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Genome characterization of the novel lytic phage vB_AbaAut_ChT04 and the antimicrobial activity of its lysin peptide against Acinetobacter baumannii isolates from different time periods

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Abstract

Acinetobacter baumannii is an important opportunistic pathogen, usually associated with immunocompromised individuals with a prolonged period of stay in a hospital. Currently, the incidence of multi-drug resistant A. baumannii (MDR-AB) and extensively drug-resistant A. baumannii (XDR-AB) is increasing rapidly in Thailand, mirroring the trend worldwide. Novel therapeutic approaches for the treatment of A. baumannii infection using bacteriophages are being evaluated, and the use of phage-derived peptides is being tested as alternative approach to fighting infection. In this study, we isolated and determined the biological features of a lytic A. baumannii phage called vB_AbaAut_ChT04 (vChT04). The vChT04 phage was classified as a member of the family Autographiviridae of the class Caudoviricetes. It showed a short latent period (10 min) and a large burst size (280 PFU cell−1), and it was able to infect 52 out of 150 clinical MDR-AB strains tested (34.67%). Most of the phage-sensitive strains were A. baumannii strains that had been isolated during the same year that the phage was isolated. The phage showed activity across a broad pH (pH 5.0–8.0) and temperature (4–37°C) range. Whole-genome analysis revealed that the vChT04 genome comprises 41,158 bp with a 39.3% GC content and contains 48 open reading frames (ORFs), 28 of which were assigned putative functions based on homology to previously identified phage genes. Comparative genomic analysis demonstrated that vChT04 had the highest similarity to phage vB_AbaP_WU2001, which was isolated in the southern part of Thailand. An endolysin gene found in the vChT04 genome was used to synthesize an antimicrobial peptide (designated as PLysChT04) and its antimicrobial activity was evaluated using minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) assays. The MIC and MBC values of peptide PLysChT04 against MDR-AB and XDR-AB were 312.5–625 µg/mL, and it was able to inhibit both phage-susceptible and phage-resistant isolates collected over different time periods. PLysChT04 showed good efficacy in killing drug-resistant A. baumannii and other bacterial strains, and it is a promising candidate for development as an alternative therapeutic agent targeting A. baumannii infections.

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Acknowledgements

We would like to thank and acknowledge the staff who collected the clinical specimens used in this study. We also thank Dr. Zhaoxia Zhou at the Loughborough Materials Characterisation Centre (LMCC) for helping and providing technical assistance with TEM.

Funding

This project was financially supported by Thailand Research Fund and Naresuan University under the Mid-Career Researcher Grant (RSA6180042). UL was supported by the Royal Golden Jubilee Ph.D. Program (PHD/0227/2560).

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Authors and Affiliations

  1. Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand

    Udomluk Leungtongkam, Supat Khongfak, Rapee Thummeepak, Kannipa Tasanapak, Jintana Wongwigkarn, Sophit Khanthawong & Sutthirat Sitthisak

  2. Department of Oriental Medicine, Chiang Rai College, Chiangrai, Thailand

    Thawatchai Kitti

  3. Chemical Engineering Department, Loughborough University, Loughborough, UK

    Aouatif Belkhiri, Henrique G. Ribeiro, John S. Turner & Danish J. Malik

  4. Centre of Excellence in Fungal Research, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand

    Sutthirat Sitthisak

  5. Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand

    Sutthirat Sitthisak

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  1. Udomluk Leungtongkam
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Contributions

Conceptualization: SS, KT, JW, DJM, and SK. Investigation: UL, TK, SK, and RT. Methodology: SS, UL, TK, and RT. TEM material preparation and investigation: DJM, UL, AB, HGR, JST. Formal analysis: UL. Resources: UL. Data curation: UL and SS. Project administration: SS. Supervision: SS. Funding acquisition: SS. Writing—original draft: UL and SS. Writing—review and editing: SS and DJM. All authors read and approved the final manuscript.

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Correspondence to Sutthirat Sitthisak.

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Leungtongkam, U., Kitti, T., Khongfak, S. et al. Genome characterization of the novel lytic phage vB_AbaAut_ChT04 and the antimicrobial activity of its lysin peptide against Acinetobacter baumannii isolates from different time periods. Arch Virol 168, 238 (2023). https://doi.org/10.1007/s00705-023-05862-y

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