Genomic insights into the phage-defense systems of Stenotrophomonas maltophilia clinical isolates

Zhuang，Zilin1; Cheng，Ying Ying2,3,7; Deng，Jie1,6; Cai，Zhao1,6; Zhong，Lin4; Qu，Jiu Xin4; Wang，Ke5; Yang，Liang1,4,6

2024

10.1016/j.micres.2023.127528

Microbiological Research   影响因子和分区

0944-5013

Stenotrophomonas maltophilia is a rapidly evolving multidrug-resistant opportunistic pathogen that can cause serious infections in immunocompromised patients. Although phage therapy is one of promising strategies for dealing with MDR bacteria, the main challenges of phage therapeutics include accumulation of phage resistant mutations and acquisition of the phage defense systems. To systematically evaluate the impact of (pro)phages in shaping genetic and evolutionary diversity of S. maltophilia, we collected 166 S. maltophilia isolates from three hospitals in southern China to analyze its pangenome, virulence factors, prophage regions, and anit-viral immune systems. Pangenome analysis indicated that there are 1328 saturated core genes and 26961 unsaturated accessory genes in the pangenome, suggesting existence of highly variable parts of S. maltophilia genome. The presence of genes in relation to T3SS and T6SS mechanisms suggests the great potential to secrete toxins by the S. maltophilia population, which is contrary to the conventional notion of low-virulence of S. maltophilia. Additionally, we characterized the pan-immune system maps of these clinical isolates against phage infections and revealed the co-harboring of CBASS and anti-CBASS in some strains, suggesting a never-ending arms race and the co-evolutionary dynamic between bacteria and phages. Furthermore, our study predicted 310 prophage regions in S. maltophilia with high genetic diversity. Six viral defense systems were found to be located at specific position of the S. maltophilia prophage genomes, indicating potential evolution of certain site/region similar to bacterial ‘defense islands’ in prophage. Our study provides novel insights of the S. maltophilia pangenome in relation to phage-defense mechanisms, which extends to our understanding of bacterial-phage interactions and might the guide application of phage therapy in combating S. maltophilia infections.

Pan-immunity Phage-defense Prophage Stenotrophomonas maltophilia Virulence

SCI ; EI

英语

第一

MICROBIOLOGY

2-s2.0-85175436755

Scopus

1.School of Medicine,Southern University of Science and Technology,Shenzhen,Guangdong,518055,China
2.Shenzhen Institute of Respiratory Diseases,Second Clinical Medical College (Shenzhen People's Hospital),Jinan University,Shenzhen,China
3.BGI Forensic,Shenzhen,518083,China
4.Shenzhen Third People's Hospital,National Clinical Research Center for Infectious Disease,The Second Affiliated Hospital of Southern University of Science and Technology,Shenzhen,518112,China
5.Department of Pulmonary and Critical Care Medicine,The First Affiliated Hospital of Guangxi Medical University,Nanning,China
6.Key University Laboratory of Metabolism and Health of Guangdong,Southern University of Science and Technology,Shenzhen,Guangdong,518055,China
7.The First Affiliated Hospital (Shenzhen People's Hospital),Southern University of Science and Technology,Shenzhen,China

Zhuang，Zilin,Cheng，Ying Ying,Deng，Jie,et al. Genomic insights into the phage-defense systems of Stenotrophomonas maltophilia clinical isolates[J]. Microbiological Research,2024,278.

Zhuang，Zilin.,Cheng，Ying Ying.,Deng，Jie.,Cai，Zhao.,Zhong，Lin.,...&Yang，Liang.(2024).Genomic insights into the phage-defense systems of Stenotrophomonas maltophilia clinical isolates.Microbiological Research,278.

Zhuang，Zilin,et al."Genomic insights into the phage-defense systems of Stenotrophomonas maltophilia clinical isolates".Microbiological Research 278(2024).