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Two novel phages, Klebsiella phage GADU21 and Escherichia phage GADU22, from the urine samples of patients with urinary tract infection

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Abstract

Phages are found in a wide variety of places where bacteria exist including body fluids. The aim of the present study was to isolate phages from the urine samples of patients with urinary tract infection. The 10 urine samples were cultured to isolate bacteria and also used as phage sources against the isolated bacteria. From 10 urine samples with positive cultures, 3 phages were isolated (33%) and two of them were further studied. The Klebsiella phage GADU21 and Escherichia phage GADU22 phages infected Klebsiella pneumonia and Escherichia coli, respectively. Among the tested 14 species for host range analysis, the Klebsiella phage GADU21 was able to infect two species which are Klebsiella pneumonia and Proteus mirabilis, and Escherichia phage GADU22 was able to infect four species which are Shigella flexneri, Shigella sonnei and Escherichia coli. Among different isolates of the indicator bacteria for each phage, GADU21 infected half of the tested 20 Klebsiella pneumonia isolates while GADU22 infected 85% of the tested 20 E. coli isolates. The genome sizes and GC ratios were 75,968 bp and 44.4%, and 168,023 bp and 35.3% for GADU21 and GADU22, respectively. GADU21 and GADU22 were both lytic and had no antibiotic resistance and virulence genes. GADU21 was homologue with Klebsiella phage vB_KpP_FBKp27 but only 88% of the genome was covered by this phage. The non-covered parts of the GADU21 genome included genes for tail-fiber-proteins and HNH-endonuclease. GADU22 had 94.8% homology with Escherichia phage vB_Eco_OMNI12 and had genes for immunity proteins. Phylogenetic analysis showed GADU21 and GADU22 were members of Schitoviridae family and Efbeekayvirus genus and Straboviridae family and Tevenvirinae genus, respectively. VIRIDIC analysis classified these phages in new species clusters. Our study demonstrated the possibility to use infected body fluids as phage sources to isolate novel phages. GADU21 is the first reported Klebsiella phage isolated from human body fluid. The absence of virulence and antibiotic resistance genes in their genomes makes the phages a potential therapeutic tool against infections.

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Data availability

The genome sequences of Klebsiella phage GADU21 and Escherichia phage GADU22 were deposited in GenBank under the accession number ON004963.1 and OQ944321, respectively.

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Acknowledgements

The author, Hanife Salih Doğan, is supported by YOK 100/2000 fellowship program during the PhD program and 2211/A National PhD Scholarship Program, The Scientific and Technological Research Council of Turkey.

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Authors and Affiliations

  1. Recombinant DNA and Recombinant Protein Center (REDPROM), Aydın Adnan Menderes University, Aydın, Turkey

    Hanife Salih Doğan, Abdulkerim Karaynir & Bülent Bozdoğan

  2. Department of Medical Services and Techniques, Gülhane Vocational School of Health, Health Sciences University, Ankara, Turkey

    Ülkü İrem Yilmaz

  3. Gülhane School of Medicine, Department of Internal Medicine, Health Sciences University, Ankara, Turkey

    Bilgin Bahadır Başgöz

  4. Gülhane School of Medicine, Department of Medical Microbiology, Health Sciences University, Ankara, Turkey

    Tuğrul Hoşbul

  5. Medical Faculty, Department of Medical Microbiology, Aydın Adnan Menderes University, Aydın, Turkey

    Bülent Bozdoğan

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  1. Hanife Salih Doğan
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Contributions

HSD: Data curation, investigation, methodology, writing—original draft, writing—review and editing, AK: Conceptualization, investigation, methodology, ÜY: Methodology, resources, BB: Methodology, resources, TH: Conceptualization, resources, supervision, writing—review and editing, BB: Conceptualization, funding acquisition, project administration, supervision, writing—review and editing.

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Correspondence to Hanife Salih Doğan.

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This study is approved under the ethical approval code of Ethical Committee of Health Sciences University Gülhane Training and Research Hospital IC-2020/315. Informed consent from the participants was obtained.

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11262_2024_2052_MOESM1_ESM.jpg

Figure S1. VipTree analysis of Klebsiella phage GADU21 and Escherichia phage GADU22 with reference dsDNA viruses (A) GADU21 and GADU22 phages were represented with stars. The outer ring indicates hosts of the phages, and the inner ring indicates the family to which the phages belong. The hosts of these phages were founded to belong to Gammaproteobacteria (Pseudomonata) phylum. (B) The taxonomic relationship for GADU21 and GADU22 phages and their relatives showed that GADU21 phage is a member of Schitoviridae family and Efbeekayvirus genus and GADU22 phage is a member of Straboviridae family and Tevenvirinae genus. Supplementary file1 (JPG 290 kb)

Supplementary file2 (DOCX 24 kb)

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Salih Doğan, H., Karaynir, A., Yilmaz, Ü.İ. et al. Two novel phages, Klebsiella phage GADU21 and Escherichia phage GADU22, from the urine samples of patients with urinary tract infection. Virus Genes 60, 208–221 (2024). https://doi.org/10.1007/s11262-024-02052-z

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