resistant P. aeruginosa across interconnected ecosystems in Northern Portugal. It underscores the importance of genomic studies in revealing the mechanisms of resistance and virulence, contributing to the broader understanding of resistance dynamics and informing future mitigation strategies.

Quorum sensing regulation by the nitrogen phosphotransferase system in Pseudomonas aeruginosa

In the opportunistic pathogen Pseudomonas aeruginosa, the nitrogen-related phosphotransferase system (PTSNtr) influences multiple virulence behaviors. The PTSNtr is comprised of three enzymes: first PtsP, then the PtsO phosphocarrier, and the final PtsN phosphoacceptor. We previously showed that ptsP inactivation increases LasI-LasR quorum sensing, a system by which P. aeruginosa regulates genes in response to population density. LasI synthesizes a diffusible autoinducer that binds and activates the LasR receptor, which activates a feedback loop by increasing lasI expression. In this study, we examined the impact of the PTSNtr on quorum sensing. Disruption of ptsP increased the expression of some, but not all, tested quorum-controlled genes, including lasI, phzM (pyocyanin biosynthesis), hcnA (hydrogen cyanide biosynthesis), and, to a lesser extent, rsaL (quorum sensing regulator). Expression of these genes remained dependent on LasR and the autoinducer, whether provided endogenously or exogenously. Increased lasI expression in ΔptsP (or ΔptsO) cells was partly due to the presence of unphosphorylated PtsN, which alone was sufficient to elevate lasI expression. However, we observed residual increases in ΔptsP or ΔptsO cells even in the absence of PtsN, suggesting that PtsP and PtsO can regulate gene expression independent of PtsN. Indeed, genetically disrupting the PtsO phosphorylation site impacted gene expression in the absence of PtsN, and transcriptomic evidence suggested that PtsO and PtsN have distinct regulons. Our results expand our view of how the PTSNtr components function both within and apart from the classic phosphorylation cascade to regulate key virulence behaviors in P. aeruginosa.

In-vitro activity of newly-developed β-lactamase inhibitors avibactam, relebactam and vaborbactam in combination with anti-pseudomonal β-lactam antibiotics against AmpC-overproducing clinical Pseudomonas aeruginosa isolates

PURPOSE

Overproduction of the intrinsic chromosomally-encoded AmpC β-lactamase is one of the main mechanisms responsible for broad-spectrum β-lactam resistance in Pseudomonas aeruginosa. Our study aimed to evaluate the in-vitro activity of anti-pseudomonal β-lactam molecules associated with the recently-developed and commercially-available β-lactamase inhibitors, namely avibactam, relebactam and vaborbactam, against P. aeruginosa isolates overproducing their AmpC.

METHODS

MIC values of ceftazidime, cefepime, meropenem, imipenem and ceftolozane with or without β-lactam inhibitor were determined for 50 AmpC-overproducing P. aeruginosa clinical isolates. MIC breakpoints for resistance were retained at 8 mg/L for β-lactams and β-lactam/β-lactamase inhibitor combinations containing ceftazidime, cefepime and meropenem, while 4 mg/L was used for those containing imipenem and ceftolozane. The concentration of all β-lactamases inhibitors was fixed at 4 mg/L, except for vaborbactam (8 mg/L).

RESULTS

The rates of isolates not being resistant to ceftazidime, cefepime, meropenem, imipenem and ceftolozane were found at 12%, 22%, 34%, 8% and 74%, respectively. When combined with avibactam, those rates increased to 60%, 62%, 60%, 46%, and 80%, respectively. The highest rates were found with relebactam-based combinations, being 76%, 64%, 66%, 76% and 84%, respectively. By contrast, associations with vaborbactam did not lead to significantly increased "non-resistance" rates.

CONCLUSION

Our results showed that all combinations including relebactam led to higher "non-resistance" rates against AmpC-overproducing P. aeruginosa clinical isolates. The best activity was achieved by combining ceftolozane and relebactam, that might therefore be considered as an excellent clinical alternative against AmpC overproducers.

Non-carbapenem-producing carbapenem-resistant Pseudomonas aeruginosa in children: Risk factors, molecular epidemiology, and resistance mechanism

BACKGROUND

The investigation into risk factors, molecular epidemiology, and resistance mechanisms of carbapenem-resistant Pseudomonas aeruginosa (CRPA) in pediatric populations in China is currently inadequate.

METHODS

To assess epidemiology, molecular characteristics, and resistance mechanisms, virulence-associated genes were analyzed, alongside multi locus sequence typing (MLST), PCR, and qRT-PCR.

FINDING

Multivariate analysis identified prolonged hospitalization (OR: 1.026; 95 % CI: 1.004-1.049; P = 0.023) and increased exposure to enzyme inhibitor complex preparations (OR: 3.165; 95 % confidence interval [CI]: 1.113-8.999; P = 0.031) as independent risk factors for CRPA healthcare-associated infections (HAIs). Mortality rates were significantly higher in the HAI group compared to the non-HAI group (19.1 % vs. 6.0 %, P = 0.021). Analysis of virulence-associated gene combinations revealed 10 and 15 distinct profiles among HAI and non-HAI isolates, respectively, characterized by exoS-/exoU+ or exoS+ /exoU- genotypes, with no isolates exhibiting both exoS+ and exoU+ genotypes concurrently. Infections predominantly correlated with CC244, with a significantly greater occurrence in the HAI group (72.1 % vs. 46.3 %, P = 0.002). Antimicrobial susceptibility testing identified that both CC244 + and HAI isolates demonstrated elevated resistance across all tested antibiotics. Furthermore, low oprD expression was observed in 77.9 % of HAI isolates and 67.2 % of non-HAI isolates, while increased ampC production and mexB gene overexpression were infrequently detected (all P > 0.05).

CONCLUSIONS

Prolonged hospital stays and an increased exposure to enzyme-inhibitor complex therapies were identified as independent risk factors for CRPA HAIs. CRPA demonstrated considerable genetic diversity, with STs predominantly represented by CC244, and virulence-associated genes have spread. The primary mechanism driving carbapenem resistance involved the downregulation of outer membrane porin protein oprD, accompanied by oprD mutation inactivation.

Pyocins and Beyond: Exploring the World of Bacteriocins in Pseudomonas aeruginosa

Pseudomonas aeruginosa significantly induces health-associated infections in a variety of species other than humans. Over the years, the opportunistic pathogen has developed resistance against commonly used antibiotics. Since most P. aeruginosa strains are multi-drug resistant, regular antibiotic treatment of its infections is becoming a dire concern, shifting the global focus towards the development of alternate antimicrobial approaches. Pyocins are one of the most diverse antimicrobial peptide combinations produced by bacteria. They have potent antimicrobial properties, mainly against bacteria from the same phylogenetic group. P. aeruginosa, whether from clinical or environmental origins, produce several different pyocins that show inhibitory activity against other multi-drug-resistant strains of P. aeruginosa. They are, therefore, good candidates for alternate therapeutic antimicrobials because they have a unique mode of action that kills antibiotic-resistant bacteria by attacking their biofilms. Here, we review pseudomonas-derived antimicrobial pyocins with great therapeutic potential against multi-drug-resistant P. aeruginosa.

The Unique Capability of Endolysin to Tackle Antibiotic Resistance: Cracking the Barrier

The lack of new antibacterial medicines and the rapid rise in bacterial resistance to antibiotics pose a major threat to individuals and healthcare systems. Despite the availability of various antibiotics, bacterial resistance has emerged for almost every antibiotic discovered to date. The increasing prevalence of multidrug-resistant bacterial strains has rendered some infections nearly untreatable, posing severe challenges to health care. Thus, the development of alternatives to conventional antibiotics is critical for the treatment of both humans and food-producing animals. Endolysins, which are peptidoglycan hydrolases encoded by bacteriophages, represent a promising new class of antimicrobials. Preliminary research suggests that endolysins are more effective against Gram-positive bacteria than Gram-negative bacteria when administered exogenously, although they can still damage the cell wall of Gram-negative bacteria. Numerous endolysins have a modular domain structure that divides their binding and catalytic activity into distinct subunits, which helps maximize their bioengineering and potential drug development. Endolysins and endolysin-derived antimicrobials offer several advantages as antibiotic substitutes. They have a unique mechanism of action and efficacy against bacterial persisters (without requiring an active host metabolism); subsequently, they target both Gram-positive and Gram-negative bacteria (including antibiotic-resistant strains), and mycobacteria. Furthermore, there has been limited evidence of endolysin being resistant. Because these enzymes target highly conserved links, resistance may develop more slowly compared to traditional antibiotics. This review provides an overview and insight of the potential applications of endolysins as novel antimicrobials.

