Phages from Ganges River curtail in vitro biofilms and planktonic growth of drug resistant Klebsiella pneumoniae in a zebrafish infection model

Sundaramoorthy, Niranjana Sri; Thothathri, Subramanian; Bhaskaran, Muthumeenakshi; ArunKumar, GaneshPrasad; Nagarajan, Saisubramanian

doi:10.1186/s13568-021-01181-0

Cited by 17 publications

(10 citation statements)

References 52 publications

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“…Nevertheless, majority of studies has compared the effect of antibiotics and phage therapy and scarce reports are available that has studied the combination of antibiotic and phage therapy. In our earlier study, we found that the combination of Streptomycin and KpG (Podoviridae phage specific to K. pneumoniae) curtailed the infection by 98% relative to untreated control, whereas KpG alone caused 77% reduction and only streptomycin resulted in 63% reduction in colony counts [39]. In the present study, U1G and colistin + U1G declined the bioburden by 0.8 and 1.4 log, respectively (Figure 7), corresponding to 86% and 95% reduction in bioburden.…”

Section: Discussionsupporting

confidence: 61%

“…No phages specific to U1007 were obtained from any other sources tested (Figure S1). We recently reported a phage KpG, belonging to Podoviridae, specific to MDR K. pneumoniae from Ganges, which was able to curtail the host's planktonic and biofilm mode of growth [39]. There are other numerous reports available on rich diversity of bacteriophages against various pathogens being isolated from The Ganges [40,41].…”

Section: Discussionmentioning

confidence: 99%

“…The same occurs in colistin + U1G group, nevertheless, the bacteria during the attempt to develop phage resistance might partially lose resistance to colistin and hence the combination can achieve enhanced killing than when individually treated. Zebrafish model has been used to study the efficiency of bacteriophages in curtailing infections caused by P. aeruginosa, K. pneumoniae, E. coli and E. faecalis [39,[47][48][49]. Nevertheless, majority of studies has compared the effect of antibiotics and phage therapy and scarce reports are available that has studied the combination of antibiotic and phage therapy.…”

Section: Discussionmentioning

confidence: 99%

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Genome Analysis of Bacteriophage (U1G) of Schitoviridae, Host Receptor Prediction using Machine Learning Tools and its Evaluation to Mitigate Colistin Resistant Clinical Isolate of Escherichia Coli In Vitro and In Vivo

Sundaramoorthy¹,

KU²,

JBB³

et al. 2023

Preprint

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The objective of the present study is to isolate phages targeting colistin resistant E. coli clinical isolates (U3790 and U1007), sequence and analyze the phage genome and use machine learning tools to predict host cell surface receptor and finally evaluate the efficiency of the phage in vitro and in vivo in a zebrafish model. Phage targeting colistin resistant U3790 could not be isolated possibly due to presence of capsule and intact prophages in genome of U3790 strain. Phage specific for E. coli U1007 was isolated from Ganges River (designated as U1G). The obtained phage was triple purified and enriched. U1G phages had a greater burst size of 195 PFU/cell and a short latent time of 25 min. TEM analysis showed that U1Gphage possessed a capsid of 70 nm in diameter with a shorter tail, which shows that U1G belongs to the family Podoviridae. Genome sequencing and analysis revealed that the size of the phage genome is 73275 bp with no tRNA sequence, antibiotic resistant or virulent genes. PHASTER annotation revealed the presence of phage RNA polymerase gene in the genome, which favors the classification of phage under a new family Schitoviridae. A machine learning (ML) based multi-class classification model using algorithms such as Random Forest, Logistic Regression, and Decision Tree were employed to predict the host receptor targeted by U1G phage and the best performing two algorithms predicted LPS O antigen as the host receptor targeted by the U1G receptor binding protein (RBP), the tail spike protein. The isolated phage was stable from pH 5.0 to 9.0 and upto 45°C. In vitro time kill assay showed an initial 5 log decline in CFU/ml of U1007 at 2 h in the presence of U1G followed by regrowth, Addition of colistin with U1G restricted the growth until 6 h, however it also resulted in a regrowth by 24 h. The phage did not pose any toxicity to zebrafish as evidenced by liver/brain enzyme profiles. In vivo intramuscular infection study showed that U1G and Col + U1G treatment caused a 0.8 log and 1.4 log decline, respectively underscoring its potential for use in phage cocktail therapy.

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Section: Discussionsupporting

confidence: 61%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genome Analysis of Bacteriophage (U1G) of Schitoviridae, Host Receptor Prediction using Machine Learning Tools and its Evaluation to Mitigate Colistin Resistant Clinical Isolate of Escherichia Coli In Vitro and In Vivo

Sundaramoorthy¹,

KU²,

JBB³

et al. 2023

Preprint

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“…Nevertheless, bacteriophages targeting MDR E. coli U1007 were isolated from The Ganges River (designated as U1G), Cooum River (CR) and Hospital Waste water(M) (Figure S1). We recently reported a phage KpG, belonging to Podoviridae, specific to MDR K. pneumoniae from which was able to curtail the host's planktonic and biofilm mode of growth [53]. There are other numerous reports available on rich diversity of bacteriophages against various pathogens being isolated from The Ganges [54,55].…”

Section: Discussionmentioning

confidence: 99%

Genome Analysis of Bacteriophage (U1G) of Schitoviridae, Host Receptor Prediction using Machine Learning Tools and its Evaluation to Mitigate Colistin Resistant Clinical Isolate of Escherichia Coli In Vitro and In Vivo

