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Phages infecting  Campylobacter jejuni  are considered a promising intervention strategy at broiler farms, yet phage sensitivity of naturally occurring poultry isolates is not well studied. Here, we investigated phage sensitivity and identified resistance mechanisms of  C. jejuni  strains originating from Danish broilers belonging to the most prevalent MLST (ST) types. Determining plaque formation of 51 phages belonging to  Fletchervirus  or  Firehammervirus  showed that 21 out of 31  C. jejuni  strains were susceptible to at least one phage. While  C. jejuni  ST-21 strains encoded the common phase variable  O -methyl phosphoramidate (MeO P N) receptor of the  Fletchervirus  and were only infected by these phages, ST-45 strains did not encode this receptor and were exclusively infected by  Firehammervirus  phages. To identify internal phage resistance mechanism in ST-21 strains, we performed comparative genomics of two strains, CAMSA2002 sensitive to almost all  Fletchervirus  phages and CAMSA2038, resistant to all 51 phages. The strains encoded diverse clustered regularly interspaced short palindromic repeats (CRISPR) spacers but none matched the tested phages. Sequence divergence was also observed in a predicted SspE homolog and putative restriction modification systems including a methyl-specific McrBC endonuclease. Furthermore, when  mcrB  was deleted, CAMSA2038 became sensitive to 17 out of 43 phages, three being  Firehammervirus  phages that otherwise did not infect any ST-21 strains. Yet, 16 phages demonstrated significantly lower efficiencies of plating on the  mcrB  mutant suggesting additional resistance mechanism still restricting phage propagation in CAMSA2038. Thus, our work demonstrates that  C. jejuni  isolates originating from broilers may have acquired several resistance mechanisms to successfully prevent phage infection in their natural habitat.

Identification of Novel Phage Resistance Mechanisms in Campylobacter jejuni by Comparative Genomics