Bacteriophage φYeO3-12, Specific forYersinia enterocolitica Serotype O:3, Is Related to Coliphages T3 and T7

Bacteriophage φYeO3-12 is a lytic phage of Yersinia enterocolitica serotype O:3. The phage receptor is the lipopolysaccharide O chain of this serotype that consists of the rare sugar 6-deoxy-l-altropyranose. A one-step growth curve of φYeO3-12 revealed eclipse and latent periods of 15 and 25 min, respectively, with a burst size of about 120 PFU per infected cell. In electron microscopy φYeO3-12 virions showed pentagonal outlines, indicating their icosahedral nature. The phage capsid was shown to be composed of at least 10 structural proteins, of which a protein of 43 kDa was predominant. N-terminal sequences of three structural proteins were determined, two of them showing strong homology to structural proteins of coliphages T3 and T7. The phage genome was found to consist of a double-stranded DNA molecule of 40 kb without cohesive ends. A physical map of the phage DNA was constructed using five restriction enzymes. The phage infection could be effectively neutralized using serum from a rabbit immunized with whole φYeO3-12 particles. The antiserum also neutralized T3 infection, although not as efficiently as that of φYeO3-12. φYeO3-12 was found to share, in addition to the N-terminal sequence homology, several common features with T3, including morphology and nonsubjectibility to F exclusion. The evidence conclusively indicated that φYeO3-12 is the first close relative of phage T3 to be described.

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Yersiniophage ϕR1-37 is a tailed bacteriophage having a 270 kb DNA genome with thymidine replaced by deoxyuridine

Microbiology ◽

10.1099/mic.0.28265-0 ◽

2005 ◽

Vol 151 (12) ◽

pp. 4093-4102 ◽

Cited By ~ 60

Author(s):

Saija Kiljunen ◽

Kristo Hakala ◽

Elise Pinta ◽

Suvi Huttunen ◽

Patrycja Pluta ◽

...

Keyword(s):

Yersinia Pseudotuberculosis ◽

Burst Size ◽

Outer Core ◽

International Committee ◽

Amino Acid Sequences ◽

Structural Proteins ◽

Virulence Plasmid ◽

O Antigen ◽

Serotype O ◽

Phage Receptor

Bacteriophage ϕR1-37 was isolated based on its ability to infect strain YeO3-R1, a virulence-plasmid-cured O antigen-negative derivative of Yersinia enterocolitica serotype O : 3. In this study, the phage receptor was found to be a structure in the outer core hexasaccharide of Y. enterocolitica O : 3 LPS. The phage receptor was present in the outer core of strains of many other Y. enterocolitica serotypes, but also in some Yersinia intermedia strains. Surprisingly, the receptor structure resided in the O antigen of Yersinia pseudotuberculosis O : 9. Electron microscopy demonstrated that ϕR1-37 particles have an icosahedral head of 88 nm, a short neck of 10 nm, a long contractile tail of 236 nm, and tail fibres of at least 86 nm. This implies that the phage belongs to the order Caudovirales and the family Myoviridae in the ICTV (International Committee for Taxonomy of Viruses) classification. ϕR1-37 was found to have a lytic life cycle, with eclipse and latent periods of 40 and 50 min, respectively, and a burst size of ∼80 p.f.u. per infected cell. Restriction digestions and PFGE showed that the ϕR1-37 genome was dsDNA and ∼270 kb in size. Enzymically hydrolysed DNA was subjected to HPLC-MS/MS analysis, which demonstrated that the ϕR1-37 genome is composed of DNA in which thymidine (T) is >99 % replaced by deoxyuridine (dU). The only organisms known to have similar DNA are the Bacillus subtilis-specific bacteriophages PBS1 and PBS2. N-terminal amino acid sequences of four major structural proteins did not show any similarity to (viral) protein sequences in databases, indicating that close relatives of ϕR1-37 have not yet been characterized. Genes for two of the structural proteins, p24 and p46, were identified from the partially sequenced ϕR1-37 genome.

