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Characterization and genome-informatic analysis of a novel lytic Pseudomonas mendocina phage vB_PmeS_STP12 suitable for phage therapy or biocontrol

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A Correction to this article was published on 05 May 2024

This article has been updated

Abstract

Background

A novel lytic bacteriophage (phage) was isolated with Pseudomonas mendocina strain STP12 (P. mendocina) from the untreated site of Sewage Treatment Plant of Lovely Professional University, India. P. mendocina is a Gram-negative, rod-shaped, aerobic bacterium belonging to the family Pseudomonadaceae and has been reported in fifteen (15) cases of economically important diseases worldwide.

Methods and results

Here, a novel phage specifically infecting and killing P. mendocina strain STP12 was isolated from sewage sample using enrichment, spot test and double agar overlay (DAOL) method and was designated as vB_PmeS_STP12. The phage vB-PmeS-STP12 was viable at wide range of pH and temperature ranging from 4 to10 and − 20 to 70 °C respectively. Host range and efficiency of plating (EOP) analysis indicated that phage vB-PmeS-STP12 was capable of infecting and killing P. mendocina strain STP6 with EOP of 0.34. Phage vB_PmeS_STP12 was found to have a significant bacterial reduction (p < 0.005) at all the doses administered, particularly at optimal MOI of 1 PFU/CFU, compared to the control. Morphological analysis using high resolution transmission electron microscopy (HR-TEM) revealed an icosahedral capsid of ~ 55 nm in diameter on average with a short, non-contractile tail. The genome of vB_PmeS_STP12 is a linear, dsDNA containing 36,212 bp in size with a GC content of 58.87% harbouring 46 open reading frames (ORFs). The 46 predicted ORFs encode proteins with functional information categorized as lysis, replication, packaging, regulation, assembly, infection, immune, and hypothetical. However, the genome of vB_PmeS_STP12 appeared to be devoid of tRNAs, integrase gene, toxins genes, virulence factors, antimicrobial resistance genes (ARGs) and CRISPR arrays. The blast analysis with phylogeny revealed that vB_PmeS_STP12 is genetically similar to Pseudomonas phage PMBT14, Pseudomonas phage Almagne and Serratia phage Serbin with a highest identity of 74.00%, 74.93% and 59.48% respectively.

Conclusions

Taken together, characterization, morphological analysis and genome-informatics indicated that vB_PmeS_STP12 is podovirus morphotype belonging to the class Caudoviticetes, family Zobellviridae which appeared to be devoid of integrase gene, ARGs, CRISPR arrays, virulence factors and toxins genes, exhibiting stability and infectivity at wide range of pH (4 to10) and temperature (–20 to 70 °C), thereby making vB_PmeS_STP12 suitable for phage therapy or biocontrol. Based on the bibliometric analysis and data availability with respect to sequences deposited in GenBank, this is the first report of a phage infecting Pseudomonas mendocina.

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Data availability

The genome sequence of Pseudomonas mendocina phage vB_PmeS_STP12 and the 16 S rRNA sequence of its host Pseudomonas mendocina strain STP12 have been deposited in the GenBank under the accession numbers OR754314 and OR188352 respectively (https://www.ncbi.nlm.nih.gov/nuccore). The 16 S rRNA sequences of the alternative hosts used for host range analysis namely P. mendocina strain STP6, S. stutzeri strain STP9, B. stratosphericus strain STP9 and P. mirabilis strain STP14 have also been deposited in the GenBank under the accession numbers OR188127, OR188486, OR186294, and OR187366 respectively (https://www.ncbi.nlm.nih.gov/nuccore).