Sundaramoorthy,

KU,

Nair

et al. 2023

Preprint

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The objective of the present study is to isolate phages targeting multidrug resistant (MDR), extended spectrum beta lactamase (ESBL) positive clinical isolate of E. coli ( U1007), sequence and analyze the phage genome and use machine learning tools to predict host cell surface receptor and finally evaluate the efficiency of monophage and phage cocktail in vitro and in vivo in a zebrafish model. Phage specific for E. coli U1007 was isolated from Ganges River (designated as U1G), Cuoom River (designated as CR) and Hospital waste water (designated as M phage). The obtained phages were triple purified and enriched. U1G phages had a greater burst size of 124 PFU/cell and a latent time of 25 min.M phage had a burst size of 150 PFU/cell with a shortlatent time of 20min. Similarly CR phage has a short latent 20 min and a burst size of 115 PFU/cell. Based on capsid architecture, U1G phage resembles Podoviridae, CR phage is structurally similar to Myoviridae and M phage has morphology that resembles Siphoviridae. Genome sequencing and analysis revealed that the size of the U1G phage genome is 73275 bp Whereas that of CR phage and M phage are 45236 bp and 45294 bp, respectively. All three genomes were marked by the absence of genes encoding tRNA sequence, antibiotic resistant or virulent genes. A machine learning (ML) based multi-class classification model using algorithms such as Random Forest, Logistic Regression, and Decision Tree were employed to predict the host receptor targeted by all 3 phages and the best performing algorithm Random Forest predicted LPS O antigen , LamB or OmpC for U1G FhuA, OmpC for CR phage and FhuA, LamB, TonB or OmpF for the M phage as the host receptor targeted by the receptor binding protein (RBP) of the phages. In vitro time kill assay showed that treatment with monophages alone and along with colistin resulted in regrowth whereas phage combinations significantly reduced the regrowth and by 24h the phage cocktail along with colistin produced a significant 3 log declinein cell counts relative to the untreated control. In vivo intramuscular infection study in zebrafish showed that phages were non toxic and a cocktail of dual (U1G +M) phage along with colsitin resulted in a significant 3.5 log decline in cell counts whereas triple phage combination along with colistin resulted in 3 log decline in cell counts probably due to host receptor competition. Our study highlights the potential of phage cocktail therapy in mitigating MDR clinical isolate of E. coli in vitro and in vivo.

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“…In addition to a mature innate immune system, zebrafish embryos are genetically similar to human, and their transparency make them ideal for investigating characteristics of infection mechanisms unreachable in standard animal models. Very recently, several zebrafish studies have been published for evaluating phage treatment upon bacterial infections, though none have studied S. aureus (Easwaran et al, 2017;Johansen et al, 2021;Sundaramoorthy et al, 2021). Bacteria can be injected into the embryo's bloodstream alongside phages, and this treatment was effective with a better survival of the infected zebrafish embryos.…”

Section: Discussion and Concluding Remarksmentioning

confidence: 99%

Bacteriophage Therapy for Staphylococcus Aureus Infections: A Review of Animal Models, Treatments, and Clinical Trials

Plumet

Ahmad-Mansour

Dunyach-Rémy

et al. 2022

Front. Cell. Infect. Microbiol.

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Staphylococcus aureus (S. aureus) is a common and virulent human pathogen causing several serious illnesses including skin abscesses, wound infections, endocarditis, osteomyelitis, pneumonia, and toxic shock syndrome. Antibiotics were first introduced in the 1940s, leading to the belief that bacterial illnesses would be eradicated. However, microorganisms, including S. aureus, began to develop antibiotic resistance from the increased use and abuse of antibiotics. Antibiotic resistance is now one of the most serious threats to global public health. Bacteria like methicillin-resistant Staphylococcus aureus (MRSA) remain a major problem despite several efforts to find new antibiotics. New treatment approaches are required, with bacteriophage treatment, a non-antibiotic strategy to treat bacterial infections, showing particular promise. The ability of S. aureus to resist a wide range of antibiotics makes it an ideal candidate for phage therapy studies. Bacteriophages have a relatively restricted range of action, enabling them to target pathogenic bacteria. Their usage, usually in the form of a cocktail of bacteriophages, allows for more focused treatment while also overcoming the emergence of resistance. However, many obstacles remain, particularly in terms of their effects in vivo, necessitating the development of animal models to assess the bacteriophage efficiency. Here, we provide a review of the animal models, the various clinical case treatments, and clinical trials for S. aureus phage therapy.

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Phages from Ganges River curtail in vitro biofilms and planktonic growth of drug resistant Klebsiella pneumoniae in a zebrafish infection model

Cited by 17 publications

References 52 publications

Genome Analysis of Bacteriophage (U1G) of <em>Schitoviridae</em>, Host Receptor Prediction using Machine Learning Tools and its Evaluation to Mitigate Colistin Resistant Clinical Isolate of<em> Escherichia Coli</em> <em>In Vitro</em> and <em>In Vivo</em>

Genome Analysis of Bacteriophage (U1G) of <em>Schitoviridae</em>, Host Receptor Prediction using Machine Learning Tools and its Evaluation to Mitigate Colistin Resistant Clinical Isolate of<em> Escherichia Coli</em> <em>In Vitro</em> and <em>In Vivo</em>

Genome Analysis of Bacteriophage (U1G) of <em>Schitoviridae</em>, Host Receptor Prediction using Machine Learning Tools and its Evaluation to Mitigate Colistin Resistant Clinical Isolate of<em> Escherichia Coli</em> <em>In Vitro</em> and <em>In Vivo</em>

Bacteriophage Therapy for Staphylococcus Aureus Infections: A Review of Animal Models, Treatments, and Clinical Trials

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