Transcriptional changes related to metabolic and iron acquisition strategies of avian pathogenic Escherichia coli are associated with embryonic survival during yolk sac infection.

INTRODUCTION

Avian pathogenic Escherichia coli (APEC) causes significant economic losses in poultry production, yet the molecular mechanisms underlying divergent infection outcomes remain poorly defined. This study aimed to elucidate the in vivo transcriptional profiles in APEC from infected chicken embryos compared to in vitro grown culture.

METHODS

Chicken embryos were experimentally infected with an APEC isolate. Subsequently, RNA sequencing was performed on APEC isolated from the yolk of experimentally infected embryos that either died or survived the infection, alongside in vitro grown controls. Differential gene expressions, functional enrichment analyses, small RNA profiling were conducted to identify key transcriptional changes. Weighted gene co-expression network analysis (WGCNA) was applied to detect bacterial gene modules associated with host outcomes.

RESULTS AND DISCUSSION: In embryos that died, APEC exhibited a transcriptionally inferred hypermetabolic program, characterized by upregulation of 443 genes involved in anaerobic respiration, nutrient scavenging, and purine and arginine biosynthesis, consistent with increased replication and virulence potential. In contrast, APEC recovered from surviving embryos displayed a transcriptionally inferred low-energy state under host immune pressure, characterized by suppression of central metabolism pathways and concurrent upregulation of genes associated with iron sequestration, toxin production, and cell envelope remodeling. WGCNA suggested the association of low-oxygen respiration and anaerobic metabolism, Fe-S cluster assembly, and purine and arginine biosynthesis genes with host lethality, while siderophore-mediated iron acquisition correlated with host survival. Arginine metabolism showed a positive association with pro-inflammatory host responses, while flagellar motility was associated with both pro- and anti-inflammatory signatures, suggesting a modulatory role of metabolic and motility pathways on host immunity. The analyses indicated that APEC survival and pathogenicity are more dependent on metabolic adaptation and iron competition than individual toxin genes. Additionally, 77 small regulatory RNAs were identified, suggesting potential regulatory roles in in vivo adaptation.These findings demonstrate the transcriptional plasticity of APEC during infection, highlighting that low-oxygen respiration and anaerobic metabolism, iron acquisition, arginine and purine metabolism and flagellar motility may contribute to bacterial survival strategies. These findings are consistent with recent host transcriptomic evidence showing mitochondrial dysfunction, hyperinflammation, and metabolic collapse in the yolk sac of infected embryos, suggesting that coordinated host-pathogen metabolic interactions influenced infection outcomes.