Isolation and characterization of a bacteriophage for Vibrio fetus

Campylobacter bacteriophage DA10: an excised temperate bacteriophage targeted by CRISPR-cas

Background

Lytic bacteriophages that infect Campylobacter spp. have been utilized to develop therapeutic/decontamination techniques. However, the association of Campylobacter spp. and bacteriophages has been the focus of several strands of research aimed at understanding the complex relationships that have developed between predators and prey over evolutionary time. The activities of endogenous temperate bacteriophages have been used to evaluate genomic rearrangements and differential protein expression in host cells, and mechanisms of resistance to bacteriophage infection in campylobacters such as phase variation and CRISPR-mediated immunity.

Results

Temperate bacteriophage DA10 represents a novel excised and infective virus capable of replication in a restricted set of C. jejuni and C. coli hosts. Whole genome sequencing reveals that DA10 (35,379 bp) forms part of a novel group of temperate bacteriophages that have limited distribution among database host genome sequences. Analysis of potential host genomes reveals a robust response against DA10 and DA10-like bacteriophages is driven by CRISPR-mediated immunity with 75% of DA10 ORFs represented as ~ 30 bp spacer sequences in numerous Campylobacter Type II-C CRISPR arrays. Several DA10-like homologues have been identified in a small sub-set of C. jejuni and C. coli genome sequences (ranging from near complete integrated prophage sequences to fragments recognisable in the sequence read archive).

Conclusions

A complete intact DA10-like prophage in C. jejuni CJ677CC520 provides evidence that the associations between host and DA10-like bacteriophages are long-standing in evolutionary timescales. Extensive nucleotide substitution and loss can be observed in the integrated DA10-like prophage of CJ677CC520 compared to other relatives as observed through pairwise genome comparisons. Examining factors that have limited the population expansion of the prophage, while others appear to have thrived and prospered (Mu-like, CJIE-like, and lytic Campylobacter bacteriophages) will assist in identifying the underlying evolutionary processes in the natural environment.

Campylobacter Phage Isolation and Characterization: What We Have Learned So Far

Lytic Campylobacter phages, which can be used to combat this pathogen in animals and on food products, have been studied for more than 30 years. Though, due to some peculiarities of the phages, which hampered their isolation and particularly their molecular analysis for a long time, progress in this research field was rather slow. Meanwhile, the situation has changed and much more is known about the biology and genetics of those phages. In this article, we address specific issues that should be considered when Campylobacter phages are studied, starting with the isolation and propagation of the phages and ending with a thorough characterization including whole-genome sequencing. The basis for advice and recommendations given here is a careful review of the scientific literature and experiences that we have had ourselves with Campylobacter phages.

Campylobacter bacteriophages and bacteriophage therapy

Members of the genus Campylobacter are frequently responsible for human enteric disease with occasionally very serious outcomes. Much of this disease burden is thought to arise from consumption of contaminated poultry products. More than 80% of poultry in the UK harbour Campylobacter as a part of their intestinal flora. To address this unacceptably high prevalence, various interventions have been suggested and evaluated. Among these is the novel approach of using Campylobacter-specific bacteriophages, which are natural predators of the pathogen. To optimize their use as therapeutic agents, it is important to have a comprehensive understanding of the bacteriophages that infect Campylobacter, and how they can affect their host bacteria. This review will focus on many aspects of Campylobacter-specific bacteriophages including: their first isolation in the 1960s, their use in bacteriophage typing schemes, their isolation from the different biological sources and genomic characterization. As well as their use as therapeutic agents to reduce Campylobacter in poultry their future potential, including their use in bio-sanitization of food, will be explored. The evolutionary consequences of naturally occurring bacteriophage infection that have come to light through investigations of bacteriophages in the poultry ecosystem will also be discussed.

Sequence variability of Campylobacter temperate bacteriophages

Background

Prophages integrated within the chromosomes of Campylobacter jejuni isolates have been demonstrated very recently. Prior work with Campylobacter temperate bacteriophages, as well as evidence from prophages in other enteric bacteria, suggests these prophages might have a role in the biology and virulence of the organism. However, very little is known about the genetic variability of Campylobacter prophages which, if present, could lead to differential phenotypes in isolates carrying the phages versus those that do not. As a first step in the characterization of C. jejuni prophages, we investigated the distribution of prophage DNA within a C. jejuni population assessed the DNA and protein sequence variability within a subset of the putative prophages found.

