Characterization and Genomic Analysis of a Novel Drexlervirial Bacteriophage IME268 with Lytic Activity Against Klebsiella pneumoniae

Relationship between biofilm formation and antibiotic resistance of Klebsiella pneumoniae and updates on antibiofilm therapeutic strategies

Klebsiella pneumoniae is a Gram-negative bacterium within the Enterobacteriaceae family that can cause multiple systemic infections, such as respiratory, blood, liver abscesses and urinary systems. Antibiotic resistance is a global health threat and K. pneumoniae warrants special attention due to its resistance to most modern day antibiotics. Biofilm formation is a critical obstruction that enhances the antibiotic resistance of K. pneumoniae. However, knowledge on the molecular mechanisms of biofilm formation and its relation with antibiotic resistance in K. pneumoniae is limited. Understanding the molecular mechanisms of biofilm formation and its correlation with antibiotic resistance is crucial for providing insight for the design of new drugs to control and treat biofilm-related infections. In this review, we summarize recent advances in genes contributing to the biofilm formation of K. pneumoniae, new progress on the relationship between biofilm formation and antibiotic resistance, and new therapeutic strategies targeting biofilms. Finally, we discuss future research directions that target biofilm formation and antibiotic resistance of this priority pathogen.

Characterization, taxonomic classification, and genomic analysis of two newly isolated bacteriophages with potential to infect Escherichia coli

Escherichia coli is a pathogenic bacterium that is widely distributed and can lead to serious illnesses in both humans and animals. As there is rising incidence of multidrug resistance among these bacteria, it has become imperative to discover alternative therapies beyond antibiotics to effectively treat such infections. Bacteriophage (phage) therapy has the potential to treat infections caused by E. coli, as phages contain enzymes that can cause lysis or destruction of bacterial cells. Simultaneously, the easy accessibility and cost-effectiveness of next-generation sequencing technologies have led to the accumulation of a vast amount of phage sequence data. Here, phages IME177 and IME267 were isolated from sewage water of a hospital in China. Modern phylogenetic approaches and key findings from the genomic analysis revealed that phages IME177 and IME267 are classified as members of the Kayfunavirus genus, Autographiviridae family, and a newly proposed Suseptimavirus genus under subfamily Gordonclarkvirinae, respectively. Further, the Kuravirus genus reshaped into three different genera: Kuravirus, Nieuwekanaalvirus, and Suspeptimavirus, which are classified together under a higher taxonomic rank (subfamily) named Gordonclarkvirinae. No genes related to virulence were detected in the genomes of the phages IME177 and IME267. Both phages exhibited a high degree of resilience to a wide range of conditions, including pH, temperature, exposure to chloroform, and UV radiation. Phages IME177 and IME267 are promising biological agents that can infect E. coli, making them suitable candidates for use in phage therapies.IMPORTANCEBiological and taxonomic characterization of phages is essential for facilitating the development of effective strategies for phage therapy and disease control. Escherichia coli phages are incredibly diverse, and their isolation and classification help us understand the scope and nature of this diversity. By identifying new phages and grouping them into families, we can better understand the genetic and structural variations between phages and how they affect their infectivity and interactions with bacteria. Overall, the isolation and classification of E. coli phages have broad implications for both basic and applied research, clinical practice, and public health.

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.

Alterations in the gut virome in patients with ankylosing spondylitis

Introduction

Ankylosing spondylitis (AS), a chronic autoimmune disease, has been linked to the gut bacteriome.

Methods

To investigate the characteristics of the gut virome in AS, we profiled the gut viral community of 193 AS patients and 59 healthy subjects based on a metagenome-wide analysis of fecal metagenomes from two publicly available datasets.

