Comparative metabolomics revealed key pathways associated with the synergistic killing of multidrug-resistant Klebsiella pneumoniae by a bacteriophage-polymyxin combination

Proteomic profile of multidrug-resistant Serratia marcescens under meropenem challenge

Serratia marcescens is an opportunistic bacterium implicated in the prevalence of serious nosocomial infections and increased outbreaks in Intensive Care Units (ICUs) and Neonatal Intensive Care Units (NICUs). S. marcescens strains are resistant to several antimicrobial classes and express numerous virulence factors that promote pathogenicity. In the present study, the proteomic profile of the multidrug-resistant (MDR) S. marcescens clinical isolate challenged with the antimicrobial meropenem was evaluated. The proteins obtained were analyzed using liquid chromatography coupled with tandem mass spectrometry (LC-MSE). A total of 199 induced proteins were identified revealing that multidrug-resistant S. marcescens promotes increasing of proteins related to energy metabolism and efflux pump and decreases synthesis of proteins related to oxidative stress response and cell mobility upon meropenem challenge, shedding some light on the relationship between expressed proteins and bacterial pathogenicity after antimicrobial induction.

Construction and validation of a predictive model for the risk of multidrug-resistant Klebsiella pneumoniae infection based on machine learning algorithms - a multicenter retrospective study

OBJECTIVE

The development of a reliable predictive model for Multi-drug-resistant Klebsiella pneumoniae (MDR-KP) infections is imperative for the timely identification of at-risk individuals.

METHODS

This study analyzed data from 3,554 patients with KP infection at multiple hospitals. By comparing six machine learning algorithms (Logistic Regression(LR), Efficient Neural Network (ENet), Decision Tree(DT), MultiLayer Perceptron(MLP), Support Vector Machine(SVM), and Extreme Gradient Boosting(XGBoost)), we constructed and validated the prediction model. Furthermore, the model interpretation was conducted through SHapley Additive exPlanations (SHAP) analysis. Subsequently, nomograms were developed to estimate the risk of MDR-KP infection in hospitalized individuals. Finally, the association between independent variables and the risk of MDR-KP acquisition was elucidated through Restricted Cubic Spline (RCS) analysis.

RESULTS

The results of the multivariable logistic regression analysis indicated that C-reactive protein (CRP), Uric Acid (UA), Urea, Platelet (PLT), Hemoglobin (HB), Red blood cell counts (RBC), Age, and Gender were identified as independent risk factors. We incorporated these independent risk factors into six machine learning, and found that the XGBoost-based model exhibited superior performance compared to other machine learning algorithms, achieving a recall of 0.732, an F1 score of 0.707, and an AUC of 0.777. Furthermore, the SHAP method highlighted Urea, UA, and PLT as the primary decision factors predicted by the machine learning model, and the RCS analysis revealed a nonlinear relationship between Age, CRP, RBC, HB, UA, UREA, and the risk of MDR-KP infection.

CONCLUSION

This study has developed an effective risk prediction model for MDR-KP infection. The model has the potential to assist healthcare providers in early identification of high-risk patients, enabling timely implementation of preventive and therapeutic interventions.

Phage-antibiotic combinations against Klebsiella pneumoniae: impact of methodological approaches on effect evaluation

Background

The combined use of bacteriophages and antibiotics represents a promising strategy for combating multidrug-resistant bacterial pathogens. However, the lack of uniformity in methods for assessing combination effects and experimental protocols has resulted in inconsistent findings across studies. This study aimed to evaluate the effects of interactions between phages and antibiotics on Klebsiella pneumoniae strains using various statistical approaches to formalize combination effects.

Methods

Effects were assessed for four antibiotics from distinct classes (gentamicin, levofloxacin, meropenem, chloramphenicol), three phages from different genera (Dlv622, Seu621, FRZ284), and a depolymerase (Dep622) on three K. pneumoniae strains of the KL23 capsule type. Antibiotics were used at Cmax concentrations, and phages at sublethal levels. A modified t-test, Bliss independence model, two-way ANOVA, and checkerboard assay were employed to evaluate the results.

Results

Among 48 combinations, 33 effects were statistically significant, including 26 cases of synergy and 7 of antagonism. All statistical methods showed consistency in identifying effects; however, the t-test and Bliss method detected a greater number of effects. The strongest synergy was observed with levofloxacin in combination with Seu621 or Dep622 across all bacterial strains. Checkerboard assays confirmed synergy in selected cases but indicated that combined effects could vary with antimicrobial concentrations.