Results

Southern blotting of C. jejuni DNA using probes from genes within the three putative prophages of the C. jejuni sequenced strain RM 1221 demonstrated the presence of at least one prophage gene in a large proportion (27/35) of isolates tested. Of these, 15 were positive for 5 or more of the 7 Campylobacter Mu-like phage 1 (CMLP 1, also designated Campylobacter jejuni integrated element 1, or CJIE 1) genes tested. Twelve of these putative prophages were chosen for further analysis. DNA sequencing of a 9,000 to 11,000 nucleotide region of each prophage demonstrated a close homology with CMLP 1 in both gene order and nucleotide sequence. Structural and sequence variability, including short insertions, deletions, and allele replacements, were found within the prophage genomes, some of which would alter the protein products of the ORFs involved. No insertions of novel genes were detected within the sequenced regions. The 12 prophages and RM 1221 had a % G+C very similar to C. jejuni sequenced strains, as well as promoter regions characteristic of C. jejuni. None of the putative prophages were successfully induced and propagated, so it is not known if they were functional or if they represented remnant prophage DNA in the bacterial chromosomes.

Conclusion

These putative prophages form a family of phages with conserved sequences, and appear to be adapted to Campylobacter. There was evidence for recombination among groups of prophages, suggesting that the prophages had a mosaic structure. In many of these properties, the Mu-like CMLP 1 homologs characterized in this study resemble temperate bacteriophages of enteric bacteria that are responsible for contributions to virulence and host adaptation.

Free-range layer chickens as a source of Campylobacter bacteriophage

Bacteriophage specific for Campylobacter were isolated from chicken excreta collected from established free-range layer breed stock. Bacteriophage were either propagated on a Campylobacter jejuni host with broad susceptibility to bacteriophage (NCTC 12662) or on Campylobacter isolates from the same samples. Campylobacters were confirmed as being C. jejuni and or C. coli, using a combination of standard biochemical tests and PCR analysis with genus and species specific primers. The bacteriophage displayed differential patterns of susceptibility against reference NCTC strains and contemporary C. jejuni /C. coli isolates from chicken excreta. Electron microscopy demonstrated that the phage possessed icosahedral heads and rigid contractile tails. Pulsed-field gel electrophoresis revealed the bacteriophage genomes to be double stranded DNA in the range of 140 kb in size and the restriction enzyme patterns of the DNAs indicate they are genetically related members of the Myoviridae family. This study showed that Campylobacter bacteriophage could easily be isolated from free-range chickens and form part of their normal microbiological biota of environmentally exposed birds.

Development of a bacteriophage typing system for Campylobacter jejuni and Campylobacter coli

A bacteriophage typing system for Campylobacter jejuni and Campylobacter coli was developed with phages isolated from poultry feces. Data for phage selection were generated from a set of isolates of C. jejuni and C. coli from humans in Illinois. Selection of 14 phages from the 47 phages available was assisted by determination of the Sneath-Jaccard similarity coefficients and subsequent unweighted pair-group arithmetic averaging cluster analysis. The typing set was reproducible and stable in the 255 isolates from Illinois. Of these isolates, 94.5% were typable, with 46% represented by the four most common phage patterns. In a set of 51 isolates from humans outside of Illinois, 88.1% of the C. jejuni isolates were typable. Phage typing for C. jejuni and C. coli has excellent epidemiologic potential and should serve as a useful adjunct or alternative to serotyping systems in current use.

Isolation of Campylobacter fetus from recent cases of human vibriosis

Campylobacter fetus was isolated from five recent cases of human vibriosis, of which two were adults and three were children. One adult presented with pericarditis and the other with recurrent pyrexia. Campylobacter fetus subsp. intestinalis which resembled cattle strains serologically, was isolated under CO2 or anaerobic conditions from blood cultures of these patients. Two of the three children had kwashiorkor and the third was only 8 days old. Isolates identified as Campylobacter fetus subsp. jejuni were cultured from blood of these patients, two of whom had diarrhoea. Three patients succumbed, despite adequate antibiotic therapy. The epidemiology of the disease is discussed and it is suggested that infection may have been from the patients' own flora.

Lytic activity of vibrio phages on strains of Vibrio fetus isolated from man and animals

Five phages isolated from lysogenic strains of Vibrio fetus var. venerealis and two from V. fetus var. intestinalis were tested for lytic activity on 95 V. fetus strains from various animal and human hosts. In addition, virion and plaque morphology of the seven phages were compared. Electron micrographs showed that all were the kite-tailed variety with minor variations in head and tail dimensions. Plaques of V45 and V2 were small, clear and irregular; those of V3, V8, and V19 were large, clear and regular at the edge; the plaques of V16 and V20 were intermediate in size, clear, and very irregular at the edge with satellite plaques. The number of strains lysed by one or more phages were as follows: 29 of 30 from cattle; 7 of 11 from sheep; 1 of 5 from pigs; 1 of 1 from a monkey; and 33 of 42 from human hosts. Four natural groups of phages were derived by statistical measures of percentage of similarity in lytic activity. Group III lysed more strains (46 of 95) than any of the others. Twenty-five strains were lysed by group IV, 23 strains by group I, and 19 strains by group II. Results of this study indicate that phage typing should be a practical supplement to other differential tests for V. fetus.