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Klebsiella pneumoniae subsp. pneumoniae-bacteriophage combination from the caecal effluent of a healthy woman.

Hoyles L, Murphy J, Neve H, Heller KJ, Turton JF, Mahony J, Sanderson JD, Hudspith B, Gibson GR, McCartney AL, van Sinderen D - PeerJ (2015)

Bottom Line: 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.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."

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Microbiology, University College Cork , Cork , Ireland ; Department of Biomedical Sciences, University of Westminster , London , United Kingdom.

ABSTRACT
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."

No MeSH data available.


Related in: MedlinePlus

Genome structures of the four members of the genus “Kp36likevirus”.Phages KLPN1, KP36 and 1513 are virulent to K. pneumoniae, while F20 is virulent to Enterobacter aerogenes (Mishra, Choi & Kang, 2012).
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fig-3: Genome structures of the four members of the genus “Kp36likevirus”.Phages KLPN1, KP36 and 1513 are virulent to K. pneumoniae, while F20 is virulent to Enterobacter aerogenes (Mishra, Choi & Kang, 2012).

Mentions: The genome of KLPN1 was 49,037 bp with a G + C content of 50.53%, similar to previously sequenced Klebsiella Siphoviridae phages such as KP36 (Table 2). Initial genome annotation was performed using Genemark (Besemer & Borodovsky, 1999), from which a gff file was generated to allow visualisation of the predicted ORFs in Artemis v10.0 (Rutherford et al., 2000). Each ORF with a minimum amino acid content of 30, a start and stop codon as well as a ribosomal-binding site was retained (Table 3). The genome of KLPN1 was predicted to encompass 73 ORFs divided into four clusters, two rightward and two leftward (Fig. 3, Table 3). Of the 73 predicted ORFs, 23 were assigned a function with the remainder representing hypothetical proteins with no assignable function (Table 3). BLAST analysis of the complete nucleotide sequence indicated that KLPN1 is closely related to the Klebsiella phages KP36 (95% identity across 86% of the genome; Kęsik-Szeloch et al., 2013), F20 (84% identity across 82% of the genome, GenBank accession no. JN672684; Mishra, Choi & Kang, 2012) and phage 1513 (95% identity across 85% of the genome, GenBank accession no. KP658157; Cao et al., 2015). Furthermore, partial identity was observed against Shigella phage Shfl1 as well as enterobacterial phages T1 (Roberts, Martin & Kropinski, 2004) and RTP (Wietzorrek et al., 2006) (GenBank accession numbers HM035024, AY216660 and AM156909, respectively). A comparative analysis of KLPN1 was performed against both known members (KP36, F20) of the genus “Kp36likevirus” (Niu et al., 2014; Table 3, Fig. 3). For completion, KLPN1 was also compared with previously sequenced Klebsiella phages (Table 2). KLPN1 was shown not to share detectable homology with Klebsiella phages belonging to the family Podoviridae or Myoviridae. Based on the amino acid percentage identities presented in Table 3, the genomes of KLPN1 and related phages were divided into functional conserved modules: packaging, phage particle morphogenesis and DNA replication (Fig. 3, Table 3). Sections of the KLPN1 genome were shown to exhibit homology to the Siphoviridae phage phiKO2 genome, although such homology was confined to the tail morphogenesis region and one hypothetical protein (Table 3). Of the 73 predicted ORFs, only three appeared unique to KLPN1: two genes encoding hypothetical proteins located at the 5’ end of the genome and a putative homing endonuclease-gene positioned in the capsid morphogenesis module (Table 3).


Klebsiella pneumoniae subsp. pneumoniae-bacteriophage combination from the caecal effluent of a healthy woman.

Hoyles L, Murphy J, Neve H, Heller KJ, Turton JF, Mahony J, Sanderson JD, Hudspith B, Gibson GR, McCartney AL, van Sinderen D - PeerJ (2015)

Genome structures of the four members of the genus “Kp36likevirus”.Phages KLPN1, KP36 and 1513 are virulent to K. pneumoniae, while F20 is virulent to Enterobacter aerogenes (Mishra, Choi & Kang, 2012).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4525690&req=5

fig-3: Genome structures of the four members of the genus “Kp36likevirus”.Phages KLPN1, KP36 and 1513 are virulent to K. pneumoniae, while F20 is virulent to Enterobacter aerogenes (Mishra, Choi & Kang, 2012).
Mentions: The genome of KLPN1 was 49,037 bp with a G + C content of 50.53%, similar to previously sequenced Klebsiella Siphoviridae phages such as KP36 (Table 2). Initial genome annotation was performed using Genemark (Besemer & Borodovsky, 1999), from which a gff file was generated to allow visualisation of the predicted ORFs in Artemis v10.0 (Rutherford et al., 2000). Each ORF with a minimum amino acid content of 30, a start and stop codon as well as a ribosomal-binding site was retained (Table 3). The genome of KLPN1 was predicted to encompass 73 ORFs divided into four clusters, two rightward and two leftward (Fig. 3, Table 3). Of the 73 predicted ORFs, 23 were assigned a function with the remainder representing hypothetical proteins with no assignable function (Table 3). BLAST analysis of the complete nucleotide sequence indicated that KLPN1 is closely related to the Klebsiella phages KP36 (95% identity across 86% of the genome; Kęsik-Szeloch et al., 2013), F20 (84% identity across 82% of the genome, GenBank accession no. JN672684; Mishra, Choi & Kang, 2012) and phage 1513 (95% identity across 85% of the genome, GenBank accession no. KP658157; Cao et al., 2015). Furthermore, partial identity was observed against Shigella phage Shfl1 as well as enterobacterial phages T1 (Roberts, Martin & Kropinski, 2004) and RTP (Wietzorrek et al., 2006) (GenBank accession numbers HM035024, AY216660 and AM156909, respectively). A comparative analysis of KLPN1 was performed against both known members (KP36, F20) of the genus “Kp36likevirus” (Niu et al., 2014; Table 3, Fig. 3). For completion, KLPN1 was also compared with previously sequenced Klebsiella phages (Table 2). KLPN1 was shown not to share detectable homology with Klebsiella phages belonging to the family Podoviridae or Myoviridae. Based on the amino acid percentage identities presented in Table 3, the genomes of KLPN1 and related phages were divided into functional conserved modules: packaging, phage particle morphogenesis and DNA replication (Fig. 3, Table 3). Sections of the KLPN1 genome were shown to exhibit homology to the Siphoviridae phage phiKO2 genome, although such homology was confined to the tail morphogenesis region and one hypothetical protein (Table 3). Of the 73 predicted ORFs, only three appeared unique to KLPN1: two genes encoding hypothetical proteins located at the 5’ end of the genome and a putative homing endonuclease-gene positioned in the capsid morphogenesis module (Table 3).

Bottom Line: 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.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."

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Microbiology, University College Cork , Cork , Ireland ; Department of Biomedical Sciences, University of Westminster , London , United Kingdom.

ABSTRACT
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."

No MeSH data available.


Related in: MedlinePlus