Bispecific Thio-Linked Disaccharides as Inhibitors of Pseudomonas Aeruginosa Lectins LecA (PA-IL) and LecB (PA-IIL): Dual-Targeting Strategy

Pseudomonas aeruginosa is a prevalent opportunistic human pathogen, particularly associated with cystic fibrosis. Among its virulence factors are the LecA and LecB lectins. Both lectins play an important role in the adhesion to the host cells and display cytotoxic activity. In this study, we successfully synthesized hardly hydrolysable carbohydrate ligands targeting these pathogenic lectins, including two bispecific glycans. The interactions between LecA/LecB lectins and synthetic glycans were evaluated using hemagglutination (yeast agglutination) inhibition assays, comparing their efficacy with corresponding monosaccharides. Additionally, the binding affinities of bispecific glycans were assessed using isothermal titration calorimetry (ITC). Structural insight into the lectin-ligand interaction was obtained by determining the crystal structures of LecA/LecB lectins in complex with one of the bispecific ligands using X ray crystallography. This comprehensive investigation into the inhibitory potential of synthetic glycosides against P. aeruginosa lectins sheds light on their potential application in antimicrobial therapy.

Caspase-11 drives macrophage hyperinflammation in models of Polg-related mitochondrial disease

Mitochondrial diseases (MtD) represent a significant public health challenge due to their heterogenous clinical presentation, often severe and progressive symptoms, and lack of effective therapies. Environmental exposures, such bacterial and viral infection, can further compromise mitochondrial function and exacerbate the progression of MtD. Infections in MtD patients more frequently progress to sepsis, pneumonia, and other detrimental inflammatory endpoints. However, the underlying immune alterations that enhance immunopathology in MtD remain unclear, constituting a key gap in knowledge that complicates treatment and increases mortality in this vulnerable population. Here we employ in vitro and in vivo approaches to clarify the molecular and cellular basis for innate immune hyperactivity in models of polymerase gamma (Polg)-related MtD. We reveal that type I interferon (IFN-I)-mediated upregulation of caspase-11 and guanylate-binding proteins (GBPs) increase macrophage sensing of the opportunistic microbe Pseudomonas aeruginosa (PA) in Polg mutant mice. Furthermore, we show that excessive cytokine secretion and activation of pyroptotic cell death pathways contribute to lung inflammation and morbidity after infection with PA. Our work sheds new light on innate immune dysregulation in MtD and reveals potential targets for limiting infection- and inflammation-related complications in Polg-related MtD.

Genetic determinants of silver nanoparticle resistance and the impact of gamma irradiation on nanoparticle stability

BACKGROUND

One of the main issues facing public health with microbial infections is antibiotic resistance. Nanoparticles (NPs) are among the best alternatives to overcome this issue. Silver nanoparticle (AgNPs) preparations are widely applied to treat multidrug-resistant pathogens. Therefore, there is an urgent need for greater knowledge regarding the effects of improper and excessive use of these medications. The current study describes the consequences of long-term exposure to sub-lethal concentrations of AgNPs on the bacterial sensitivity to NPs and the reflection of this change on the bacterial genome.

RESULTS

Chemical methods have been used to prepare AgNPs and gamma irradiation has been utilized to produce more stable AgNPs. Different techniques were used to characterize and identify the prepared AgNPs including UV-visible spectrophotometer, Fourier Transform Infrared (FT-IR), Dynamic light scattering (DLS), and zeta potential. Transmission electron microscope (TEM) and Scanning electron microscope (SEM) showed 50-100 nm spherical-shaped AgNPs. Eleven gram-negative and gram-positive bacterial isolates were collected from different wound infections. The minimum inhibitory concentrations (MICs) of AgNPs against the tested isolates were evaluated using the agar dilution method. This was followed by the induction of bacterial resistance to AgNPs using increasing concentrations of AgNPs. All isolates changed their susceptibility level to become resistant to high concentrations of AgNPs upon recultivation at increasing concentrations of AgNPs. Whole genome sequencing (WGS) was performed on selected susceptible isolates of gram-positive Staphylococcus lentus (St.L.1), gram-negative Klebsiella pneumonia (KP.1), and their resistant isolates St.L_R.Ag and KP_R.Ag to detect the genomic changes and mutations.

CONCLUSIONS

For the detection of single-nucleotide polymorphisms (SNPs) and the identification of all variants (SNPs, insertions, and deletions) in our isolates, the Variation Analysis Service tool available in the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) was used. Compared to the susceptible isolates, the AgNPs-resistant isolates St.L_R.Ag and KP_R.Ag had unique mutations in specific efflux pump systems, stress response, outer membrane proteins, and permeases. These findings might help to explain how single-nucleotide variants contribute to AgNPs resistance. Consequently, strict regulations and rules regarding the use and disposal of nano waste worldwide, strict knowledge of microbe-nanoparticle interaction, and the regulated disposal of NPs are required to prevent pathogens from developing nanoparticle resistance.

Multidrug efflux pumps of Pseudomonas aeruginosa show selectivity for their natural substrates

Antibiotic-resistant Gram-negative bacteria are an increasing threat to human health. Strategies to restore antibiotic efficacy include targeting multidrug efflux pumps by competitive efflux pump inhibitors. These could be derived from natural substrates of these efflux systems. In this work, we aimed to elucidate the natural substrates of the clinically relevant Mex efflux pumps of Pseudomonas aeruginosa by an untargeted metabolomic approach. We constructed a PA14 mutant, genetically deleted in the major multidrug efflux pumps MexAB-OprM, MexCD-OprJ, MexXY-OprM, and MexEF-OprN and expressed in this mutant each efflux pump individually from an inducible promoter. Comparative analysis of the exo-metabolomes identified 210 features that were more abundant in the supernatant of efflux pump overexpressors compared to the pump-deficient mutant. Most of the identified features were efflux pump specific, while only a few were shared among several Mex pumps. We identified by-products of secondary metabolites as well as signaling molecules. Supernatants of the pump-deficient mutant also showed decreased accumulation of fatty acids, including long chain homoserine lactone quorum sensing molecules. Our data suggests that Mex efflux pumps of P. aeruginosa appear to have dedicated roles in extruding signaling molecules, metabolic by-products, as well as oxidized fatty acids. These findings represent an interesting starting point for the development of competitive efflux pump inhibitors.

Dose optimization of piperacillin/tazobactam, cefepime, and ceftazidime for carbapenem-resistant Pseudomonas aeruginosa isolates in Türkiye

INTRODUCTION

Although CRPA may test susceptible to other β-lactams such as ceftazidime (CAZ), cefepime (FEP), and piperacillin/tazobactam (TZP), reduced potency has been observed. We assessed the adequacy of EUCAST Susceptible (S) or Susceptible Increased Exposure (SIE)/(I) doses for CAZ, FEP, and TZP against CRPA clinical isolates.

METHODS

CRPA isolates were collected from patients at three Turkish hospitals. CAZ, FEP, and TZP MICs were determined using broth microdilution. Monte Carlo simulations were performed to determine the probability of target attainment (PTA) for a free time above the MIC (fT > MIC) targets for various doses of each agent against isolates defined as susceptible. fT > MIC targets were 70% for CAZ or FEP and 50% for TZP. Cumulative fraction of response (CFR) was calculated. Optimal PTA and CFR was 90% target achievement.

RESULTS

The percentages of isolates SIE/I to CAZ, FEP, and TZP were 49,8%, 47%, and 31,8% respectively. Reduced potency was noted with 54,1% of CAZ-S isolates having MICs of 4 or 8 mg/L. Of the FEP and TZP-S isolates, MICs at the breakpoint (8 and 16 mg/L, respectively) were the mode with 45,2 and 53,9% of isolates for each, respectively. At an MIC of 8 mg/L for CAZ, the EUCAST standard dose was insufficient (CFR of 85%). 3 h infusions of EUCAST SIE doses were required for 90% PTA at MIC of 8 mg/L and an optimized CFR of 100%. For FEP, the SIE dose of 2 g q8h 0.5 h infusion of was effective (CFR 96%), utilization of an extended 3 h infusion further optimized the PTA at 8 mg/L (CFR 99%). For TZP, the standard dose of 4.5 q6h administered as a 0.5 h infusion was inadequate (CFR 86%). A standard TZP dose with an extended infusion (4.5 g q8h over 4 h) and the SIE dose 4.5 g q6h 3 h infusion resulted in CFRs > 95%.

