AUTHOR=Sørensen Martine C. H. , Gencay Yilmaz Emre , Fanger Florian , Chichkova Mariana A. T. , Mazúrová Mária , Klumpp Jochen , Nielsen Eva M. , Brøndsted Lone 

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

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.780559

DOI=10.3389/fmicb.2021.780559

ISSN=1664-302X

ABSTRACT=<p>Phages infecting <italic>Campylobacter jejuni</italic> 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 <italic>C. jejuni</italic> strains originating from Danish broilers belonging to the most prevalent MLST (ST) types. Determining plaque formation of 51 phages belonging to <italic>Fletchervirus</italic> or <italic>Firehammervirus</italic> showed that 21 out of 31 <italic>C. jejuni</italic> strains were susceptible to at least one phage. While <italic>C. jejuni</italic> ST-21 strains encoded the common phase variable <italic>O</italic>-methyl phosphoramidate (MeO<italic>P</italic>N) receptor of the <italic>Fletchervirus</italic> and were only infected by these phages, ST-45 strains did not encode this receptor and were exclusively infected by <italic>Firehammervirus</italic> phages. To identify internal phage resistance mechanism in ST-21 strains, we performed comparative genomics of two strains, CAMSA2002 sensitive to almost all <italic>Fletchervirus</italic> 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 <italic>mcrB</italic> was deleted, CAMSA2038 became sensitive to 17 out of 43 phages, three being <italic>Firehammervirus</italic> phages that otherwise did not infect any ST-21 strains. Yet, 16 phages demonstrated significantly lower efficiencies of plating on the <italic>mcrB</italic> mutant suggesting additional resistance mechanism still restricting phage propagation in CAMSA2038. Thus, our work demonstrates that <italic>C. jejuni</italic> isolates originating from broilers may have acquired several resistance mechanisms to successfully prevent phage infection in their natural habitat.</p>