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A BACTERIOPHAGE THAT ATTACKS NUMEROUS PHYTOPATHOGENIC XANTHOMONAS SPECIES

Canadian Journal of Microbiology ◽

10.1139/m58-053 ◽

1958 ◽

Vol 4 (5) ◽

pp. 493-497 ◽

Cited By ~ 7

Author(s):

M. D. Sutton ◽

H. Katznelson ◽

C. Quadling

Keyword(s):

Burst Size ◽

Lytic Phage ◽

Plant Materials ◽

Single Burst ◽

Xanthomonas Species ◽

One Step ◽

Average Burst Size ◽

Step Growth ◽

Rot Disease

This paper reports the isolation of a lytic phage that attacks in vitro numerous phytopathogenic Xanthomonas species, including X. campestris (Pammel) Dowson, the cause of black rot disease of crucifers. Although 'one-step' growth experiments suggested an average burst size of ca. four for this phage-host system, 'single burst' experiments indicated a burst size of ca. one hundred phage particles per bacterium. The particles have typical phage morphology, as determined by electron microscopy. This phage gave satisfactory results when used in the rapid plaque count test for detection of phage-sensitive bacteria in plant materials.

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Biological characteristics and anti-biofilm activity of a lytic phage against vancomycin-resistant Enterococcus faecium

Iranian Journal of Microbiology ◽

10.18502/ijm.v13i5.7436 ◽

2021 ◽

Author(s):

Forough Goodarzi ◽

Masoumeh Hallajzadeh ◽

Mohammad Sholeh ◽

Malihe Talebi ◽

Vahid Pirhajati Mahabadi ◽

...

Keyword(s):

Enterococcus Faecium ◽

Burst Size ◽

Biological Properties ◽

Lytic Phage ◽

Wide Range ◽

One Step ◽

Vancomycin Resistant ◽

Hospital Sewage ◽

Phage Growth ◽

And Control

Background and Objectives: An important leading cause of the emergence of vancomycin-resistant enterococci, especially Enterococcus faecium, is the inefficiency of antibiotics in the elimination of drug-resistant pathogens. Consequently, the need for alternative treatments is more necessary than ever. Materials and Methods: A highly effective bacteriophage against vancomycin-resistant E. faecium called vB-EfmS-S2 was isolated from hospital sewage. The biological properties of phage S2 and its effect on biofilm structures were determined. Results: Phage S2 was specifically capable of lysing a wide range of clinical E. faecium isolates. According to Electron mi- croscopy observations, the phage S2 belonged to the Siphoviridea family. Suitable pH spectra for phage survival was 5-11, at which the phage showed 100% activity. The optimal temperature for phage growth was 30-45°C, with the highest growth at 37°C. Based on one-step growth curve results, the latent period of phage S2 was 14 min with a burst size of 200 PFU/ml. The phage S2 was also able to tolerate bile at concentrations of 1 and 2% and required Mg2+ for an effective infection cycle. Biofilms were significantly inhibited and disrupted in the presence of the phage. Conclusion: According to the results, phage S2 could potentially be an alternative for the elimination and control of vancomycin-resistant E. faecium biofilm.

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Aztreonam Lysine Increases the Activity of Phages E79 and phiKZ against Pseudomonas aeruginosa PA01

Microorganisms ◽

10.3390/microorganisms9010152 ◽

2021 ◽

Vol 9 (1) ◽

pp. 152

Author(s):

Carly M. Davis ◽

Jaclyn G. McCutcheon ◽

Jonathan J. Dennis

Keyword(s):