CONCLUSION

These data support the EUCAST SIE breakpoints for FEP and TZP. To optimize PTA at the SIE breakpoint for CAZ, prolonged infusion is required.

Molecular Epidemiology of Carbapenemase-Producing Pseudomonas aeruginosa: An Iranian Referral Hospital-Based Study

In recent years, there has been a significant increase in infections caused by carbapenemase-producing strains, with carbapenem-resistant Pseudomonas aeruginosa (CRPA) emerging as a priority pathogen according to the World Health Organization. This study aimed to evaluate the molecular epidemiology of CRPA isolated from patients referred to Children's Medical Center in Tehran, Iran. P. aeruginosa isolates collected from different children's wards were screened for common carbapenem-resistant genes by polymerase chain reaction (PCR). Genetic relatedness between isolates was assessed by pulsed-field gel electrophoresis (PFGE). The study included 133 participants, with 50% being male, and revealed a median age of 2 years (interquartile range: 6 months to 6 years). Carbapenem resistance was detected in 15% of cases (n = 20), with CRPA isolates predominantly found in the emergency ward (60%). The median age of patients with CRPA was significantly higher than those with carbapenem-susceptible P. aeruginosa (6 years vs. 1 year). PCR analysis revealed metallo-β-lactamase production in 45% of CRPA isolates (n = 9), with blaNDM being the most prevalent gene. PFGE analysis of the CRPA isolates identified three clusters (Cluster I, II, and III). Cluster I, comprising 65% of all isolates (n = 13), was predominantly found in the emergency ward. Notably, blaNDM-producing strains were prevalent in the emergency ward. Our study highlights the significant prevalence of CRPA in the emergency ward of our hospital and underscores the importance of targeted surveillance and infection control measures to curb its spread within health care settings.

Mobilization of an ICEclc-Like Element as a Potential Mechanism for the Spread of IMP-13 Carbapenemase in Pseudomonas aeruginosa

Carbapenem-resistant Pseudomonas aeruginosa is a global public health concern. IMP-13 is a carbapenemase that was described for the first time in 2001 but is often underestimated due to poor hydrolysis of carbapenems and a lack of molecular detection. The aim of this study was to characterize the genetic support of blaIMP-13 in P. aeruginosa and to assess the ability of mobile genetic elements to disseminate this resistance. A retrospective analysis conducted between 2010 and 2020 revealed eight multiresistant P. aeruginosa isolates by their production of the carbapenemase IMP-13 in Bordeaux. Additionally, three of the studied isolates exhibited high-level resistance to imipenem and imipenem-relebactam that was linked to an insertion sequence in the oprD gene. Successful mating was achieved, and transconjugants and parental clinical isolate genomes were sequenced. All clinical isolates were found to be ST621 strains. The data revealed that blaIMP-13 was carried on an Integrative and Conjugative Element (ICEclc-like) of 88,589 bp with a 62% GC content harboring 85 CDSs, and was inserted at the tRNAGly locus PA0729.1. The ICE was identical in the eight studied clinical isolates and in all the ST621 strains found in the databases. The conjugation rate was low, at approximately 10-8 transconjugants per donor and ICE transfer appeared to mobilize some adjacent parental genes located immediately downstream of the ICE. In conclusion, these results suggest that even if the spread of blaIMP-13 is mainly due to an epidemic ST621 clone, the mobilization of a blaIMP-13-carrying ICEclc-like element is possible and should not be underestimated.

Genomic epidemiology and ceftazidime-avibactam high-level resistance mechanisms of Pseudomonas aeruginosa in China from 2010 to 2022

Ceftazidime-avibactam (CZA) resistance is a huge threat in the clinic; however, the underlying mechanism responsible for high-level CZA resistance in Pseudomonas aeruginosa (PA) isolates remains unknown. In this study, a total of 5,763 P. aeruginosa isolates were collected from 2010 to 2022 to investigate the ceftazidime-avibactam (CZA) high-level resistance mechanisms of Pseudomonas aeruginosa (PA) isolates in China. Fifty-six PER-producing isolates were identified, including 50 isolates carrying blaPER-1 in PA, and 6 isolates carrying blaPER-4. Of these, 82.1% (46/56) were classified as DTR-PA isolates, and 76.79% (43/56) were resistant to CZA. Importantly, blaPER-1 and blaPER-4 overexpression led to 16-fold and >1024-fold increases in the MICs of CZA, respectively. WGS revealed that the blaPER-1 gene was located in two different transferable IncP-2-type plasmids and chromosomes, whereas blaPER-4 was found only on chromosomes and was carried by a class 1 integron embedded in a Tn6485-like transposon. Overexpression of efflux pumps may be associated with high-level CZA resistance in blaPER-1-positive strains. Kinetic parameter analysis revealed that PER-4 exhibited a similar kcat/Km with ceftazidime and a high (∼3359-fold) IC50 value with avibactam compared to PER-1. Our study found that overexpression of PER-1 combined with enhanced efflux pump expression and the low affinity of PER-4 for avibactam contributes to high-level resistance to CZA. Additionally, the Tn6485-like transposon plays a significant role in disseminating blaPER. Urgent active surveillance is required to prevent the further spread of high-level CZA resistance in DTR-PA isolates.

Collateral susceptibility-guided alternation of ceftolozane/tazobactam with imipenem prevents resistance development in XDR Pseudomonas aeruginosa biofilms

Objectives

New combinations of β-lactams and β-lactamase inhibitors, such as ceftolozane/tazobactam could be useful to combat biofilm-driven chronic infections by extensively resistant (XDR) Pseudomonas aeruginosa but resistance development by mutations in the Ω-loop of AmpC has been described. However, these mutations confer collateral susceptibility to carbapenems. Thus we aimed to evaluate the therapeutic efficacy and the prevention of resistance development of regimen alternating ceftolozane/tazobactam and imipenem.

Methods

A carbapenem-resistant XDR P. aeruginosa clinical strain (ST175, 104-B7) and its isogenic imipenem-susceptible ceftolozane/tazobactam-resistant mutant derivative (AmpC T96I, 104-I9) were used. Experiments of single strains and mixed (104-B7 and 104-I9, 1:0.01 ratio) biofilms were performed. 48h biofilms (flow cell system) were treated for 6 days with either ceftolozane/tazobactam, 4/4 mg/L or the alternation of ceftolozane/tazobactam (2 days)-imipenem 4 mg/L (2 days) - ceftolozane/tazobactam (2 days). After treatment, biofilms were collected and plated on Mueller-Hinton agar± ceftolozane/tazobactam 4/4 mg/L. Structural dynamics were monitored using confocal laser scanning microscopy and images were processed with IMARIS software. At least, three independent triplicate experiments per condition were performed. Emerging resistant mutants were characterized through whole genome sequencing (Illumina).

Results

Ceftolozane/tazobactam monotherapy failed to reduce the biofilms of the 104-B7 XDR strain and led to the selection of resistant mutants that showed AmpC Ω-loop mutations (T96I, L244R or aa236Δ7). On the contrary, alternation with imipenem enhanced activity (3 Logs reduction at day 6) and prevented the emergence of ceftolozane/tazobactam-resistant mutants. Likewise, treatment with ceftolozane/tazobactam dramatically amplified the resistant strain 104-I9 in mixed biofilms (>90 % of the population), while the alternation regimen counterselected it.

Conclusions

Collateral susceptibility-guided alternation of ceftolozane/tazobactam with imipenem effectively prevented the selection of resistant mutants and thus could be a potential therapeutic strategy for the treatment of P. aeruginosa XDR chronic infections.

Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains

In current genomic research, the widely used methods for predicting antimicrobial resistance (AMR) often rely on prior knowledge of known AMR genes or reference genomes. However, these methods have limitations, potentially resulting in imprecise predictions owing to incomplete coverage of AMR mechanisms and genetic variations. To overcome these limitations, we propose a pan-genome-based machine learning approach to advance our understanding of AMR gene repertoires and uncover possible feature sets for precise AMR classification. By building compacted de Brujin graphs (cDBGs) from thousands of genomes and collecting the presence/absence patterns of unique sequences (unitigs) for Pseudomonas aeruginosa, we determined that using machine learning models on unitig-centered pan-genomes showed significant promise for accurately predicting the antibiotic resistance or susceptibility of microbial strains. Applying a feature-selection-based machine learning algorithm led to satisfactory predictive performance for the training dataset (with an area under the receiver operating characteristic curve (AUC) of > 0.929) and an independent validation dataset (AUC, approximately 0.77). Furthermore, the selected unitigs revealed previously unidentified resistance genes, allowing for the expansion of the resistance gene repertoire to those that have not previously been described in the literature on antibiotic resistance. These results demonstrate that our proposed unitig-based pan-genome feature set was effective in constructing machine learning predictors that could accurately identify AMR pathogens. Gene sets extracted using this approach may offer valuable insights into expanding known AMR genes and forming new hypotheses to uncover the underlying mechanisms of bacterial AMR.

