Giant viruses as reservoirs of antibiotic resistance genes

Xinzhu Yi, Jie-Liang Liang, Ping Wen, Pu Jia, Shi-wei Feng, Shen-yan Liu, Yuan-yue Zhuang, Yu-qian Guo, Jing-li Lu, Sheng-ji Zhong, Bin Liao, Zhang Wang, Wen-sheng Shu and Jin-tian Li ()
Additional contact information
Xinzhu Yi: South China Normal University
Jie-Liang Liang: South China Normal University
Ping Wen: South China Normal University
Pu Jia: South China Normal University
Shi-wei Feng: South China Normal University
Shen-yan Liu: South China Normal University
Yuan-yue Zhuang: South China Normal University
Yu-qian Guo: South China Normal University
Jing-li Lu: South China Normal University
Sheng-ji Zhong: South China Normal University
Bin Liao: Sun Yat-sen University
Zhang Wang: South China Normal University
Wen-sheng Shu: South China Normal University
Jin-tian Li: South China Normal University

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.

Date: 2024
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DOI: 10.1038/s41467-024-51936-z

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