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Complete genome sequence of bacteriophage Ab4316 isolated from clinical Acinetobacter baumannii 4316
Korean J. Microbiol. 2022;58(1):53-54
Published online March 31, 2022
© 2022 The Microbiological Society of Korea.

Kyeongmin Kim1†, Md. Maidul Islam1†, Jungmin Kim1, Je Chul Lee1, Yoo Chul Lee1, Chang-Won Hong2, and Minsang Shin1*

1Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
2Department of Physiology, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
Correspondence to: E-mail: shinms@knu.ac.kr; Tel.: +82-53-420-4841; Fax: +82-53-427-5664
These authors contributed equally to this work.
Received February 7, 2022; Revised February 27, 2022; Accepted February 28, 2022.
Abstract
Acinetobacter baumannii is an opportunistic pathogen with multidrug resistance (MDR). Bacteriophages are bacterial viruses that can infect bacteria and serves as an alternative approach to treat multidrug resistant bacterial infection because of its specificity to the host bacteria. Bacteriophage Ab4316 was isolated from clinical A. baumannii strain and showed specificity to A. baumannii strains. Here we report the whole-genome sequence of Ab4316, which was 41,332 bp long, and the G + C content is 41%. The genome consists of 46 predicted open reading frames, and among them, host cell lysis enzyme, such as endolysin, are present.
Keywords : Acinetobacter baumannii, bacteriophage, endolysin, multidrug resistance, whole-genome sequence
Body

Acinetobacter spp. are Gram-negative nosocomial pathogen that causes respiratory tract infection, especially among patients admitted to intensive care units. About 30% of A. baumannii clinical strains are resistant to major classes of antibiotics (Lockhart et al., 2007). Therefore, bacteriophages can be used to treat multidrug-resistant bacterial infections, known as phage therapy (Kortright et al., 2019). Additionally, genomic properties of the bacteriophage genome provide valuable information regarding gene content. Here, we present the whole-genome sequence and annotation result of the bacteriophage Ab4316 genome.

The bacteriophage Ab4316 was isolated from clinical isolates of A. baumannii obtained from Kyungpook National University Hospital National Culture Collection for Pathogens (KNUH-NCCP), South Korea using the Mitomycin C induction method. To confirm the presence of bacteriophage and its lytic potential, clinical A. baumannii strain (obtained from the same source) and isolated phage were mixed and poured on brain heart infusion agar plates (with 0.75% top soft agar) to see the plaque formation. Phage DNA was isolated using a Phage DNA isolation Kit (Norgen Biotek), and genome sequencing was performed at Macrogen Inc. using the Illumina platform. Quality-filtered data were assembled using a de novo assembler, SPAdes. Gene annotation was performed using Prokka (v.1.12), and gene functions were identified with BLASTp search (https://blast.ncbi.nlm.nih.gov).

The complete genome sequence of bacteriophage Ab4316 is summarized in Table 1, comprising 41,332 bp, with an average G + C content of 41%. The genome comprised 46 protein-coding genes, no tRNA genes were detected; among them, 26 functional and 20 putative hypothetical proteins were detected. BLASTp search (Camacho et al., 2009) was used to predict gene function. Predicted genes might be involved in structural roles, transcriptional regulation, translocation, and host lysis, such as endolysin (Chang et al., 2010; Kim et al., 2021). The bacteriophage Ab4316 was used to infect with different bacterial species including A. baumannii standard and clinical strains and ESKAPE pathogens, but the bacteriophage showed specific activity to A. baumannii only.

Genomic features of A. baumannii phage Ab4316

Feature type Genomic feature
Contig 1
Genome size (bp) 41,322
G + C content (%) 41
Genes 46
Protein-coding genes (CDSs) 46


Conclusively, the genomic information of Ab4316 from this study can provide useful information to understand the host specificity of this bacteriophage and can be used to treat multidrug-resistant A. baumannii infection.

Nucleotide sequence accession number

The complete genome sequence of the bacteriophage Ab4316 has been deposited at GenBank under the accession number OM334891.

적 요

Acinetobacter baumannii는 다제내성을 가진 기회감염 병원체이다. 박테리아의 바이러스인 박테리오파지는 숙주 박테리아에만 감염하는 숙주 특이성을 가지기 때문에 다제내성 박테리아 감염 치료에 대안적 접근 방식을 제공하고 있다. 박테리오파지 Ab4316은 A. baumannii임상 분리균으로부터 분리되었으며 A. baumannii 균주들에 대한 특이적 활성을 보였다. 본 연구에서는 Ab4316의 완전한 게놈 서열 분석을 통해 41,332 bp의 전장 게놈 길이와 41%의 G + C 함량을 확인하였다. 본 게놈은 46개의 단백질 암호화 유전자로 구성되었으며, 그 중 엔도리신과 같은 세균 용해 효소가 존재함을 확인하였다.

Acknowledgments

This research was supported by a grant from the Korea Government National Research Foundation Grants 2016R1D1 A1B01008962 (to M.S.).

Conflict of Interest

The authors declare no conflict of interest.

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