Conclusion

The choice of analytical method substantially impacts the detection of phage-antibiotic effects. The t-test and Bliss method, due to their simplicity and sensitivity, may be optimal for clinical application, while two-way ANOVA for confirming strong interactions. These results emphasize the need to consider interaction characteristics when designing therapeutic strategies.

Re-Emergence of Bacteriophages and Their Products as Antibacterial Agents: An Overview

Microbes possess diverse genetic and metabolic traits that help them withstand adverse conditions. Microbial pathogens cause significant economic losses and around 7.7 million human deaths annually. While antibiotics have historically been a lifesaving treatment, their effectiveness is declining due to antibiotic-resistant strains, prompting the exploration of bacterial predation as an alternative. Bacteriophages (BPhs) have reemerged as antibacterial agents, offering advantages over antibiotics, such as (i) high specificity, (ii) self-replication, and (iii) strong killing capacity. This review explores BPh- and enzyme-based antibacterial strategies for infectious disease treatment, discussing phage-antibiotic synergy, the risks of BPh resistance, and the role of quorum sensing in BPh therapy.

Exploring Structure-Activity Relationships and Modes of Action of Laterocidine

A significant increase in life-threatening infections caused by Gram-negative "superbugs" is a serious threat to global health. With a dearth of new antibiotics in the developmental pipeline, antibiotics with novel mechanisms of action are urgently required to prevent a return to the preantibiotic era. A key strategy to develop novel anti-infective treatments is to discover new natural scaffolds with distinct mechanisms of action. Laterocidine is a unique cyclic lipodepsipeptide with activity against multiple problematic multidrug-resistant Gram-negative pathogens, including Pseudomonas aeruginosa, Acinetobacter baumannii, and Enterobacterales. Here, we developed a total chemical synthesis methodology for laterocidine and undertook systematic structure-activity relationship studies with chemical biology and NMR. We discovered important structural features that drive the antimicrobial activity of laterocidine, leading to the discovery of an engineered peptide surpassing the efficacy of the original peptide. This engineered peptide demonstrated complete inhibition of the growth of a polymyxin-resistant strain of Pseudomonas aeruginosa in static time-kill experiments.

Systematic genome-wide discovery of host factors governing bacteriophage infectivity

Bacterial host factors regulate the infection cycle of bacteriophages. Except for some well-studied host factors (e.g., receptors or restriction-modification systems), the contribution of the rest of the host genome on phage infection remains poorly understood. We developed PHAGEPACK, a pooled assay that systematically and comprehensively measures each host-gene impact on phage fitness. PHAGEPACK combines CRISPR interference with phage packaging to link host perturbation to phage fitness during active infection. Using PHAGEPACK, we constructed a genome-wide map of genes impacting T7 phage fitness in permissive E. coli, revealing pathways previously unknown to affect phage packaging. When applied to the non-permissive E. coli O121, PHAGEPACK identified pathways leading to host resistance; their removal increased phage susceptibility up to a billion-fold. Bioinformatic analysis indicates phage genomes carry homologs or truncations of key host factors, potentially for fitness advantage. In summary, PHAGEPACK offers valuable insights into phage-host interactions, phage evolution, and bacterial resistance.

The Safety of Bacteriophages in Treatment of Diseases Caused by Multidrug-Resistant Bacteria

Given the urgency due to the rapid emergence of multidrug-resistant (MDR) bacteria, bacteriophages (phages), which are viruses that specifically target and kill bacteria, are rising as a potential alternative to antibiotics. In recent years, researchers have begun to elucidate the safety aspects of phage therapy with the aim of ensuring safe and effective clinical applications. While phage therapy has generally been demonstrated to be safe and tolerable among animals and humans, the current research on phage safety monitoring lacks sufficient and consistent data. This emphasizes the critical need for a standardized phage safety assessment to ensure a more reliable evaluation of its safety profile. Therefore, this review aims to bridge the knowledge gap concerning phage safety for treating MDR bacterial infections by covering various aspects involving phage applications, including phage preparation, administration, and the implications for human health and the environment.