Results

AS patients revealed a significant decrease in gut viral richness and a considerable alteration of the overall viral structure. At the family level, AS patients had an increased abundance of Gratiaviridae and Quimbyviridae and a decreased abundance of Drexlerviridae and Schitoviridae. We identified 1,004 differentially abundant viral operational taxonomic units (vOTUs) between patients and controls, including a higher proportion of AS-enriched Myoviridae viruses and control-enriched Siphoviridae viruses. Moreover, the AS-enriched vOTUs were more likely to infect bacteria such as Flavonifractor, Achromobacter, and Eggerthellaceae, whereas the control-enriched vOTUs were more likely to be Blautia, Ruminococcus, Collinsella, Prevotella, and Faecalibacterium bacteriophages. Additionally, some viral functional orthologs differed significantly in frequency between the AS-enriched and control-enriched vOTUs, suggesting the functional role of these AS-associated viruses. Moreover, we trained classification models based on gut viral signatures to discriminate AS patients from healthy controls, with an optimal area under the receiver operator characteristic curve (AUC) up to 0.936, suggesting the clinical potential of the gut virome for diagnosing AS.

Discussion

This work provides novel insight into the AS gut virome, and the findings may guide future mechanistic and therapeutic studies for other autoimmune diseases.

Alterations of the gut virome in patients with systemic lupus erythematosus

Background

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that has been linked to the dysbiosis of the gut microbiome and virome. However, the potential characterization of the gut virome in SLE patients needs to be explored more extensively.

Methods

Herein, we analyzed the gut viral community of 16 SLE patients and 31 healthy controls using both bulk and virus-like particle (VLP)-based metagenomic sequencing of their fecal samples. A total of 15,999 non-redundant viral operational taxonomic units (vOTUs) were identified from the metagenomic assembled contigs and used for gut virome profiling.

Results

SLE patients exhibited a significant decrease in gut viral diversity in the bulk metagenome dataset, but this change was not significant in the VLP metagenome dataset. Also, considerable alterations of the overall gut virome composition and remarkable changes in the viral family compositions were observed in SLE patients compared with healthy controls, as observed in both two technologies. We identified 408 vOTUs (177 SLE-enriched and 231 control-enriched) with significantly different relative abundances between patients and controls in the bulk virome, and 18 vOTUs (17 SLE-enriched in 1 control-enriched) in the VLP virome. The SLE-enriched vOTUs included numerous Siphoviridae, Microviridae, and crAss-like viruses and were frequently predicted to infect Bacteroides, Parabacteroides, and Ruminococcus_E, while the control-enriched contained numerous members of Siphoviridae and Myoviridae and were predicted to infect Prevotella and Lachnospirales_CAG-274. We explored the correlations between gut viruses and bacteria and found that some Lachnospirales_CAG-274 and Hungatella_A phages may play key roles in the virus-bacterium network. Furthermore, we explored the gut viral signatures for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of above 0.95, suggesting the potential of the gut virome in the prediction of SLE.

Conclusion

Our findings demonstrated the alterations in viral diversity and taxonomic composition of the gut virome of SLE patients. Further research into the etiology of SLE and the gut viral community will open up new avenues for treating and preventing SLE and other autoimmune diseases.

Isolation and genomic characterization of a novel Autographiviridae bacteriophage IME184 with lytic activity against Klebsiella pneumoniae

Klebsiella pneumoniae, a multidrug resistant bacterium that causes nosocomial infections including septicemia, pneumonia etc. Bacteriophages are potential antimicrobial agents for the treatment of antibiotic resistant bacteria. In this study, a novel bacteriophage IME184, was isolated from hospital sewage against clinical multi-drug resistant Klebsiella pneumoniae. Transmission electron microscopy and genomic characterization exhibited this phage belongs to the Molineuxvirinae genus, Autographiviridae family. Phage IME184 possessed a double-stranded DNA genome composed of 44,598 bp with a GC content of 50.3%. The phage genome encodes 57 open reading frames, out of 26 are hypothetical proteins while 31 had assigned putative functions. No tRNA, virulence related or antibiotic resistance genes were found in phage genome. Comparative genomic analysis showed that phage IME184 has 94% similarity with genomic sequence of Klebsiella phage K1-ULIP33 (MK380014.1). Multiplicity of infection, one step growth curve and host range of phage were also measured. According to findings, Phage IME184 is a promising biological agent that infects Klebsiella pneumoniae and can be used in future phage therapies.