Phenotypic and molecular characterization of extended spectrum- and metallo- beta lactamase producing Pseudomonas aeruginosa clinical isolates from Egypt

BACKGROUND

Antimicrobial resistance among Pseudomonas aeruginosa (P. aeruginosa), a leading cause of nosocomial infections worldwide, is escalating. This study investigated the prevalence of extended-spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs) among 104 P. aeruginosa clinical isolates from Alexandria Main University Hospital, Alexandria, Egypt.

METHODS

Antimicrobial susceptibility testing was performed using agar dilution technique, or broth microdilution method in case of colistin. ESBL and MBL prevalence was assessed phenotypically and genotypically using polymerase chain reaction (PCR). The role of plasmids in mediating resistance to extended-spectrum β-lactams was studied via transformation technique using plasmids isolated from ceftazidime-resistant isolates.

RESULTS

Antimicrobial susceptibility testing revealed alarming resistance rates to carbapenems, cephalosporins, and fluoroquinolones. Using PCR as the gold standard, phenotypic methods underestimated ESBL production while overestimating MBL production. Eighty-five isolates (81.7%) possessed only ESBL encoding genes, among which 69 isolates harbored a single ESBL gene [blaOXA-10 (n = 67) and blaPER (n = 2)]. Four ESBL-genotype combinations were detected: blaPER + blaOXA-10 (n = 8), blaVEB-1 + blaOXA-10 (n = 6), blaPSE + blaOXA-10 (n = 1), and blaPER + blaVEB-1 + blaOXA-10 (n = 1). Three isolates (2.9%) possessed only the MBL encoding gene blaVIM. Three ESBL + MBL- genotype combinations: blaOXA-10 + blaAIM, blaOXA-10 + blaVIM, and blaPER + blaOXA-10 + blaAIM were detected in 2, 1 and 1 isolate(s), respectively. Five plasmid preparations harboring blaVEB-1 and blaOXA-10 were successfully transformed into chemically competent Escherichia coli DH5α with transformation efficiencies ranging between 6.8 × 10 3 and 3.7 × 10 4    CFU/μg DNA plasmid. Selected tested transformants were ceftazidime-resistant and harbored plasmids carrying blaOXA-10.

CONCLUSIONS

The study highlights the importance of the expeditious characterization of ESBLs and MBLs using genotypic methods among P. aeruginosa clinical isolates to hinder the development and dissemination of multidrug resistant strains.

Pseudomonas aeruginosa faces a fitness trade-off between mucosal colonization and antibiotic tolerance during airway infection

Pseudomonas aeruginosa frequently causes antibiotic-recalcitrant pneumonia, but the mechanisms driving its adaptation during human infections remain unclear. To reveal the selective pressures and adaptation strategies at the mucosal surface, here we investigated P. aeruginosa growth and antibiotic tolerance in tissue-engineered airways by transposon insertion sequencing (Tn-seq). Metabolic modelling based on Tn-seq data revealed the nutritional requirements for P. aeruginosa growth, highlighting reliance on glucose and lactate and varying requirements for amino acid biosynthesis. Tn-seq also revealed selection against biofilm formation during mucosal growth in the absence of antibiotics. Live imaging in engineered organoids showed that biofilm-dwelling cells remained sessile while colonizing the mucosal surface, limiting nutrient foraging and reduced growth. Conversely, biofilm formation increased antibiotic tolerance at the mucosal surface. Moreover, mutants with exacerbated biofilm phenotypes protected less tolerant but more cytotoxic strains, contributing to phenotypic heterogeneity. P. aeruginosa must therefore navigate conflicting physical and biological selective pressures to establish chronic infections.

Prevalence and Antimicrobial Susceptibility of Wound Pathogens in a Tertiary Care Hospital in Kashmir: A Cross-sectional Study

BACKGROUND

Wound infections significantly impact morbidity, mortality, and healthcare costs globally. The Kashmir Valley's unique geographical and climatic conditions, coupled with resource constraints and antibiotic misuse, complicate managing these infections effectively. This study aimed to identify predominant bacterial pathogens in wound infections at a tertiary care hospital in Kashmir, determine their antibiotic susceptibility profiles, and estimate the prevalence of multidrug-resistant (MDR) strains.

MATERIALS AND METHODS

A prospective cross-sectional study was conducted from January to June 2023 at the Government Medical College, Srinagar. Pus samples from wound infections were aseptically collected and processed following standard microbiological protocols. Antibiotic susceptibility testing utilized the Kirby-Bauer disk diffusion method, adhering to Clinical and Laboratory Standards Institute guidelines. Data were analyzed using IBM SPSS statistics.

RESULTS

Out of 4,378 samples analyzed, bacterial growth was observed in 1,921 samples, representing 43.9% of the total. Among the bacterial isolates, Gram-negative bacilli accounted for 73.5%, with Escherichia coli being the most prevalent at 27.9%. Among Gram-positive cocci, Staphylococcus aureus predominated, comprising 25.9% of the isolates. Methicillin-resistant S. aureus exhibited 100% susceptibility to linezolid but low susceptibility to erythromycin (27.0%) and clindamycin (24.0%). E. coli demonstrated high susceptibility to tigecycline (97.4%) and amikacin (75.0%), but lower susceptibility to imipenem (45.0%) and piperacillin-tazobactam (57.8%).

CONCLUSION

The substantial wound infection burden and high MDR prevalence in Kashmir necessitate comprehensive antimicrobial stewardship and infection control programs. Regular surveillance, education, and research are crucial to address antibiotic resistance and ensure effective wound infection management in the region.

Antibiotic resistance in Pseudomonas aeruginosa: mechanisms and emerging treatment

Pseudomonas aeruginosa, able to survive on the surfaces of medical devices, is a life-threatening pathogen that mainly leads to nosocomial infection especially in immunodeficient and cystic fibrosis (CF) patients. The antibiotic resistance in P. aeruginosa has become a world-concerning problem, which results in reduced and ineffective therapy efficacy. Besides intrinsic properties to decrease the intracellular content and activity of antibiotics, P. aeruginosa develops acquired resistance by gene mutation and acquisition, as well as adaptive resistance under specific situations. With in-depth research on drug resistance mechanisms and the development of biotechnology, innovative strategies have emerged and yielded benefits such as screening for new antibiotics based on artificial intelligence technology, utilizing drugs synergistically, optimizing administration, and developing biological therapy. This review summarizes the recent advances in the mechanisms of antibiotic resistance and emerging treatments for combating resistance, aiming to provide a reference for the development of therapy against drug-resistant P. aeruginosa.

Investigation of Carbapenemase-Producing Pseudomonas aeruginosa at Secondary Care Hospital in Bolu, Turkey

The global increase in carbapenem resistance poses a significant public health threat due to the potential emergence of multidrug-resistant pathogens and limited treatment options. To learn more about this issue and offer potential solutions, we conducted a study of carbapenem-resistant Pseudomonas aeruginosa (CRPA) infections in a secondary care hospital setting. The study utilized the carbapenem inactivation method (CIM), a leading phenotypic analysis, to determine carbapenemase activity in 63 CRPA isolates. Additionally, polymerase chain reaction (PCR) analysis was conducted to test for the presence of carbapenemase genes associated with the production or expression of various carbapenemase enzymes, including blaKPC, blaNDM, blaVIM, blaOXA-48, blaIMP, and blaGES. Arbitrary primed PCR (AP-PCR) was performed to assess the clonal relationship between different isolates. The isolates were also classified as either health care-associated infections or community-acquired infections, and their clonal relationship and gene positivity were evaluated. A total of 63 CRPA samples underwent evaluation, with 14 isolates determined to be carbapenemase producers via CIM tests. PCR assays revealed that 14 isolates carried carbapenemase genes, with 9 carrying blaNDM, 2 carrying blaGES, 2 carrying blaVIM, and 1 carrying blaIMP. CRPA exhibited a 22% prevalence of carbapenemase genes, of which 64% were attributed to the NDM gene responsible for multidrug resistance. AP-PCR revealed high clonal diversity among the isolates. Molecular epidemiological evaluation also showed no dominant outbreak strain among PA isolates. This study presents significant data on the prevalence and distribution of carbapenemase-producing CRPA strains isolated from secondary health care facilities. Typically, the literature focuses on resistance rates in tertiary care public hospitals. These findings may aid in understanding resistance and its mechanisms, as well as in developing effective treatment strategies and infection control measures.

