# Integrated Pathogen–Host Analysis of Citrobacter braakii SCGY-1L: Genomic Determinants and Host Transcriptional Dynamics During Infection

## TL;DR

This study explores the genome and infection mechanisms of Citrobacter braakii, revealing its virulence and resistance traits and how it affects host gene expression.

## Contribution

The study provides the first integrated genomic and transcriptomic analysis of Citrobacter braakii SCGY-1L and its host response.

## Key findings

- The C. braakii strain SCGY-1L has a 5.75 Mb genome with 738 virulence genes and 366 antibiotic resistance genes.
- Host infection leads to significant changes in gene expression, particularly in immune-related pathways.
- The LD50 of the strain is 1.28 × 10^6 CFU/mL, with severe organ damage observed in infected hosts.

## Abstract

Citrobacter braakii is an emerging opportunistic pathogen of escalating clinical significance in animal hosts, though its pathogenic mechanisms remain poorly characterized. This study isolated a C. braakii strain (SCGY-1L) from diseased Siniperca chuatsi and confirmed its identity through integrated morphological, physiological, and molecular analyses. Comprehensive genomic sequencing revealed a 5.75 Mb genome comprising one circular chromosome and two plasmids. A Circos plot was constructed to visualize the genomic architecture of strain SCGY-1L, revealing 5482 protein-coding genes, 25 tRNA genes, and 86 rRNA genes. Additionally, 738 virulence-associated genes and 366 antibiotic resistance determinants were annotated, elucidating multidrug-resistant phenotypes including insensitivity to erythromycin and penicillin. Pathogenicity assessment established an LD50 of 1.28 × 106 CFU/mL in infected hosts, with histopathological analysis showing significant hemorrhage and necrosis in target organs (liver, spleen, kidney). Host transcriptome profiling generated 41.21 Gb of high-quality clean data, identifying 2201 differentially expressed genes post-infection (1568 up-regulated; 633 down-regulated). These were significantly enriched in phagocytosis, cytokine-mediated signaling, and inflammatory regulation pathways. These molecular insights establish C. braakii’s mechanistic framework for pathogenesis and host adaptation, providing critical targets for diagnostics and therapeutics against emerging Citrobacter infections.