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Background   Campylobacter jejuni  is the leading cause of bacterial gastroenteritis in humans and the handling or consumption of contaminated poultry meat is a key source of infection. Selective breeding of poultry that exhibit elevated resistance to  Campylobacter  is an attractive control strategy. Here we studied the global transcriptional response of inbred chicken lines that differ in resistance to  C. jejuni  colonisation at a key site of bacterial persistence.    Results  Three-week-old chickens of line 6 1  and N were inoculated orally with  C. jejuni  strain M1 and caecal contents and tonsils were sampled at 1 and 5 days post-infection. Caecal colonisation was significantly lower in line 6 1  compared to line N at 1 day post-infection, but not 5 days post-infection. RNA-Seq analysis of caecal tonsils of both lines revealed a limited response to  C. jejuni  infection compared to age-matched uninfected controls. In line N at days 1 and 5 post-infection, just 8 and 3 differentially expressed genes (DEGs) were detected (fold-change > 2 and false-discovery rate of < 0.05) relative to uninfected controls, respectively. In the relatively resistant line 6 1 , a broader response to  C. jejuni  was observed, with 69 DEGs relating to immune regulation, cell signalling and metabolism at 1 day post-infection. However, by day 5 post-infection, no DEGs were detected. By far, the greatest number of DEGs were between uninfected birds of the two lines implying that differential resistance to  C. jejuni  is intrinsic. Of these genes, several Major Histocompatibility Complex class I-related genes ( MHCIA1 ,  MHCBL2  and  MHCIY ) and antimicrobial peptides ( MUC2 ,  AvBD10  and  GZMA ) were expressed to a greater extent in line N. Two genes within quantitative trait loci associated with  C. jejuni  colonisation were also more highly expressed in line N ( ASIC4  and  BZFP2 ). Quantitative reverse-transcriptase PCR analysis of a subset of transcripts confirmed the RNA-Seq results.    Conclusions  Our data indicate a limited transcriptional response in the caecal tonsils of inbred chickens to intestinal colonisation by  Campylobacter  but identify a large number of differentially transcribed genes between lines 6 1  and N that may underlie variation in heritable resistance to  C. jejuni .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07748-2.

Transcriptomic analysis of caecal tissue in inbred chicken lines that exhibit heritable differences in resistance to Campylobacter jejuni