Non-antibiotic pharmaceutical phenylbutazone binding to MexR reduces the antibiotic susceptibility of Pseudomonas aeruginosa

Antimicrobial resistance has been an increasingly serious threat to global public health. The contribution of non-antibiotic pharmaceuticals to the development of antibiotic resistance has been overlooked. Our study found that the anti-inflammatory drug phenylbutazone could protect P. aeruginosa against antibiotic mediated killing by binding to the efflux pump regulator MexR. In this study, antibiotic activity against P. aeruginosa alone or in combination with phenylbutazone was evaluated in vitro and in vivo. Resazurin accumulation assay, transcriptomic sequencing, and PISA assay were conducted to explore the underlying mechanism for the reduced antibiotic susceptibility caused by phenylbutazone. Then EMSA, ITC, molecular dynamic simulations, and amino acid substitutions were used to investigate the interactions between phenylbutazone and MexR. We found that phenylbutazone could reduce the susceptibility of P. aeruginosa to multiple antibiotics, including parts of β-lactams, fluoroquinolones, tetracyclines, and macrolides. Phenylbutazone could directly bind to MexR, then promote MexR dissociating from the mexA-mexR intergenic region and de-repress the expression of MexAB-OprM efflux pump. The overexpressed MexAB-OprM pump resulted in the reduced antibiotic susceptibility. And the His41 and Arg21 residues of MexR were involved in the phenylbutazone-MexR interaction. We hope this study would imply the potential risk of antibiotic resistance caused by non-antibiotic pharmaceuticals.

Genomic and metagenomic analyses of the domestic mite Tyrophagus putrescentiae identify it as a widespread environmental contaminant and a host of a basal, mite-specific Wolbachia lineage (supergroup Q)

Tyrophagus putrescentiae (mould mite) is a global, microscopic trophic generalist that commonly occurs in various human-created habitats, causing allergies and damaging stored food. Its ubiquity and extraordinary ability to penetrate research samples or cultures through air currents or by active walking through tights spaces (such as treads of screw caps) may lead to sample contamination and introduction of its DNA to research materials in the laboratory. This prompts a thorough investigation into potential sequence contamination in public genomic databases. The trophic success of T. putrescentiae is primarily attributed to the symbiotic bacteria housed in specialized internal mite structures, facilitating adaptation to varied nutritional niches. However, recent work suggests that horizontal transfer of bacterial/fungal genes related to nutritional functionality may also contribute to the mite's trophic versatility. This aspect requires independent confirmation. Additionally, T. putrescentiae harbors an uncharacterized and genetically divergent bacterium, Wolbachia, displaying blocking and microbiome-modifying effects. The phylogenomic position and supergroup assignment of this bacterium are unknown. Here, we sequenced and assembled the T. putrescentiae genome, analyzed its microbiome, and performed detailed phylogenomic analyses of the mite-specific Wolbachia. We show that T. putrescentiae DNA is a substantial source of contamination of research samples. Its DNA may inadvertently be co-extracted with the DNA of the target organism, eventually leading to sequence contamination in public databases. We identified a diversity of bacterial species associated with T. putrescentiae, including those capable of rapidly developing antibiotic resistance, such as Escherichia coli. Despite the presence of diverse bacterial communities in T. putrescentiae, we did not detect any recent horizontal gene transfers in this mite species and/or in astigmatid (domestic) mites in general. Our phylogenomic analysis of Wolbachia recovered a basal, mite-specific lineage (supergroup Q) represented by two Wolbachia spp. from the mould mite and a gall-inducing plant mite. Fluorescence in situ hybridization confirmed the presence of Wolbachia inside the mould mite. The discovery of an early derivative Wolbachia lineage (supergroup Q) in two phylogenetically unrelated and ecologically dissimilar mites suggests that this endosymbiotic bacterial lineage formed a long-term association with mites. This finding provides a unique insight into the early evolution and host associations of Wolbachia. Further discoveries of Wolbachia diversity in acariform mites are anticipated.

Case Report: Pan-Drug Resistant Pseudomonas aeruginosa from a Child with an Infected Burn Wound at the University Teaching Hospital of Kigali, Rwanda

Background

Pseudomonas aeruginosa is a significant cause of morbidity and mortality in intensive care units, and is prevalent in nosocomial infections and cystic fibrosis. The increasing rates of antimicrobial resistance (AMR) complicate the treatment of P. aeruginosa infections, especially because of the multidrug resistance (MDR), extensively drug-resistant (XDR), and pan-drug resistant (PDR) strains.

Case Presentation

We report the case of a 4-year-old male with severe burns covering 45% of his body surface who developed nosocomial PDR P. aeruginosa infection at the University Teaching Hospital of Kigali (CHUK) in Rwanda. A wound culture yielded a PDR P. aeruginosa isolate that was resistant to all the tested antimicrobials, with intermediate resistance to colistin. However, the patient improved with a combination of ceftazidime and amikacin following cessation of fever and successful skin grafting. The patient was discharged on day 95.

Conclusion

P. aeruginosa is a common hospital-acquired pathogen that is particularly challenging to treat, owing to its antimicrobial resistance profile and biofilm production. Antibiotic-resistant strains are a significant public health threat, especially in pediatric burn units. This case underscores the critical need to strengthen infection prevention and control measures together with robust antimicrobial stewardship programs. Molecular characterization of this PDR strain will yield further details regarding its virulence and genotyping.

The contribution of neutrophils to bacteriophage clearance and pharmacokinetics in vivo

With the increasing prevalence of antimicrobial-resistant bacterial infections, there is interest in using bacteriophages (phages) to treat such infections. However, the factors that govern bacteriophage pharmacokinetics in vivo remain poorly understood. Here, we have examined the contribution of neutrophils, the most abundant phagocytes in the body, to the pharmacokinetics of i.v. administered bacteriophage in uninfected mice. A single dose of LPS-5, a bacteriophage recently used in human clinical trials to treat drug-resistant Pseudomonas aeruginosa, was administered i.v. to both immunocompetent BALB/c and neutropenic CD1 mice. Phage concentrations were assessed in peripheral blood and spleen at 0.25, 1, 2, 4, 8, 12, and 24 hours after administration by plaque assay and qPCR. We observed that the phage clearance was only minimally affected by neutropenia. Indeed, the half-lives of phages in blood in BALB/c and CD1 mice were 3.45 and 3.66 hours, respectively. These data suggest that neutrophil-mediated phagocytosis is not a major determinant of phage clearance. Conversely, we observed a substantial discrepancy in circulating phage levels over time when measured by qPCR versus plaque assay, suggesting that significant inactivation of circulating phages occurs over time. These data indicate that alternative factors, but not neutrophils, inactivate i.v. administered phages.

The OprF porin as a potential target for the restoration of carbapenem susceptibility in Pseudomonas aeruginosa expressing acquired carbapenemases

Carbapenem resistance in Pseudomonas aeruginosa is primarily due to the acquisition of carbapenemases and is often associated with a diminution of the membrane permeability. The outer membrane protein, OprD, is a well-known route, by which carbapenems, predominantly imipenem, can enter the cell, and its loss has been associated with reduced susceptibility to imipenem. In this study, we investigated the antibiotic susceptibility patterns of isogenic P. aeruginosa mutants containing various acquired β-lactamases, including carbapenemases, in a porin-depleted background. We identified that the deletion of oprF was associated with some recovery of susceptibility to carbapenems.