Change history

Abbreviations

AMR:

Antimicrobial resistance

Anti-CRISPRdb:

Anti- Clustered regularly interspaced short palindromic repeats database

Anti-CRISPR proteins:

Anti- Clustered regularly interspaced short palindromic repeats proteins

ARGs:

Antimicrobial resistance genes

BLASTn:

Basic local alignment search tool for nucleotide

BLASTP:

Basic local alignment search tool for proteins

BOD:

Biochemical oxygen demand

CARD:

Comprehensive antibiotic research database

CIF:

Central instrumentation facility

COD:

Chemical oxygen demand

CRISPR-arrays:

Clustered regularly interspaced short palindromic repeats-arrays

CRISPRCasFinder:

Clustered regularly interspaced short palindromic repeats-CRISPR-associated protein finder

DAOL:

Double agar overlay

DHF:

Dihydrofolate

DNA:

Deoxyribonucleic acid

DO:

Dissolved oxygen

DSBs:

DNA double-strand breaks

dsDNA:

Double-stranded DNA

dUMP:

2’-deoxyuridine- 5’-monophosphate

dTMP:

2’-deoxythymidine-5’-monophosphate

eggNOG:

Evolutionary genealogy of genes:Non- supervised Orthologous Group

EC:

Electrical conductivity

EPA:

Environmental protection agency

HR-TEM:

High resolution-transmission electron microscopy

HQ:

High quality

HiFi:

High fidelity

ICTV:

International Committee on Taxonomy of Viruses

IISER:

Indian institute of science research and education

LB:

Luria Bertani

LPU:

Lovely Professional University

MDR Bacteria:

Multidrug-resistant bacteria

MMseqs:

Many-against-Many sequence searching

MOI:

Multiplicity of infection

mTHF:

5,10-methylenetetrahydrofolate

NCBI:

National Center for Biotechnology Information

NT:

Nucleotide

NR:

Non-redundant

ON:

Overnight

ORFs:

Open reading frames

PCR:

Polymerase chain reaction

PFU:

Plaque forming unit

PE:

Pair-end

RNA:

Ribonucleic acid

rRNA:

ribosomal RNA

SM buffer:

Sodium magnesium buffer

ssDNA:

Single-stranded DNA

STP:

Sewage treatment plant

TDS:

Total dissolved solid

TEM:

Transmission electron microscopy

TMHMM:

Transmembrane hidden Markov model

tRNA:

Transfer RNA

tRNAscan-SE:

Transfer RNA scan in genomic sequence

TSS:

Total suspended solid

US:

United States

UV light:

Ultraviolet light

VFDB:

Virulence factor database

WGS:

Whole-genome sequencing

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Acknowledgements

We would like to thank Lovely Professional University for providing the facilities to carry out the present study; Associate Professor Gabriel Magno de Freitas Almeida of UiT The Arctic University of Norway for his constructive guidance; the CIF, IISER Thiruvananthapuram for conducting the HR-TEM analysis.

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  1. Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab, 144401, India

    Sani Sharif Usman & Evangeline Christina

  2. Department of Biological Sciences, Faculty of Science, Federal University of Kashere, P.M.B. 0182, Gombe, Nigeria

    Sani Sharif Usman

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  1. Sani Sharif Usman
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  2. Evangeline Christina
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Sani Sharif Usman: Conceptualization, Formal analysis, Investigation, Project administration, Software, Writing – original draft, Writing – review & editing. Evangeline Christina: Conceptualization, Formal analysis, Investigation, Project administration, Software, Supervision, Writing – original draft, Writing – review & editing. The authors read and approved the final manuscript as well as agreed to authorship and submission of the manuscript for publication.

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Correspondence to Evangeline Christina.

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The original online version of this article was revised: The article title is corrected as ‘Characterization and genome-informatic analysis of a novel lytic Pseudomonas mendocina phage vB_PmeS_STP12 suitable for phage therapy or biocontrol’

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Usman, S.S., Christina, E. Characterization and genome-informatic analysis of a novel lytic Pseudomonas mendocina phage vB_PmeS_STP12 suitable for phage therapy or biocontrol. Mol Biol Rep 51, 419 (2024). https://doi.org/10.1007/s11033-024-09362-3

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