Pseudomonas Aeruginosa ◽

Morphological Changes ◽

Burst Size ◽

Type Iv Pili ◽

Biofilm Growth ◽

Promising Alternative ◽

Type Iv ◽

Alternative Treatment Option ◽

One Step ◽

Step Growth

Pseudomonas aeruginosa is a pernicious bacterial pathogen that is difficult to treat because of high levels of antibiotic resistance. A promising alternative treatment option for such bacteria is the application of bacteriophages; the correct combination of phages plus antibiotics can produce synergistic inhibitory effects. In this study, we describe morphological changes induced by sub-MIC levels of the antibiotic aztreonam lysine (AzLys) on P. aeruginosa PA01, which may in part explain the observed phage–antibiotic synergy (PAS). One-step growth curves for phage E79 showed increased adsorption rates, decreased infection latency, accelerated time to lysis and a minor reduction in burst size. Phage E79 plus AzLys PAS was also able to significantly reduce P. aeruginosa biofilm growth over 3-fold as compared to phage treatment alone. Sub-inhibitory AzLys-induced filamentation of P. aeruginosa cells resulted in loss of twitching motility and a reduction in swimming motility, likely due to a reduction in the number of polar Type IV pili and flagella, respectively, on the filamented cell surfaces. Phage phiKZ, which uses Type IV pili as a receptor, did not exhibit increased activity with AzLys at lower sub-inhibitory levels, but still produced phage–antibiotic synergistic killing with sub-inhibitory AzLys. A one-step growth curve indicates that phiKZ in the presence of AzLys also exhibits a decreased infection latency and moderately undergoes accelerated time to lysis. In contrast to prior PAS studies demonstrating that phages undergo delayed time to lysis with cell filamentation, these PAS results show that phages undergo accelerated time to lysis, which therefore suggests that PAS is dependent upon multiple factors, including the type of phages and antibiotics used, and the bacterial host being tested.

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Lytic Myophage Abp53 Encodes Several Proteins Similar to Those Encoded by Host Acinetobacter baumannii and Phage phiKO2

Applied and Environmental Microbiology ◽

10.1128/aem.05116-11 ◽

2011 ◽

Vol 77 (19) ◽

pp. 6755-6762 ◽

Cited By ~ 14

Author(s):

Chia-Ni Lee ◽

Tsai-Tien Tseng ◽

Juey-Wen Lin ◽

Yung-Chieh Fu ◽

Shu-Fen Weng ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Burst Size ◽

Sputum Sample ◽

Polyacrylamide Gel Electrophoresis ◽

Multiple Drug ◽

Lytic Phage ◽

Tail Fiber ◽

Drug Resistant ◽

Content Type ◽

Multiple Drug Resistant

ABSTRACTAcinetobacter baumanniiis an important Gram-negative opportunistic pathogen causing nosocomial infections. The emergence of multiple-drug-resistantA. baumanniiisolates has increased in recent years. Directed toward phage therapy, a lytic phage ofA. baumannii, designated Abp53, was isolated from a sputum sample in this study. Abp53 has an isometric head and a contractile tail with tail fibers (belonging toMyoviridae), a latent period of about 10 min, and a burst size of approximately 150 PFU per infected cell. Abp53 could completely lyse 27% of theA. baumanniiisolates tested, which were all multiple drug resistant, but not other bacteria. Mg2+enhanced the adsorption and productivity of, and host lysis by, Abp53. Twenty Abp53 virion proteins were visualized in SDS-polyacrylamide gel electrophoresis, with a 47-kDa protein being the predicted major capsid protein. Abp53 has a double-stranded DNA genome of 95 kb. Sequence analyses of a 10-kb region revealed 8 open reading frames. Five of the encoded proteins, including 3 tail components and 2 hypothetical proteins, were similar to proteins encoded byA. baumanniistrain ACICU. ORF1176 (one of the tail components, 1,176 amino acids [aa]), which is also similar to tail protein gp21 ofKlebsiellaphage phiKO2, contained repeated domains similar to those within the ACICU_02717 protein ofA. baumanniiACICU and gp21. These findings suggest a common ancestry and horizontal gene transfer during evolution. As phages can expand the host range by domain duplication in tail fiber proteins, repeated domains in ORF1176 might have a similar significance in Abp53.

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Construction of a genomic map ofMoraxella (Branhamella) catarrhalisATCC 25238 and physical mapping of virulence-associated genes

Canadian Journal of Microbiology ◽

10.1139/w99-005 ◽

1999 ◽

Vol 45 (4) ◽

pp. 299-303 ◽

Cited By ~ 6

Author(s):

K T Nguyen ◽

E J Hansen ◽

M A Farinha

Keyword(s):