Characterization of acquired β-lactamases in Pseudomonas aeruginosa and quantification of their contributions to resistance

Pseudomonas aeruginosa is a highly problematic opportunistic pathogen that causes a range of different infections. Infections are commonly treated with β-lactam antibiotics, including cephalosporins, monobactams, penicillins, and carbapenems, with carbapenems regarded as antibiotics of last resort. Isolates of P. aeruginosa can contain horizontally acquired bla genes encoding β-lactamase enzymes, but the extent to which these contribute to β-lactam resistance in this species has not been systematically quantified. The overall aim of this research was to address this knowledge gap by quantifying the frequency of β-lactamase-encoding genes in P. aeruginosa and by determining the effects of β-lactamases on susceptibility of P. aeruginosa to β-lactams. Genome analysis showed that β-lactamase-encoding genes are present in 3% of P. aeruginosa but are enriched in carbapenem-resistant isolates (35%). To determine the substrate antibiotics, 10 β-lactamases were expressed from an integrative plasmid in the chromosome of P. aeruginosa reference strain PAO1. The β-lactamases reduced susceptibility to a variety of clinically used antibiotics, including carbapenems (meropenem, imipenem), penicillins (ticarcillin, piperacillin), cephalosporins (ceftazidime, cefepime), and a monobactam (aztreonam). Different enzymes acted on different β-lactams. β-lactamases encoded by the genomes of P. aeruginosa clinical isolates had similar effects to the enzymes expressed in strain PAO1. Genome engineering was used to delete β-lactamase-encoding genes from three carbapenem-resistant clinical isolates and increased susceptibility to substrate β-lactams. Our findings demonstrate that acquired β-lactamases play an important role in β-lactam resistance in P. aeruginosa, identifying substrate antibiotics for a range of enzymes and quantifying their contributions to resistance.IMPORTANCEPseudomonas aeruginosa is an extremely problematic pathogen, with isolates that are resistant to the carbapenem class of β-lactam antibiotics being in critical need of new therapies. Genes encoding β-lactamase enzymes that degrade β-lactam antibiotics can be present in P. aeruginosa, including carbapenem-resistant isolates. Here, we show that β-lactamase genes are over-represented in carbapenem-resistant isolates, indicating their key role in resistance. We also show that different β-lactamases alter susceptibility of P. aeruginosa to different β-lactam antibiotics and quantify the effects of selected enzymes on β-lactam susceptibility. This research significantly advances the understanding of the contributions of acquired β-lactamases to antibiotic resistance, including carbapenem resistance, in P. aeruginosa and by implication in other species. It has potential to expedite development of methods that use whole genome sequencing of infecting bacteria to inform antibiotic treatment, allowing more effective use of antibiotics, and facilitate the development of new antibiotics.

Alpinia officinarum Hance Essential Oil as Potent Antipseudomonal Agent: Chemical Profile, Antibacterial Activity, and Computational Study

Alpinia officinarum Hance, is an aromatic and medicinal herb with a very interesting history and prominent chemical and biological prospects. We aimed to investigate the antibacterial activity of Alpinia officinarum essential oil and the preferred molecular targets of its constituents together with their pharmacokinetic properties and toxicity profile. According to GC-MS analysis, eucalyptol was the main compound (27.52 %) identified in Alpinia officinarum essential oil, followed by α-terpineol, and β-sesquiphellandrene. As opposed to the weak antiradical activity estimated by DPPH and ABTS tests, the essential oil caused inhibition of all the bacteria following well-diffusion and microdilution methods, especially the gram-negative Pseudomonas aeruginosa and Escherichia coli. It displayed exceptionally remarkable activity against Pseudomonas aeruginosa by totally inhibiting its growth on the agar plate exceeding the effect of chloramphenicol standard. This bactericidal effect was confirmed by very low MIC and MBC values of 0.82 and 6.562 μg/mL, respectively. The molecular docking showed interesting binding affinity between the major compounds and various drug targets in Pseudomonas aeruginosa, also good pharmacokinetic and toxicity behavior. These encouraging findings are particularly relevant in light of the increasingly pressing challenge to find alternative substances with antibacterial aptitude to address the issue of antibiotic resistance among infectious bacteria.

Bismuth-based drugs sensitize Pseudomonas aeruginosa to multiple antibiotics by disrupting iron homeostasis

Pseudomonas aeruginosa infections are difficult to treat due to rapid development of antibiotic drug resistance. The synergistic combination of already-in-use drugs is an alternative to developing new antibiotics to combat antibiotic-resistant bacteria. Here we demonstrate that bismuth-based drugs (bismuth subsalicylate, colloidal bismuth subcitrate) in combination with different classes of antibiotics (tetracyclines, macrolides, quinolones, rifamycins and so on) can eliminate multidrug-resistant P. aeruginosa and do not induce development of antibiotic resistance. Bismuth disrupts iron homeostasis by binding to P. aeruginosa siderophores. Inside cells, bismuth inhibits the electron transport chain, dissipates the proton motive force and impairs efflux pump activity by disrupting iron-sulfur cluster-containing enzymes, including respiration complexes. As a result, bismuth facilitates antibiotic accumulation inside bacteria, enhancing their efficacy. The combination therapy shows potent antibacterial efficacy and low toxicity in an ex vivo bacteraemia model and increases the survival rate of mice in in vivo mouse lung-infection models. Our findings highlight the potential of bismuth-based drugs to be repurposed to combat P. aeruginosa infections in combination with clinically used antibiotics.

ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics

The rise of antibiotic resistance and a dwindling antimicrobial pipeline have been recognized as emerging threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria for which effective therapies were rapidly needed. Now, entering the third decade of the twenty-first century, and despite the introduction of several new antibiotics and antibiotic adjuvants, such as novel β-lactamase inhibitors, these organisms continue to represent major therapeutic challenges. These bacteria share several key biological features, including adaptations for survival in the modern health-care setting, diverse methods for acquiring resistance determinants and the dissemination of successful high-risk clones around the world. With the advent of next-generation sequencing, novel tools to track and combat the spread of these organisms have rapidly evolved, as well as renewed interest in non-traditional antibiotic approaches. In this Review, we explore the current epidemiology and clinical impact of this important group of bacterial pathogens and discuss relevant mechanisms of resistance to recently introduced antibiotics that affect their use in clinical settings. Furthermore, we discuss emerging therapeutic strategies needed for effective patient care in the era of widespread antimicrobial resistance.

The Potential of Thymus serpyllum Essential Oil as an Antibacterial Agent against Pseudomonas aeruginosa in the Preservation of Sous Vide Red Deer Meat

Foodborne infections caused by microbes are a serious health risk. Regarding this, customer preferences for "ready-to-eat" or minimally processed (MP) deer meat are one of the main risk factors. Given the health dangers associated with food, essential oil (EO) is a practical substitute used to decrease pathogenic germs and extend the shelf-life of MP meals. Nonetheless, further data regarding EO use in MP meals are required. In order to evaluate new, safer alternatives to chemicals for disease control and food preservation, this research was carried out in the following areas to assess the antibacterial and antibiofilm characteristics of Thymus serpyllum (TSEO) essential oil, which is extracted from dried flowering stalks. Furthermore, this study applied an essential oil of wild thyme and inoculated the sous vide deer meat with Pseudomonas aeruginosa for seven days at 4 °C in an effort to prolong its shelf-life. Against P. aeruginosa, the essential oil exhibited potent antibacterial action. The findings of the minimal biofilm inhibition concentration (MBIC) crystal violet test demonstrated the substantial antibiofilm activity of the TSEO. The TSEO modified the protein profiles of bacteria on glass and plastic surfaces, according to data from MALDI-TOF MS analysis. Moreover, it was discovered that P. aeruginosa was positively affected by the antibacterial properties of TSEO. The anti-Pseudomonas activity of the TSEO was marginally higher in vacuum-packed sous vide red deer meat samples than in control samples. The most frequently isolated species from sous vide deer meat, if we do not consider the applied bacteria Pseudomonas aeruginosa, were P. fragi, P. lundensis, and P. taetrolens. These results highlight the antibacterial and antibiofilm qualities of TSEO, demonstrating its potential for food preservation and extending the shelf-life of deer meat.

Structural and functional diversity of Resistance-Nodulation-Division (RND) efflux pump transporters with implications for antimicrobial resistance

SUMMARYThe discovery of bacterial efflux pumps significantly advanced our understanding of how bacteria can resist cytotoxic compounds that they encounter. Within the structurally and functionally distinct families of efflux pumps, those of the Resistance-Nodulation-Division (RND) superfamily are noteworthy for their ability to reduce the intracellular concentration of structurally diverse antimicrobials. RND systems are possessed by many Gram-negative bacteria, including those causing serious human disease, and frequently contribute to resistance to multiple antibiotics. Herein, we review the current literature on the structure-function relationships of representative transporter proteins of tripartite RND efflux pumps of clinically important pathogens. We emphasize their contribution to bacterial resistance to clinically used antibiotics, host defense antimicrobials and other biocides, as well as highlighting structural similarities and differences among efflux transporters that help bacteria survive in the face of antimicrobials. Furthermore, we discuss technical advances that have facilitated and advanced efflux pump research and suggest future areas of investigation that will advance antimicrobial development efforts.

Clonal Distribution and Its Association With the Carbapenem Resistance Mechanisms of Carbapenem-Non-Susceptible Pseudomonas aeruginosa Isolates From Korean Hospitals

Background

Carbapenem resistance in Pseudomonas aeruginosa is a serious global health problem. We investigated the clonal distribution and its association with the carbapenem resistance mechanisms of carbapenem-non-susceptible P. aeruginosa isolates from three Korean hospitals.

