Campylobacter phages use hypermutable polyG tracts to create phenotypic diversity and evade bacterial resistance

Sørensen, Martine C. Holst; Vitt, Amira R.; Neve, Horst; Soverini, Matteo; Ahern, Stephen J.; Klumpp, Jochen; Brøndsted, Lone

doi:10.1016/j.celrep.2021.109214

Cited by 18 publications

(39 citation statements)

References 66 publications

(90 reference statements)

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“…We previously demonstrated that phase variable expression of CPS surface structures acts as a major defense mechanism against the Fletchervirus phages also in the chicken gut ( Sørensen et al, 2011 ; Holst Sørensen et al, 2012 ; Aidley et al, 2017 ; Gencay et al, 2018 ). Yet, we recently discovered that phages belonging to this genus can encode up to four different receptor binding protein which allows these phages to infect C. jejuni in the absence of the common phase variable MeO P N receptor ( Sørensen et al, 2021 ). This supports the need for complementary phage defense mechanisms in C. jejuni to efficiently prevent infection by this group of phages.…”

Section: Discussionmentioning

confidence: 99%

“…In contrast, the Fletchervirus phages rely on CPS for infection and the phase variable MeO P N modification has been identified as a phage receptor recognized by many of these phages ( Sørensen et al, 2011 ; Holst Sørensen et al, 2012 ; Gencay et al, 2018 ). We recently demonstrated that Fletchervirus phages encode up to four different receptor binding proteins (RBP1 to RBP4) ( Sørensen et al, 2021 ). While RBP1 is responsible for binding to the common phase variable MeO P N receptor, phase variable expression of RBP2 ensures binding to another currently unknown receptor when MeO P N is not expressed ( Sørensen et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…We recently demonstrated that Fletchervirus phages encode up to four different receptor binding proteins (RBP1 to RBP4) ( Sørensen et al, 2021 ). While RBP1 is responsible for binding to the common phase variable MeO P N receptor, phase variable expression of RBP2 ensures binding to another currently unknown receptor when MeO P N is not expressed ( Sørensen et al, 2021 ). Thus, as a counter-resistance mechanism to phase variable expression of the common MeO P N receptor, Fletchervirus phages encode multiple receptor binding proteins including two that are phase variably expressed creating phenotypically diverse phage populations ( Sørensen et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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 (MeOPN) 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.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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“…In fact, phase variability through hypermutable poly-G tracts (a rapid adaptation mechanism that provides a stochastic on/off switch for gene expression via homopolymeric nucleotide stretches encoded within open reading frames [57]) has recently been reported in Campylobacter phages [58]. As C. jejuni expresses at least 30 phase-variable genes, many of them governing surface structure expression [26,57,59], it is not surprising to find that Campylobacter phages have evolved similar mechanisms to ensure evolutionary dominance over such a variable host. Tracts of only 6-7 nucleotides in length would not be predicted to switch on and off as frequently as longer tracts, given the slipped-strand mispairing mechanism that leads to variation at these loci, but would still be reasonably expected to represent a mechanism of variation that could provide an adaptive advantage for the encoding biological entity.…”

Section: Discussionmentioning

confidence: 99%

Reduced Infection Efficiency of Phage NCTC 12673 on Non-Motile Campylobacter jejuni Strains Is Related to Oxidative Stress

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Javed

Crippen

et al. 2021

Viruses

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Campylobacter jejuni is a Gram-negative foodborne pathogen that causes diarrheal disease and is associated with severe post-infectious sequelae. Bacteriophages (phages) are a possible means of reducing Campylobacter colonization in poultry to prevent downstream human infections. However, the factors influencing phage-host interactions must be better understood before this strategy can be predictably employed. Most studies have focused on Campylobacter phage binding to the host surface, with all phages classified as either capsule- or flagella-specific. Here we describe the characterization of a C. jejuni phage that requires functional flagellar glycosylation and motor genes for infection, without needing the flagella for adsorption to the cell surface. Through phage infectivity studies of targeted C. jejuni mutants, transcriptomic analysis of phage-resistant mutants, and genotypic and phenotypic analysis of a spontaneous phage variant capable of simultaneously overcoming flagellar gene dependence and sensitivity to oxidative stress, we have uncovered a link between oxidative stress, flagellar motility, and phage infectivity. Taken together, our results underscore the importance of understanding phage-host interactions beyond the cell surface and point to host oxidative stress state as an important and underappreciated consideration for future phage-host interaction studies.

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“…Previous studies highlighted the need for (i) a lytic phage collection directed against current Campyobacter field strains ( Carrillo et al, 2005 ), (ii) more precise and faster methods to identify and select useful phages ( Xie et al, 2018 ; Zbikowska et al, 2020 ), and (iii) a better understanding of bacteriophage kinetics to allow for advanced considerations concerning dosing and timing of phage applications ( Cairns et al, 2009 ; Hammerl et al, 2014 ; Loessner et al, 2020 ). Furthermore, genome determination of Campylobacter phages was also shown to be laborious due to prevailing DNA modification and extensive repetitive sequences, including hypermutable polyGtracts, resulting in low amounts of extracted DNA and/or incomplete genomes ( Hammerl et al, 2011 ; Carvalho et al, 2012 ; Jackel et al, 2015 ; Crippen et al, 2019 ; Sorensen et al, 2021 ). However, all Campylobacter phages described to date are closely related in their genetic composition and exhibit highly conserved nucleotide sequences.…”

Section: Introductionmentioning

confidence: 99%

Isolation and Characterization of Group III Campylobacter jejuni–Specific Bacteriophages From Germany and Their Suitability for Use in Food Production

et al. 2021

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Campylobacter spp. are a major cause of bacterial foodborne diarrhea worldwide. While thermophilic Campylobacter species asymptomatically colonize the intestines of chickens, most human infections in industrial countries have been attributed to consumption of chicken meat or cross-contaminated products. Bacteriophages (phages) are natural predators of bacteria and their use at different stages of the food production chain has been shown to reduce the public health burden of human campylobacteriosis. However, regarding regulatory issues, the use of lytic phages in food is still under discussion and evaluation. This study aims to identify lytic phages suitable for reducing Campylobacter bacteria along the food production chain. Therefore, four of 19 recently recovered phages were further characterized in detail for their lytic efficacy against different Campylobacter field strains and their suitability under food production settings at different temperatures and pH values. Based on the results of this study, the phages vB_CjM-LmqsCP1-4 and vB_CjM-LmqsCP1-5 appear to be promising candidates for the reduction of Campylobacter jejuni in food production settings.

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Campylobacter phages use hypermutable polyG tracts to create phenotypic diversity and evade bacterial resistance

Cited by 18 publications

References 66 publications

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

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

Reduced Infection Efficiency of Phage NCTC 12673 on Non-Motile Campylobacter jejuni Strains Is Related to Oxidative Stress

Isolation and Characterization of Group III Campylobacter jejuni–Specific Bacteriophages From Germany and Their Suitability for Use in Food Production

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