Gel Electrophoresis ◽

Moraxella Catarrhalis ◽

Southern Hybridization ◽

Physical Map ◽

Outer Membrane Proteins ◽

Restriction Enzymes ◽

Pulsed Field Gel Electrophoresis ◽

Respiratory Pathogens ◽

Circular Chromosome ◽

Pulsed Field

A physical genome map of the Moraxella catarrhalis type strain (ATCC 25238) has been constructed using pulsed field gel electrophoresis. Macrorestriction analyses of the genome of M. catarrhalis were performed by digestion with the restriction enzymes SmaI, NotI, and RsrII, which cleave the single circular chromosome into 9, 10, and 6 fragments, respectively. The chromosomal fragments generated by pulsed field gel electrophoresis were converted to a linkage map utilizing a combination of partial digestions, and cross-hybridizations. Moraxella catarrhalis, like a number of other respiratory pathogens, has a relatively small genome estimated at 1750 kilobase pairs or about 40% of the size of the Escherichia coli genome. The locations of the four ribosomal RNA operons (rrnLS) were determined by Southern hybridization and by digestion with I-CeuI endonuclease. A number of genes involved in virulence have been placed onto the physical map by Southern hybridization including those encoding the predominant outer-membrane proteins and the chromosomal gene encoding beta-lactamase.Key words: Moraxella catarrhalis, physical map, genome analysis, pulsed-field gel electrophoresis, virulence.

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Characterization and Full Genome Sequence of Novel KPP-5 Lytic Phage against Klebsiella pneumoniae Responsible for Recalcitrant Infection

Biomedicines ◽

10.3390/biomedicines9040342 ◽

2021 ◽

Vol 9 (4) ◽

pp. 342

Author(s):

Ahmed R. Sofy ◽

Noha K. El-Dougdoug ◽

Ehab E. Refaey ◽

Rehab A. Dawoud ◽

Ahmed A. Hmed

Keyword(s):

Klebsiella Pneumoniae ◽

Burst Size ◽

Phylogenetic Analyses ◽

Foodborne Pathogen ◽

Gc Content ◽

Full Genome Sequence ◽

Multiple Drug ◽

Lytic Phage ◽

Trna Genes ◽

Bacteriophage Therapy

Klebsiella pneumoniae is a hazardous opportunistic pathogen that is involved in many serious human diseases and is considered to be an important foodborne pathogen found in many food types. Multidrug resistance (MDR) K. pneumoniae strains have recently spread and increased, making bacteriophage therapy an effective alternative to multiple drug-resistant pathogens. As a consequence, this research was conducted to describe the genome and basic biological characteristics of a novel phage capable of lysing MDR K. pneumoniae isolated from food samples in Egypt. The host range revealed that KPP-5 phage had potent lytic activity and was able to infect all selected MDR K. pneumoniae strains from different sources. Electron microscopy images showed that KPP-5 lytic phage was a podovirus morphology. The one-step growth curve exhibited that KPP-5 phage had a relatively short latent period of 25 min, and the burst size was about 236 PFU/infected cells. In addition, KPP-5 phage showed high stability at different temperatures and pH levels. KPP-5 phage has a linear dsDNA genome with a length of 38,245 bp with a GC content of 50.8% and 40 predicted open reading frames (ORFs). Comparative genomics and phylogenetic analyses showed that KPP-5 is most closely associated with the Teetrevirus genus in the Autographviridae family. No tRNA genes have been identified in the KPP-5 phage genome. In addition, phage-borne virulence genes or drug resistance genes were not present, suggesting that KPP-5 could be used safely as a phage biocontrol agent.

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Characterization of a New and Efficient Polyvalent Phage Infecting E. coli O157:H7, Salmonella spp., and Shigella sonnei

Microorganisms ◽

10.3390/microorganisms9102105 ◽

2021 ◽

Vol 9 (10) ◽

pp. 2105

Author(s):

Su-Hyeon Kim ◽

Damilare Adeyemi ◽

Mi-Kyung Park

Keyword(s):