Methods

A total of 155 carbapenem-non-susceptible P. aeruginosa isolates collected between 2011 and 2019 were analyzed for sequence types (STs), antimicrobial susceptibility, and carbapenem resistance mechanisms, including carbapenemase production, the presence of resistance genes, OprD mutations, and the hyperproduction of AmpC β-lactamase.

Results

Sixty STs were identified in carbapenem-non-susceptible P. aeruginosa isolates. Two high-risk clones, ST235 (N=41) and ST111 (N=20), were predominant; however, sporadic STs were more prevalent than high-risk clones. The resistance rate to amikacin was the lowest (49.7%), whereas that to piperacillin was the highest (92.3%). Of the 155 carbapenem-non-susceptible isolates, 43 (27.7%) produced carbapenemases. Three metallo-β-lactamase (MBL) genes, blaIMP-6 (N=38), blaVIM-2 (N=3), and blaNDM-1 (N=2), were detected. blaIMP-6 was detected in clonal complex 235 isolates. Two ST773 isolates carried blaNDM-1 and rmtB. Frameshift mutations in oprD were identified in all isolates tested, regardless of the presence of MBL genes. Hyperproduction of AmpC was detected in MBL gene-negative isolates.

Conclusions

Frameshift mutations in oprD combined with MBL production or hyperproduction of AmpC are responsible for carbapenem resistance in P. aeruginosa. Further attention is required to curb the emergence and spread of new carbapenem-resistant P. aeruginosa clones.

In vitro activity of ceftolozane/tazobactam against Gram-negative bacilli isolated from pediatric patients: Results from the Study for Monitoring Antimicrobial Resistance Trends (SMART) 2017-2021, China

OBJECTIVES

Ceftolozane-tazobactam (C/T) is a combination of a cephalosporin and a β-lactamase inhibitor with activity against Gram-negative bacilli (GNB). The study aims were to evaluate the activity of C/T in vitro vs. comparators against clinical GNB isolated from Chinese paediatric patients.

METHODS

From 2017-2021, 660 GNB isolates were collected from 20 hospitals across China. The minimum inhibitory concentrations were tested using a Trek Diagnostic System (Thermo Fisher Scientific). Susceptibility was determined by CLSI broth microdilution and the results were interpreted according to CLSI M100 (2021) breakpoints.

RESULTS

GNB isolates were obtained from paediatric patients < 18 years old, mainly from the bloodstream (n = 146), intraperitoneal cavity (n = 138), lower respiratory (n = 278) and urinary tract (n = 96). Overall, C/T was active against 76.6% of 436 Enterobacterales, with a descending susceptibility rate of 100.0% to S. marcescens, 92.2% to E. coli, 83.3% to K. oxytoca, 66.7% to K. aerogenes, 66.7% to P. mirabilis, 58.6% to K. pneumoniae and 57.1% to E. cloacae. The susceptibility of P. aeruginosa to C/T was 89.4%, which was the highest among the β-lactam antibiotics and was second only to amikacin (92.9%). Isolates of respiratory tract infection (RTI) derived P. aeruginosa were highly susceptible (93.8%) to C/T, while <75% of isolates of RTI derived P. aeruginosa were susceptible to the other β-lactam antibiotics tested, except for ceftazidime-avibactam (91.2%).

CONCLUSION

GNBs collected from paediatric patients in China showed a high susceptibility to C/T making this drug combination an effective choice for treating the paediatric population, especially those infected with P. aeruginosa.

Efflux pump-mediated resistance to new beta lactam antibiotics in multidrug-resistant gram-negative bacteria

The emergence and spread of bacteria resistant to commonly used antibiotics poses a critical threat to modern medical practice. Multiple classes of bacterial efflux pump systems play various roles in antibiotic resistance, and members of the resistance-nodulation-division (RND) transporter superfamily are among the most important determinants of efflux-mediated resistance in gram-negative bacteria. RND pumps demonstrate broad substrate specificities, facilitating extrusion of multiple chemical classes of antibiotics from the bacterial cell. Several newer beta-lactams and beta-lactam/beta-lactamase inhibitor combinations (BL/BLI) have been developed to treat infections caused by multidrug resistant bacteria. Here we review recent studies that suggest RND efflux pumps in clinically relevant gram-negative bacteria may play critical but underappreciated roles in the development of resistance to beta-lactams and novel BL/BLI combinations. Improved understanding of the genetic and structural basis of RND efflux pump-mediated resistance may identify new antibiotic targets as well as strategies to minimize the emergence of resistance.

Optimized Dosing and Delivery of Bacteriophage Therapy for Wound Infections

Lytic bacteriophages, viruses that lyse (kill) bacteria, hold great promise for treating infections, including wound infections caused by antimicrobial-resistant Pseudomonas aeruginosa. However, the optimal dosing and delivery strategies for phage therapy remain unclear. In a mouse wound infection model, we investigated the impact of dose, frequency, and administration route on the efficacy of phage therapy. We find that topical but not intravenous delivery is effective in this model. High-doses of phage reduces bacterial burden more effectively than low-doses, and repeated dosing achieves the highest eradication rates. Building on these insights, we developed "HydroPhage", a hyaluronan-based hydrogel system that uses dynamic covalent crosslinking to deliver high-titre phages over one week. HydroPhage eradicates infections five times more effectively than intravenous injection. We conclude that hydrogel-based sustained phage delivery enhances the efficacy of phage therapy and offers a practical, well-tolerated option for topical application.

Pseudomonas aestus Isolation from the Nasal Cavity of a Cat with Chronic Rhinitis

The Pseudomonas genus includes ubiquitous bacteria frequently described as animal and human opportunistic pathogens. A 9-year-old cat was referred for rhinoscopy at the Veterinary Hospital of the Faculty of Veterinary Medicine, University of Lisbon, Portugal, for an investigation of the chronic respiratory signs. Upon rhinoscopy, nasal and nasopharyngeal discharge were observed, and the nasal turbinates showed signs of inflammation. The nasal biopsies were evaluated by histopathology and mycological and bacterial cultures. The histopathology revealed chronic lymphoplasmacytic inflammation. The mycological culture was negative, but the bacterial culture revealed the growth of a bacterial isolate in the pure culture, identified as P. aestus by the sequencing of a 1750 bp PCR amplicon obtained with BCR1 and BCR2 primers, followed by homologous sequences analysis using the NCBI database. The isolate's susceptibility profile towards 14 antimicrobials was evaluated through the disk diffusion method, being observed that it presented a multidrug resistance profile. The studies available on this environmental Pseudomonas strain focused on its potential use for biocide production and application in agricultural settings, and, to the authors' best knowledge, there are no reports describing its association with infectious diseases in humans or animals, highlighting the importance of establishing protocols aiming at the identification and characterization of non-traditional, multidrug-resistant Pseudomonas in the clinical setting.

Resistance to ceftazidime-avibactam and other new β-lactams in Pseudomonas aeruginosa clinical isolates: a multi-center surveillance study

New β-lactam-β-lactamase inhibitor combinations represent last-resort antibiotics to treat infections caused by multidrug-resistant Pseudomonas aeruginosa. Carbapenemase gene acquisition can limit their spectrum of activity, and reports of resistance toward these new molecules are increasing. In this multi-center study, we evaluated the prevalence of resistance to ceftazidime-avibactam (CZA) and comparators among P. aeruginosa clinical isolates from bloodstream infections, hospital-acquired or ventilator-associated pneumonia, and urinary tract infections, circulating in Southern Italy. We also investigated the clonality and content of relevant β-lactam resistance mechanisms of CZA-resistant (CZAR) isolates. A total of 120 P. aeruginosa isolates were collected. CZA was among the most active β-lactams, retaining susceptibility in the 81.7% of cases, preceded by cefiderocol (95.8%) and followed by ceftolozane-tazobactam (79.2%), meropenem-vaborbactam (76.1%), imipenem-relebactam (75%), and aztreonam (69.6%). Among non-β-lactams, colistin and amikacin were active against 100% and 85.8% of isolates respectively. In CZAR strains subjected to whole-genome sequencing (n = 18), resistance was mainly due to the expression of metallo-β-lactamases (66.6% VIM-type and 5.5% FIM-1), followed by PER-1 (16.6%) and GES-1 (5.5%) extended-spectrum β-lactamases, mostly carried by international high-risk clones (ST111 and ST235). Of note, two strains producing the PER-1 enzyme were resistant to all β-lactams, including cefiderocol. In conclusion, the CZA resistance rate among P. aeruginosa clinical isolates in Southern Italy remained low. CZAR isolates were mostly metallo-β-lactamases producers and belonging to ST111 and ST253 epidemic clones. It is important to implement robust surveillance systems to monitor emergence of new resistance mechanisms and to limit the spread of P. aeruginosa high-risk clones.

