Identification of essential genes by transposon insertion sequencing and genome-scale metabolic model construction in Streptococcus suis

Bacterial essential genes are indispensable for the survival of bacteria and therefore are attractive targets for novel anti-microbial drugs. Identifying essential genes provides a roadmap for developing novel antibiotics and anti-microbial therapies. In this study, combining high-throughput transposon sequencing (Tn-seq) and genome-scale metabolic model (GEM) construction, essential genes of Streptococcus suis, an important emerging zoonotic bacterial pathogen, were analyzed. A highly efficient transposon (Tn) mutagenesis system was developed in S. suis. This system facilitated the construction of a high-density library containing over 160,000 Tn mutants. By sequencing the library and data analysis, more than 21,000 insertion sites and 150 essential genes for growth in the rich medium were identified. Subsequently, a GEM of S. suis SC19 strain was constructed, and 165 essential genes were predicted via flux balance analysis (FBA). A total of 244 essential genes were obtained by combining the results of Tn-seq, and FBA performed. Gene identity analysis revealed 101 essential genes as potential anti-bacterial drug targets. Among them, apart from many known antibiotic targets, some interesting essential genes were also identified, including those involved in capsule biosynthesis, aminoacyl-tRNA biosynthesis, lipid biosynthesis, cell division, and cell signaling. This work identified essential genes of S. suis at the whole-genome level, providing a reference for the mining of novel anti-microbial drug targets.IMPORTANCEAnti-microbial resistance (AMR) presents an escalating challenge, making anti-microbial drug development an urgent need. Bacterial essential genes represent promising targets for anti-microbial drugs. However, conventional approaches to identifying bacterial essential genes are time and labor intensive. Techniques such as Tn-seq and GEM construction offer a high-throughput approach for this identification. Streptococcus suis is an emerging zoonotic bacterial pathogen, posing a big threat to public health as well as the pig industry, and the levels of AMR are increasing. Our study has successfully identified essential genes in S. suis, providing crucial insights for the discovery of new anti-microbial drug targets.