Complete Genome of Citrobacter freundii Siphophage Stevie

Shaw, Justin P.; Medina, Carlos A. Aviles; Chen, Yi; Luna, Adrian J.; Hernández, Adriana C.; Everett, Gabriel F. Kuty

doi:10.1128/genomea.01434-14

Cited by 12 publications

(12 citation statements)

References 18 publications

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“…4 ). A BLASTP search of the predicted 213 aa fusion protein showed it shares 47% identity (E-value 3 × 10 −56 ) with the tape measure chaperone of the Citrobacter Siphoviridae phage Stevie, reported to have a conserved translational frameshift ( Shaw et al, 2015 ; Fig. 4 ).…”

Section: Resultsmentioning

confidence: 99%

Klebsiella pneumoniaesubsp.pneumoniae–bacteriophage combination from the caecal effluent of a healthy woman

Hoyles

Murphy

Neve

et al. 2015

PeerJ

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A sample of caecal effluent was obtained from a female patient who had undergone a routine colonoscopic examination. Bacteria were isolated anaerobically from the sample, and screened against the remaining filtered caecal effluent in an attempt to isolate bacteriophages (phages). A lytic phage, named KLPN1, was isolated on a strain identified as Klebsiella pneumoniae subsp. pneumoniae (capsular type K2, rmpA+). This Siphoviridae phage presents a rosette-like tail tip and exhibits depolymerase activity, as demonstrated by the formation of plaque-surrounding haloes that increased in size over the course of incubation. When screened against a panel of clinical isolates of K. pneumoniae subsp. pneumoniae, phage KLPN1 was shown to infect and lyse capsular type K2 strains, though it did not exhibit depolymerase activity on such hosts. The genome of KLPN1 was determined to be 49,037 bp (50.53 %GC) in length, encompassing 73 predicted ORFs, of which 23 represented genes associated with structure, host recognition, packaging, DNA replication and cell lysis. On the basis of sequence analyses, phages KLPN1 (GenBank: KR262148) and 1513 (a member of the family Siphoviridae, GenBank: KP658157) were found to be two new members of the genus “Kp36likevirus.”

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Section: Resultsmentioning

confidence: 99%

Klebsiella pneumoniaesubsp.pneumoniae–bacteriophage combination from the caecal effluent of a healthy woman

Hoyles

Murphy

Neve

et al. 2015

PeerJ

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“…Citrobacter freundii exists in the natural environment, especially in healthcare settings and is difficult to eradicate [Chaudhry et al, 2014]. Many infections are caused by C. freundii, including severe peritonitis [Kataria and Saad, 2015], wound infections [Akbar et al, 2015], urinary tract infections [Shaw et al, 2015], brain abscesses [Nguyen et al, 2015], pneumonia [Nguyen et al, 2015], and emphysematous pyelonephritis [Yanagawa et al, 2013]. To identify potentially effective treatments targeting this pathogen, C. freundii phages merit further attention, as these phages may provide good alternatives to conventional antibiotics, especially for antibiotic-resistant pathogenic bacteria [Hong et al, 2013].…”

Section: Introductionmentioning

confidence: 99%

“…LK1 has a narrow host range and was classified as a member of the Podoviridae family; it has an icosahedral head and a short tail, with a genome described as doublestranded (ds) DNA (20-23 kb), but no detailed genomic sequence information [Chaudhry et al, 2014] was published. Recently, the complete genome sequences of the following four C. freundii phages were submitted to GenBank by Kuty Everett and colleagues [Edwards et al, 2015;Hwang et al, 2015;Nguyen et al, 2015;Shaw et al, 2015]: Moogle (KM236239), Miller (NC025414), Stevie (KM236241), and Moon (KM236240); Miller belongs to the Myoviridae family [Hwang et al, 2015], Stevie belongs to the Siphoviridae family [Shaw et al, 2015], and Moogle and Moon are unclassified phages [Edwards et al, 2015;Nguyen et al, 2015]. Additionally, none of these phages have been described or studied in detail as yet.…”