IMPORTANCE

Multidrug-resistant Pseudomonas aeruginosa infections are a growing threat due to the limited therapeutic options available. Ceftazidime-avibactam (CZA) is among the last-resort antibiotics for the treatment of difficult-to-treat P. aeruginosa infections, although resistance due to the acquisition of transferable β-lactamase genes is increasing. With this work, we report that CZA represents a highly active antipseudomonal β-lactam compound (after cefiderocol), and that metallo-β-lactamases (VIM-type) and extended-spectrum β-lactamases (GES and PER-type) production is the major factor underlying CZA resistance in isolates from Southern Italian hospitals. In addition, we reported that such resistance mechanisms were mainly carried by the international high-risk clones ST111 and ST235.

Capsid structure of bacteriophage ΦKZ provides insights into assembly and stabilization of jumbo phages

Jumbo phages are a group of tailed bacteriophages with large genomes and capsids. As a prototype of jumbo phage, ΦKZ infects Pseudomonas aeruginosa, a multi-drug-resistant (MDR) opportunistic pathogen leading to acute or chronic infection in immunocompromised individuals. It holds potential to be used as an antimicrobial agent and as a model for uncovering basic phage biology. Although previous low-resolution structural studies have indicated that jumbo phages may have more complicated capsid structures than smaller phages such as HK97, the detailed structures and the assembly mechanism of their capsids remain largely unknown. Here, we report a 3.5-Å-resolution cryo-EM structure of the ΦKZ capsid. The structure unveiled ten minor capsid proteins, with some decorating the outer surface of the capsid and the others forming a complex network attached to the capsid's inner surface. This network seems to play roles in driving capsid assembly and capsid stabilization. Similar mechanisms of capsid assembly and stabilization are probably employed by many other jumbo viruses.

Characterization of selected phages for biocontrol of food-spoilage pseudomonads

Pseudomonas spp., such as P. fluorescens group, P. fragi, and P. putida, are the major psychrophilic spoilage bacteria in the food industry. Bacteriophages (phages) are a promising tool for controlling food-spoilage and food-poisoning bacteria; however, there are few reports on phages effective on food-spoilage bacteria such as Pseudomonas spp. In this study, 12 Pseudomonas phages were isolated from chicken and soil samples. Based on the host range and lytic activity at 30 °C and 4 °C and various combinations of phages, phages vB_PflP-PCS4 and vB_PflP-PCW2 were selected to prepare phage cocktails to control Pseudomonas spp. The phage cocktail consisting of vB_PflP-PCS4 and vB_PflP-PCW2 showed the strongest lytic activity and retarded regrowth of P. fluorescens and P. putida at 30 °C, 8 °C, and 4 °C at a multiplicity of infection of 100. Nucleotide sequence analysis of the genomic DNA indicated that vB_PflP-PCS4 and vB_PflP-PCW2 phages were lytic phages of the Podoviridae family and lacked tRNA, toxin, or virulence genes. A novel endolysin gene was found in the genomic DNA of phage vB_PflP-PCS4. The results of this study suggest that the phage cocktail consisting of vB_PflP-PCS4 and vB_PflP-PCW2 is a promising tool for the biocontrol of psychrophilic food-spoilage pseudomonads during cold storage and distribution.

Beyond antibiotics: Emerging antivirulence strategies to combat Pseudomonas aeruginosa in cystic fibrosis

Pseudomonas aeruginosa is an opportunistic pathogen that poses a significant threat to individuals suffering from cystic fibrosis (CF). The pathogen is highly prevalent in CF individuals and is responsible for chronic infection, resulting in severe tissue damage and poor patient outcome. Prolonged antibiotic administration has led to the emergence of multidrug resistance in P. aeruginosa. In this direction, antivirulence strategies achieving targeted inhibition of bacterial virulence pathways, including quorum sensing, efflux pumps, lectins, and iron chelators, have been explored against CF isolates of P. aeruginosa. Hence, this review article presents a bird's eye view on the pulmonary infections involving P. aeruginosa in CF patients by laying emphasis on factors contributing to bacterial colonization, persistence, and disease progression along with the current line of therapeutics against P. aeruginosa in CF. We further collate scientific literature and discusses various antivirulence strategies that have been tested against P. aeruginosa isolates from CF patients.

A Simple Allelic Exchange Method for Efficient Seamless Knockout of Up to 34-kbp-Long Gene Cassettes in Pseudomonas

Gene knockout is a widely used technique for engineering bacterial genomes, investigating the roles of genes in metabolism, and conferring biological characteristics. Herein, we developed a rapid, efficient, and simple method for the knockout of long gene cassettes in Pseudomonas spp., based on a traditional allelic exchange strategy. The upstream and downstream sequences of the target gene cluster to be deleted were amplified using primers with 5'-end sequences identical to the multiple cloning sites of a suicide plasmid (mutant allele insert vector). The sequences were then fused with the linearized suicide plasmid in one step via seamless cloning. The resulting allelic exchange vector (recombinant plasmid) was introduced from the donor strain (Escherichia coli SM 10) into recipient cells (Pseudomonas putida, P. composti, and P. khazarica) via conjugation. Single-crossover merodiploids (integrates the vector into host chromosome by homologous recombination) were screened based on antibiotic resistance conferred by the plasmid, and double-crossover haploids (deleting the target gene clusters and inserted alien plasmid backbone) were selected using sucrose-mediated counterselection. Unlike other approaches, the method described herein introduces no selective marker genes into the genomes of the knockout mutants. Using our method, we successfully deleted polysaccharide-encoding gene clusters in P. putida, P. composti, and P. khazarica and generated four mutants with single-gene cassette deletions up to 18 kbp and one mutant with double-gene cassette deletion of approximately 34 kbp. Collectively, our results indicate that this method is ideal for the deletion of long genetic sequences, yielding seamless mutants of various Pseudomonas spp.

Non-interchangeable functions of efflux transporters of Pseudomonas aeruginosa in survival under infection-associated stress

Pseudomonas aeruginosa is a challenging opportunistic pathogen due to its intrinsic and acquired mechanisms of antibiotic resistance. A large repertoire of efflux transporters actively expels antibiotics, toxins, and metabolites from cells and enables growth of P. aeruginosa in diverse environments. In this study, we analyzed the roles of representative efflux pumps from the Resistance-Nodulation-Division (RND), Major Facilitator Superfamily (MFS), and Small Multidrug Resistance (SMR) families of proteins in the susceptibility of P. aeruginosa to antibiotics and bacterial growth under stresses imposed by human hosts during bacterial infections: an elevated temperature, osmotic stress, low iron, bile salts, and acidic pH. We selected five RND pumps MexAB-OprM, MexEF-OprN, MexCD-OprJ, MuxABC-OpmB, and TriABC-OpmH that differ in their substrate specificities and expression profiles, two MFS efflux pumps PA3136-3137 and PA5158-5160 renamed here into MfsAB and MfsCD-OpmG, respectively, and an SMR efflux transporter PA1540-1541 (MdtJI). We found that the most promiscuous RND pumps such as MexEF-OprN and MexAB-OprM are integrated into diverse survival mechanisms and enable P. aeruginosa growth under various stresses. MuxABC-OpmB and TriABC-OpmH pumps with narrower substrate spectra are beneficial only in the presence of the iron chelator 2,2'-dipyridyl and bile salts, respectively. MFS pumps do not contribute to antibiotic efflux but play orthogonal roles in acidic pH, low iron, and in the presence of bile salts. In contrast, MdtJI protects against polycationic antibiotics but does not contribute to survival under stress. Thus, efflux pumps play specific, non-interchangeable functions in P. aeruginosa cell physiology and bacterial survival under stresses.

IMPORTANCE

The role of multidrug efflux pumps in the intrinsic and clinical levels of antibiotic resistance in Pseudomonas aeruginosa and other gram-negative bacteria is well-established. Their functions in bacterial physiology, however, remain unclear. The P. aeruginosa genome comprises an arsenal of efflux pumps from different protein families, the substrate specificities of which are typically assessed by measuring their impact on susceptibility to antibiotics. In this study, we analyzed how deletions and overproductions of efflux pumps affect P. aeruginosa growth under human-infection-induced stresses. Our results show that the physiological functions of multidrug efflux pumps are non-redundant and essential for the survival of this important human pathogen under stress.