Burst Size ◽

Genomic Analysis ◽

Cesium Chloride ◽

Shigella Sonnei ◽

Health Concern ◽

Lytic Phage ◽

Salmonella Spp ◽

E Coli ◽

Significant Public Health ◽

Ph Range

Ongoing outbreaks of foodborne diseases remain a significant public health concern. Lytic phages provide promising attributes as biocontrol agents. This study characterized KFS-EC3, a polyvalent and lytic phage, which was isolated from slaughterhouse sewage and purified by cesium chloride density centrifugation. Host range and efficiency of plating analyses revealed that KFS-EC3 is polyvalent and can efficiently infect E. coli O157:H7, Salmonella spp., and Shigella sonnei. KFS-EC3 had a latent time of 20 min and burst size of ~71 phages/infected cell. KFS-EC3 was stable and infectious following storage at a pH range of 3 to 11 and a temperature range of −70°C to 60°C. KFS-EC3 could inhibit E. coli O157:H7 growth by 2 logs up to 52 h even at the lowest MOI of 0.001. Genomic analysis of KFS-EC3 revealed that it consisted of 167,440 bp and 273 ORFs identified as functional genes, without any genes associated with antibiotic resistance, virulence, allergenicity, and lysogenicity. This phage was finally classified into the Tequatrovirus genus of the Myoviridae family. In conclusion, KFS-EC3 could simultaneously infect E. coli O157:H7, S. sonnei, and Salmonella spp. with the lowest MOI values over long periods, suggesting its suitability for simultaneous pathogen control in foods.

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A Novel Benthic Phage Infecting Shewanella with Strong Replication Ability

Viruses ◽

10.3390/v11111081 ◽

2019 ◽

Vol 11 (11) ◽

pp. 1081 ◽

Cited By ~ 3

Author(s):

Zengmeng Wang ◽

Jiulong Zhao ◽

Long Wang ◽

Chengcheng Li ◽

Jianhui Liu ◽

...

Keyword(s):

Burst Size ◽

Coastal Sediments ◽

The Yellow Sea ◽

Comparative Genomic ◽

Lytic Phage ◽

Host Interactions ◽

Metabolic Genes ◽

Double Stranded Dna ◽

Auxiliary Metabolic Genes ◽

Structure Assembly

The coastal sediments were considered to contain diverse phages playing important roles in driving biogeochemical cycles based on genetic analysis. However, till now, benthic phages in coastal sediments were very rarely isolated, which largely limits our understanding of their biological characteristics. Here, we describe a novel lytic phage (named Shewanella phage S0112) isolated from the coastal sediments of the Yellow Sea infecting a sediment bacterium of the genus Shewanella. The phage has a very high replication capability, with the burst size of ca. 1170 phage particles per infected cell, which is 5–10 times higher than that of most phages isolated before. Meanwhile, the latent period of this phage is relatively longer, which might ensure adequate time for phage replication. The phage has a double-stranded DNA genome comprising 62,286 bp with 102 ORFs, ca. 60% of which are functionally unknown. The expression products of 16 ORF genes, mainly structural proteins, were identified by LC-MS/MS analysis. Besides the general DNA metabolism and structure assembly genes in the phage genome, there is a cluster of auxiliary metabolic genes that may be involved in 7-cyano-7-deazaguanine (preQ0) biosynthesis. Meanwhile, a pyrophosphohydrolase (MazG) gene being considered as a regulator of programmed cell death or involving in host stringer responses is inserted in this gene cluster. Comparative genomic and phylogenetic analysis both revealed a great novelty of phage S0112. This study represents the first report of a benthic phage infecting Shewanella, which also sheds light on the phage–host interactions in coastal sediments.

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Linkage Map of Escherichia coli K-12, Edition 10: The Physical Map

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.62.3.985-1019.1998 ◽

1998 ◽

Vol 62 (3) ◽

pp. 985-1019 ◽

Cited By ~ 72

Author(s):

Kenneth E. Rudd

Keyword(s):

Escherichia Coli ◽

Physical Map ◽

Restriction Enzymes ◽

Open Reading Frames ◽

Sequence Elements ◽

Systematic Nomenclature ◽

Repetitive Extragenic Palindrome ◽

Complete Set ◽

K 12 ◽

Reading Frames

SUMMARY A physical map, EcoMap10, of the now completely sequenced Escherichia coli chromosome is presented. Calculated genomic positions for the eight restriction enzymes BamHI, HindIII, EcoRI, EcoRV, BglI, KpnI, PstI, and PvuII are depicted. Both sequenced and unsequenced Kohara/Isono miniset clones are aligned to this calculated restriction map. DNA sequence searches identify the precise locations of insertion sequence elements and repetitive extragenic palindrome clusters. EcoGene10, a revised set of genes and functionally uncharacterized open reading frames (ORFs), is also depicted on EcoMap10. The complete set of unnamed ORFs in EcoGene10 are assigned provisional names beginning with the letter “y” by using a systematic nomenclature.

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