Genome Analysis and Therapeutic Evaluation of a Novel Lytic Bacteriophage of Salmonella Typhimurium: Suggestive of a New Genus in the Subfamily Vequintavirinae

Sattar, Sadia; Ullah, Inam; Khanum, Sofia; Bailie, Marc; Shamsi, Bushra; Ahmed, Ibrar; Shah, S. P.; Javed, Sundus; Ghafoor, Aamir; Pervaiz, Amna; Sohail, Fakiha; Kaleem, Imdad; Tariq, Aamira; Bostan, Nazish; Ali, Ijaz; Altermann, Eric

doi:10.3390/v14020241

Cited by 6 publications

(3 citation statements)

References 56 publications

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“…Rivera et al [52] described Salmonella phage STGO-35-1, and Wara-like receptorbinding proteins and tail tube proteins were identified, along with structural protein major capsid and DNA polymerase. A Salmonella phage, SSBI34, was reported by Sattar et al, [53] and like our study, it encoded a DNA ligase and DNA polymerase I and III, indicating independence from host polymerases for DNA replication. The A1-protein-encoding gene was detected in Wara, which is involved in the degradation of host DNA and the shutoff of host genes and phage pre-early genes (https://www.uniprot.org/uniprotkb/Q6QGT3/entry, accessed on 15 January 2022).…”

Section: Discussionsupporting

confidence: 86%

Molecular Characterization of Salmonella Phage Wara Isolated from River Water in Brazil

et al. 2023

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Antimicrobial resistance is increasing despite new treatments being employed, so novel strategies are required to ensure that bacterial infections remain treatable. Bacteriophages (phages; bacteria viruses) have the potential to be used as natural antimicrobial methods to control bacterial pathogens such as Salmonella spp. A Salmonella phage, Wara, was isolated from environmental water samples at the Subaé River Basin, Salvador de Bahia, Brazil. The basin has environmental impacts in its main watercourses arising from the dumping of domestic and industrial effluents and agricultural and anthropological activities. The phage genome sequence was determined by Oxford Nanopore Technologies (ONT) MinION and Illumina HiSeq sequencing, and assembly was carried out by Racon (MinION) and Unicycler (Illumina, Illumina + MinION). The genome was annotated and compared to other Salmonella phages using various bioinformatics approaches. MinION DNA sequencing combined with Racon assembly gave the best complete genome sequence. Phylogenetic analysis revealed that Wara is a member of the Tequintavirus genus. A lack of lysogeny genes, antimicrobial resistance, and virulence genes indicated that Wara has therapeutic and biocontrol potential against Salmonella species in healthcare and agriculture.

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Section: Discussionsupporting

confidence: 86%

Molecular Characterization of Salmonella Phage Wara Isolated from River Water in Brazil

et al. 2023

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“…The phage's latent period was calculated from the OSG graph and is considered somewhat short. Previous studies have linked optimal latent time qualities to good viral fitness [48]. The latent duration of phage SA14 after infection was 25 min, which is less than that of other E. faecalis phages reported earlier (30-50 min) [49].…”

Section: Discussionmentioning

confidence: 69%

Isolation and phenotypic characterization of bacteriophage SA14 with lytic- and anti-biofilm activity against multidrug-resistant Enterococcus faecalis