Lipid A Modification and Metabolic Adaptation in Polymyxin-Resistant, New Delhi Metallo-β-Lactamase-Producing Klebsiella pneumoniae

Polymyxins are last-line antibiotics employed against multidrug-resistant (MDR) Klebsiella pneumoniae. Worryingly, polymyxin resistance is rapidly on the rise globally. Polymyxins initially target lipid A of lipopolysaccharides (LPSs) in the cell outer membrane (OM), causing disorganization and cell lysis. While most studies focus on how genetic variations confer polymyxin resistance, the mechanisms of membrane remodeling and metabolic changes in polymyxin-resistant strains remain unclear, thus hampering the development of effective therapies to treat severe K. pneumoniae infections. In the present study, lipid A profiling, OM lipidomics, genomics, and metabolomics were integrated to elucidate the global mechanisms of polymyxin resistance and metabolic adaptation in a polymyxin-resistant strain (strain S01R; MIC of >128 mg/L) obtained from K. pneumoniae strain S01, a polymyxin-susceptible (MIC of 2 mg/L), New Delhi metallo-β-lactamase (NDM)-producing MDR clinical isolate. Genomic analysis revealed a novel in-frame deletion at position V258 of PhoQ in S01R, potentially leading to lipid A modification with 4-amino-4-deoxy-l-arabinose (L-Ara4N) despite the absence of polymyxin B. Comparative metabolomic analysis revealed slightly elevated levels of energy production and amino acid metabolism in S01R compared to their levels in S01. Exposure to polymyxin B (4 mg/L for S01 and 512 mg/L for S01R) substantially altered energy, nucleotide, and amino acid metabolism and resulted in greater accumulation of lipids in both strains. Furthermore, the change induced by polymyxin B treatment was dramatic at both 1 and 4 h in S01 but only significant at 4 h in S01R. Overall, profound metabolic adaptation was observed in S01R following polymyxin B treatment. These findings contribute to our understanding of polymyxin resistance mechanisms in problematic NDM-producing K. pneumoniae strains and may facilitate the discovery of novel therapeutic targets. IMPORTANCE Antimicrobial resistance (AMR) is a major threat to global health. The emergence of resistance to the polymyxins that are the last line of defense in so-called Gram-negative "superbugs" has further increased the urgency to develop novel therapies. There are frequent outbreaks of K. pneumoniae infections in hospitals being reported, and polymyxin usage is increasing remarkably. Importantly, the polymyxin-resistant K. pneumoniae strains are imposing more severe consequences to health systems. Using metabolomics, lipid A profiling, and outer membrane lipidomics, our findings reveal (i) changes in the pentose phosphate pathway and amino acid and nucleotide metabolism in a susceptible strain following polymyxin treatment and (ii) how cellular metabolism, lipid A modification, and outer membrane remodeling were altered in K. pneumoniae following the acquisition of polymyxin resistance. Our study provides, for the first time, mechanistic insights into metabolic responses to polymyxin treatment in a multidrug-resistant, NDM-producing K. pneumoniae clinical isolate with acquired polymyxin resistance. Overall, these results will assist in identifying new therapeutic targets to combat and prevent polymyxin resistance.

New Bacteriophages Members of the Ackermannviridae Family Specific for Klebsiella pneumoniae ST258

Background

Carbapenem-resistant Klebsiella pneumoniae, particularly isolates classified as sequence-type 258 (ST258), are multidrug-resistant strains that are strongly associated with poor-prognosis nosocomial infections, as current therapeutic options are limited and ineffective. In recent years, phage therapy has emerged as a promising treatment option for these scenarios.

Methodology and Results

We report the isolation and characterization of three new phages against Klebsiella pneumoniae ST258 strains recovered from Machángara river wastewater. These new members of the Ackermannviridae family showed stability over a wide temperature and pH range and burst sizes ranging from 6 to 44 plaque-forming units per bacteria. Their genomes were about 157 kilobases, with an average guanine-cytosine content of 46.4% and showed presence of several transfer RNAs, which also allowed us to predict in silico a lytic replicative cycle due to the presence of endolysins and lysozymes.

Conclusion

Three lytic phages of Ackermannviridae family were recovered against Klebsiella pneumoniae ST258 strains from sewage; however, further characterization is needed for future consideration as therapeutic alternatives.

