[WIP] The Pan-Genome of Streptococcus iniae Reveals Recent Tetracycline Adaptation, Cadmium Resistance Plasmids, and Lineage-Specific Gastrointestinal Niche Specialization

🧬 [WIP] The Pan-Genome of Streptococcus iniae Reveals Recent Tetracycline Adaptation, Cadmium Resistance Plasmids, and Lineage-Specific Gastrointestinal Niche Specialization CreatorANDRES, Quentin Ludovic Stephane (Author)🔗 ORCID: 0009-0003-3434-1778🎓 Department of Fisheries, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand📧 Contact: [email protected] 🧠 Key Results 🧬 Strictly clonal population structure→ No significant homologous recombination across 90 genomes (r/m = 0.00) 💊 Tetracycline resistance element→ tet(M) gene on a Tn916 conjugative transposon detected in a single isolate (QMA0371) ☢️ Cadmium resistance operons→ Plasmid-encoded cadA/cadC modules detected in multiple isolates, flanked by IS elements 🧫 Accessory genome variability→ 3,001 total genes: 1538 core, 110 soft-core, 321 shell, 1032 cloud 🧬 Lineage-specific gene blocks→ Stress response, metabolism, plasmid maintenance, toxin–antitoxin systems 🌐 Global diversity across 10 countries→ Sampling from 1976–2023, across 4 continents and multiple host species 🧪 No vaccine targets discussed in this work — strict focus on genomics and evolutionary adaptation 🧾 Description This article presents a large-scale comparative genomic analysis of the aquatic zoonotic pathogen Streptococcus iniae. Five newly sequenced isolates from diseased Lates calcarifer (Asian seabass) in Thailand were analyzed alongside 85 publicly available genomes, spanning multiple hosts and regions worldwide. Population structure was resolved using both SNP-based (FastBAPS) and k-mer–based (PopPUNK) approaches. Accessory genome structure was analyzed using Roary and Panaroo, while homologous recombination and mobile genetic element mapping were performed with Gubbins and ISMapper, respectively. The findings demonstrate a largely clonal species with limited evidence of recent horizontal gene transfer, but with notable lineage-specific traits—including antimicrobial resistance, metal detoxification plasmids, and accessory modules likely related to ecological adaptation. 🔬 Organism Species: Streptococcus iniae Hosts: Fish (Asian seabass, trout, pangasius, flounder, etc.) and human zoonotic isolates 🧪 Technologies Illumina HiSeq 2000 (151 bp paired-end) 🧰 Methodologies Whole-genome sequencing and annotation (Prokka, PGAP) Reference-guided assembly and synteny analysis (Bowtie2, ProgressiveMauve) Core-SNP phylogeny (Panaroo, Core-SNP-Filter, IQ-TREE2) Pangenome analysis (Roary, Panaroo) IS element detection (ISMapper, PanISa) Population structure (FastBAPS, PopPUNK) Homologous recombination detection (Gubbins) 🌍 Dataset Overview 🧫 Total genomes analyzed: 90 🌍 Countries: Australia, USA, China, Thailand, Honduras, Israel, Canada, South Korea, Reunion, Taiwan 📅 Sampling years: 1976–2023 📦 Genome size: ~2.0 Mb | GC content ~36.7% 📂 Data Access 🧬 BioProject: PRJNA933632 🧬 Genome accession: SIKU01 – GenBank CP121692.1 💾 Raw sequencing data: SRR23406918–SRR23406922 (SIKU01–SIKU05) 📎 Keywords: Streptococcus iniae, comparative genomics, population structure, pangenome, tetracycline resistance, cadmium plasmids, IS elements, clonal population, aquaculture pathogens, mobile genetic elements