Section: Introductionmentioning

confidence: 99%

Characterization of phiCFP‐1, a virulent bacteriophage specific for Citrobacter freundii

Zhao

Huang

Zhao

et al. 2015

Journal of Medical Virology

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Citrobacter freundii, a Gram-negative bacterium, causes many opportunistic infections. Bacteriophage phiCFP-1 was isolated and characterized by its ability to lyse the multidrug-resistant clinical C. freundii strain P10159. Transmission electron microscopy showed that the phage has an icosahedral head and a short tail, making it a Podoviridae family member. In a single-step growth experiment, phiCFP-1 exhibited an eclipse period of 20 min and a burst size of 100 particles per cell. Its genome assembled as a circular molecule when genomic sequencing was completed. However, based on genome content and organization, it was categorized as a classic T7-related phage, and such phages are known to have linear genomes with direct terminal repeats. With the quick and simple method established herein, the 38,625-bp linear double-stranded DNA with 229-bp direct terminal repeats was accurately identified. The genome contained 43 putative open reading frames and no tRNA genes. Using a proteomics-based approach, seven viral and two host proteins from purified phiCFP-1 particles were identified. Comparative genomics and recombination analyzes revealed close genetic relatedness among phiCFP-1, phiYeO3-12/vB_YenP_AP5 (from Yersinia enterocolitica O3), and phiSG-JL2 (from Salmonella enterica).

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“…And yet, only a limited number of Citrobacter phages have been previously described, most of which only at the genome nucleotide level. Furthermore, most previously characterized phages infect C. freundii, including members related to T4virus (Merlin, Miller, Moon) (14-16), FelixO1virus (Michonne, Mordin, Moogle) (17)(18)(19), T1virus (Stevie) (20), and T7virus (phiCFP-1, SH1, SH2, SH3, SH4, SH5) (21,22) genera. Genome sequences are also publically available for the T7virus related phages CR8 and CR44b that specifically infect C. rodentium (23).…”

Section: Introductionmentioning

confidence: 99%

Isolation and characterization of bacteriophages that infect Citrobacter rodentium, a model pathogen for investigating human intestinal diseases

Luong

Cedarstrom

et al. 2018

Preprint

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Citrobacter rodentium is a mouse-restricted pathogen that has long been used as an in vivo model for two important human intestinal pathogen enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC). And yet, in contrast to E. coli, little is known about the bacteriophages (phages) -bacterial viruses -that infect C. rodentium, reflecting in part a need to isolate and compare phages associated with this bacterial species. Here, we isolated two novel virulent phages CrRp3 and CrRp10 that infect C. rodentium and conduct in vitro and comparative genomic studies with other, related phages. We show that CrRp3 should be considered as a new species within the genus Sp6virus in the family Podoviridae, having relatively close relations to E. coli phages K1-E and K1-5 in both gene content and genome organization. By contrast, CrRp10 genome is 98% identical to that of E. coli phage Ime09 and thus should be considered as a new strain of the latter phage. We provide evidence that genomes of CrRp3 and CrRp10 have been shaped by both horizontal genetic exchange and genetic drift. Furthermore, phylogenetic analyses showed that these phages are more closely related to E. coli phages than to those infecting members of the Citrobacter genus, suggesting that CrRp3 and CrRp10 may have evolved from E. coli phages following a host-switch event.

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Complete Genome of Citrobacter freundii Siphophage Stevie

Cited by 12 publications

References 18 publications

Klebsiella pneumoniaesubsp.pneumoniae–bacteriophage combination from the caecal effluent of a healthy woman

Klebsiella pneumoniaesubsp.pneumoniae–bacteriophage combination from the caecal effluent of a healthy woman

Characterization of phiCFP‐1, a virulent bacteriophage specific for Citrobacter freundii

Isolation and characterization of bacteriophages that infect Citrobacter rodentium, a model pathogen for investigating human intestinal diseases

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