Phages for treatment of Klebsiella pneumoniae infections

Klebsiella pneumoniae is an opportunistic pathogen involved in both hospital- and community-acquired infections. K. pneumoniae is associated with various infections, including pneumonia, septicemia, meningitis, urinary tract infection, and surgical wound infection. K. pneumoniae possesses serious virulence, biofilm formation ability, and severe resistance to many antibiotics especially hospital-acquired strains, due to excessive use in healthcare systems. This limits the available effective antibiotics that can be used for patients suffering from K. pneumoniae infections; therefore, alternative treatments are urgently needed. Bacteriophages (for short, phages) are prokaryotic viruses capable of infecting, replicating, and then lysing (lytic phages) the bacterial host. Phage therapy exhibited great potential for treating multidrug-resistant bacterial infections comprising K. pneumoniae. Hence, this chapter emphasizes and summarizes the research articles in the PubMed database from 1948 until the 15th of December 2022, addressing phage therapy against K. pneumoniae. The chapter provides an overview of K. pneumoniae phages covering different aspects, including phage isolation, different morphotypes of isolated phages, in vitro characterization, anti-biofilm activity, various therapeutic forms, in vivo research and clinical studies.

Untargeted Metabolomics Analysis of Gentamicin-Induced Tolerant Colonies of Klebsiella pneumoniae

PURPOSE

Antibiotic resistance development in pathogenic bacteria like Klebsiella pneumoniae seriously threatens humankind. Therefore, it is important to understand the interaction of bacteria with antibiotic agents and how it acquires resistance at the molecular level. The current study describes metabolomics analysis of K. pneumoniae sensitive strains and its gentamicin-tolerant (resistant) strains.

METHODS

K. pneumoniae strains were treated at five different concentrations of gentamicin, increasing from a low dose (16.2 µg/mL) to the highest dose (250 µg/mL) at three incubation time periods (24h, 48h, and 72h). Colonies obtained at various concentrations and time intervals were subjected to metabolomic analysis using GC-MS.

RESULTS

A drastic change was observed in the morphology of K. pneumoniae colonies with the increasing gentamicin concentration. Moreover, K. pneumoniae strains grown at the highest concentration (250 µg/mL) were found tolerant to 1 mg/mL gentamicin (4-folds) and considered resistant strains. A total of 459 metabolites were identified. A sequential down/up-regulation in 4, 3, and 4 metabolites were observed in association with the increasing gentamicin concentration at 24h, 48h, and 72h, respectively. While with the comparative analysis of resistant and sensitive strains, a total of seven down- and sixteen up-regulated metabolites were observed. The concentration of some fatty acids and sugars have been found to increase while, a few metabolites like inosine, tyrosine, 1-propionylproline, and 2-hydroxyacetic acid have been found down-regulated in resistant samples.

CONCLUSION

These regulator metabolites might be associated with resistance development in K. pneumoniae against gentamicin and might be helpful in the rapid detection of gentamicin-resistant clinical strains.

Characterization of a Lytic Bacteriophage and Demonstration of Its Combined Lytic Effect with a K2 Depolymerase on the Hypervirulent Klebsiella pneumoniae Strain 52145

Klebsiella pneumoniae is a nosocomial pathogen. Among its virulence factors is the capsule with a prominent role in defense and biofilm formation. Bacteriophages (phages) can evoke the lysis of bacterial cells. Due to the mode of action of their polysaccharide depolymerase enzymes, phages are typically specific for one bacterial strain and its capsule type. In this study, we characterized a bacteriophage against the capsule-defective mutant of the nosocomial K. pneumoniae 52145 strain, which lacks K2 capsule. The phage showed a relatively narrow host range but evoked lysis on a few strains with capsular serotypes K33, K21, and K24. Phylogenetic analysis showed that the newly isolated Klebsiella phage 731 belongs to the Webervirus genus in the Drexlerviridae family; it has a 31.084 MDa double-stranded, linear DNA with a length of 50,306 base pairs and a G + C content of 50.9%. Out of the 79 open reading frames (ORFs), we performed the identification of orf22, coding for a trimeric tail fiber protein with putative capsule depolymerase activity, along with the mapping of other putative depolymerases of phage 731 and homologous phages. Efficacy of a previously described recombinant K2 depolymerase (B1dep) was tested by co-spotting phage 731 on K. pneumoniae strains, and it was demonstrated that the B1dep-phage 731 combination allows the lysis of the wild type 52145 strain, originally resistant to the phage 731. With phage 731, we showed that B1dep is a promising candidate for use as a possible antimicrobial agent, as it renders the virulent strain defenseless against other phages. Phage 731 alone is also important due to its efficacy on K. pneumoniae strains possessing epidemiologically important serotypes.