Ali

Dishisha

El-Gendy

et al. 2023

Beni-Suef Univ J Basic Appl Sci

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Background Antimicrobial resistance is a growing global health concern demanding more attention and action at the international-, national- and regional levels. In the present study, bacteriophage was sought as a potential alternative to traditional antibiotics. Results Vancomycin-resistant Enterococcus faecalis was isolated from a urine sample. Partial 16S rRNA-gene sequencing and VITEK®2 system were employed for its identification, biochemical characterization, and antibiotic susceptibility testing. The isolate was resistant to eight antibiotics (out of 11): vancomycin, gentamicin (high-level synergy), streptomycin (high-level synergy), ciprofloxacin, levofloxacin, erythromycin, quinupristin/dalfopristin, and tetracycline. Bacteriophage SA14 was isolated from sewage water using the multidrug-resistant isolate as a host. Transmission electron micrographs revealed that phage SA14 is a member of the Siphoviridae family displaying the typical circular head and long non-contractile tail. The phage showed characteristic stability to a wide range of solution pH and temperatures, with optimal stability at pH 7.4 and 4 °C, while showing high specificity toward their host. Based on the one-step growth curve, the phage's latent period was 25 min, and the burst size was 20 PFU/ml. The lytic activity of phage SA14 was evaluated at various multiplicities of infection (MOI), all considerably suppressed the growth of the host organism. Moreover, phage SA14 displayed a characteristic anti-biofilm activity as observed by the reduction in adhered biomass and -viable cells in the pre-formed biofilm by 19.1-fold and 2.5-fold, respectively. Conclusion Phage therapy can be a valuable alternative to antibiotics against multi-drug resistant microorganisms.

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“…Salmonella enterica serovar Typhimurium strain SE-BS17 was isolated and characterized in Molecular Virology Labs (MVL), CUI, Islamabad from retail poultry samples and its isolation procedure is published previously in [24] and [60]. This strain is also characterized by 16S rRNA typing (Macrogen, Seoul, Korea) and the resulting sequence is submitted to NCBI (GenBank Acc.…”

Section: Bacterial Strain and Bacteriophage Isolationmentioning

confidence: 99%

Isolation and Molecular Characterization of a Novel Podo-virus BIS08P22 having a Unique Terminase Enzyme Representing a new Genus in Class <em>Caudoviricetes</em>

Sattar,

Carbone,

Basharat

et al. 2023

Preprint

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Salmonella enterica includes enteric pathogens of zoonotic potential, possessing one of the largest pools of temperate phages in their genomes. One such class of phages previously called Podoviridae (Now genera placed directly under class Caudoviricetes temporarily) is the largest group of temperate phages that lysogenize clinically and economically important Salmonella enterica serovars. These phages are capable of generalized transduction and are well known for carrying foreign DNA (mobile genetic elements and resistance genes) to new bacterial species that play a major role in the evolution, pathogenicity, and host adaptability of Salmonella serovars. Here we report a novel species of podo viruses; Salmonella phage BIS08P22 (BIS08) that infects Salmonella enterica serovar Typhimurium strain SE-BS17 (Acc. NO: MZ503545). Phage BIS08 was viable only at biological pH and temperature (pH7 and 37 °C) and features 41,574 -base pair (bp) linear ds DNA genome with 47% GC content. It encodes 73 putative Open Reading Frames (ORFs), has a mosaic arrangement, and shares only 16 core genes with its closest homologs. BIS08 genome possesses only 52 % homology (genome-wide Nucleotide homology by VIRIDIC analysis) with members of the genus Lederbergvirus which is not sufficient to place it in the same genus. This phage has a unique terminase enzyme (DNA packaging motor) with no nucleotide and protein homology with any known member of the Lederbergvirus genus. We carried out a detailed phylogenetic and genome analysis of this novel phage and proposed its placement in a new genus. Our study also suggests a revision in the classification of the genus Lederbergvirus. We also performed in silico structural analysis of the BIS08 unique terminase enzyme comparing it to its close homologs.

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Genome Analysis and Therapeutic Evaluation of a Novel Lytic Bacteriophage of Salmonella Typhimurium: Suggestive of a New Genus in the Subfamily Vequintavirinae

Cited by 6 publications

References 56 publications

Molecular Characterization of Salmonella Phage Wara Isolated from River Water in Brazil

Molecular Characterization of Salmonella Phage Wara Isolated from River Water in Brazil

Isolation and phenotypic characterization of bacteriophage SA14 with lytic- and anti-biofilm activity against multidrug-resistant Enterococcus faecalis

Isolation and Molecular Characterization of a Novel Podo-virus BIS08P22 having a Unique Terminase Enzyme Representing a new Genus in Class <em>Caudoviricetes</em>

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