Chemical-Biology and Metabolomics Studies in Phage-Host Interactions

For many years, several studies have explored the molecular mechanisms involved in the infection of bacteria by their specific phages to understand the main infection strategies and the host defense strategies. The modulation of the mechanisms involved in the infection, as well as the expression of key substances in the development of the different life cycles of phages, function as a natural source of strategies capable of promoting the control of different pathogens that are harmful to human and animal health. Therefore, this chapter aims to provide an overview of the mechanisms involved in virus-bacteria interaction to explore the main compounds produced or altered as a chemical survival strategy and the metabolism modulation when occurring a host-phage interaction. In this context, emphasis will be given to the chemistry of peptides/proteins and enzymes encoded by bacteriophages in the control of pathogenic bacteria and the use of secondary metabolites recently reported as active participants in the mechanisms of phage-bacteria interaction. Finally, metabolomics strategies developed to gain new insights into the metabolism involved in the phage-host interaction and the metabolomics workflow in host-phage interaction will be presented.

Examining the effects of Salmonella phage on the caecal microbiota and metabolome features in Salmonella-free broilers

Bacteriophages selectively infect and kill their target bacterial host, being a promising approach to controlling zoonotic bacteria in poultry production. To ensure confidence in its use, fundamental questions of safety and toxicity monitoring of phage therapy should be raised. Due to its high specificity, a minimal impact on the gut ecology is expected; however, more in-depth research into key parameters that influence the success of phage interventions has been needed to reach a consensus on the impact of bacteriophage therapy in the gut. In this context, this study aimed to investigate the interaction of phages with animals; more specifically, we compared the caecum microbiome and metabolome after a Salmonella phage challenge in Salmonella-free broilers, evaluating the role of the phage administration route. To this end, we employed 45 caecum content samples from a previous study where Salmonella phages were administered via drinking water or feed for 24 h from 4, 5 to 6-weeks-old broilers. High-throughput 16S rRNA gene sequencing showed a high level of similarity (beta diversity) but revealed a significant change in alpha diversity between broilers with Salmonella-phage administered in the drinking water and control. Our results showed that the phages affected only a few genera of the microbiota's structure, regardless of the administration route. Among these, we found a significant increase in Streptococcus and Sellimonas in the drinking water and Lactobacillus, Anaeroplasma and Clostridia_vadinBB60_group in the feed. Nevertheless, the LC-HRMS-based metabolomics analyses revealed that despite few genera were significantly affected, a substantial number of metabolites, especially in the phage administered in the drinking water were significantly altered (64 and 14 in the drinking water and feed groups, respectively). Overall, our study shows that preventive therapy with bacteriophages minimally alters the caecal microbiota but significantly impacts their metabolites, regardless of the route of administration.

Identification of metabolite extraction method for targeted exploration of antimicrobial resistance associated metabolites of Klebsiella pneumoniae

Antimicrobial resistant Klebsiella pneumoniae (K. pneumoniae), as being a pathogen of critical clinical concern, urgently demands effective therapeutic options. However, the discovery of novel antibiotics over the last three decades has declined drastically and necessitates exploring novel strategies. Metabolomic modulation has been the promising approach for the development of effective therapeutics to deal with AMR; however, only limited efforts have been made to-date, possibly due to the unavailability of suitable metabolites extraction protocols. Therefore, in order to establish a detailed metabolome of K. pneumoniae and identify a method for targeted exploration of metabolites that are involved in the regulation of AMR associated processes, metabolites were extracted using multiple methods of metabolites extraction (freeze-thaw cycle (FTC) and sonication cycle (SC) method alone or in combination (FTC followed by SC; FTC + SC)) from K. pneumoniae cells and then identified using an orbitrap mass analyzer (ESI-LC-MS/MS). A total of 151 metabolites were identified by using FTC, 132 metabolites by using FTC+SC, 103 metabolites by using SC and 69 metabolites common among all the methods used which altogether enabled the identification of 199 unique metabolites. Of these 199, 70 metabolites were known to have an association with AMR phenotype and among these, the FTC + SC method yielded better (identified 55 metabolites), quantitatively and qualitatively compared to FTC and SC alone (identified 51 and 41 metabolites respectively). Each method of metabolite extraction showed a definite degree of biasness and specificity towards chemical classes of metabolites and jointly contributed to the development of a detailed metabolome of the pathogen. FTC method was observed to give higher metabolomic coverage as compared to SC alone and FTC + SC. However, FTC + SC resulted in the identification of a higher number of AMR associated metabolites of K. pneumoniae compared to FTC and SC alone.