Project proposal form
Project title: Marine bacteriophages: important players in antibiotic resistance gene transfer?
Project code:
Host institution: University of Warwick
Theme: Organisms, ‘omics and biogeochemistry
Key words: Antibiotic resistance, bacteriophage, marine
Supervisory team (including institution & email address):
Andrew Millard, University of Warwick. a.d.millard@warwick.ac.uk
Dave Scanlan, University of Warwick. d.j.scanlan@warwick.ac.uk
Project Highlights:

Isolation of broad host range bacteriophages

Functional Metagenomics to identify novel
AMR genes in viral DNA

Viral Metagenomics
Overview:
Are marine viruses important in the transfer of
antimicrobial resistance (AMR) genes in the
environment?
The rise of antibiotic resistance is a global health
problem. In the UK a report by the Chief Medical
Officer, Professor Sally Davies stated that
“Antimicrobial resistance poses a catastrophic threat.
If we don’t act now, any one of us could go into
hospital in 20 years for minor surgery and die because
of an ordinary infection that can’t be treated by
antibiotics. And routine operations like hip
replacements or organ transplants could be deadly
because of the risk of infection”. Therefore,
understanding the spread and reservoir of AMR genes
is of the up-most importance. To date, there has been
scant attention to the marine environment as a
reservoir of AMR genes, despite the Oceans covering
the nd how, these genes are being transferred
between bacteria is unknown. Based on the evidence
found in other communities it is highly likely that
bacteriophage act as mediators to transfer these AMR
genes and provide a persistent reservoir of AMR
genes. Recent studies on viral DNA obtained from
activated sludge have demonstrated they can confer
resistance to antibiotics (2), whilst in a murine model
viral DNA was shown to contribute to the transfer of
AMRs (3). Yet nothing is known of the role
bacteriophages play in the transfer of AMR genes in
the marine environment. With an estimated 1030
viruses in oceanic systems, it is essential to
understand what role they may play in the
dessimination of AMR genes. Given the recent finding
of bacteriophage that are capable of infecting a wide
range of bacterial cells from different phyla (4),
bacteriophage have the potential to mediate the
widespread transfer of AMR genes from the
environment
to
pathogenic
bacteria.
Methodology: This PhD Project aims to answer the
Figure 1: a & c : TEM image of bacteriophages
isolated from seawater. B : Novel bacteriophage
genome assembled from a viral metagenome.
key question: What role do bacteriophage play in
mediating the transfer of antibiotic resistance genes
in the marine environment? The successful applicant
will isolate and analyse a range of bacteriophages to
determine their ability to mediate the transfer of
anitbiotic resistance genes. This project is
multidisciplinary in that it emcompasses both
traditional microbiology, molecular biology and
bioinformatics, with supervisors in both the Medical
Schoool and Life Sciences.
Characterisation of bacteriophages will include host
range studies against a range of bacterial species;
Transduction assays to determine the frequencing of
horizontal gene transfer; High throughput sequencing
of bacteriophage isolates; Construction of
metagenomic libraries from the viral DNA fraction to
identify novel AMR genes via functional genomics.
Bioinformatic analysis of both bacteriophage genomes
and viral metagenomes.
Training and skills:
CENTA students are required to complete 45 days
training throughout their PhD including a 10 day
placement. In the first year, students will be trained as
a single cohort on environmental science, research
methods and core skills. Throughout the PhD, training
will progress from core skills sets to master classes
specific to the student's projects and themes.
More specifically, this PhD project will offer the
student a unique opportunity to learn cutting edge
genomics and metagenomics skills, alongside
advanced bioinformatics analysis of viral
metagenomes and bacteriophage genomes.
Combined with the opportunity to isolate a range of
novel bacteriophages against a diverse group of
marine bacteria the opportunity to discover novel
traits carried by these bacteriophage is clearly
apparent.
Partners and collaboration (including CASE):
Possible timeline:
Year 1:
 Isolation of bacteriophages infecting marine
bacteria.
 Host range studies on bacteriophage isolates
 Characterisation of bacteriophages -TEM
Year 2:
 Genome sequencing and
analysis of genomes
bioinformatic



Year 3:




Concentration of phage from seawater
Construction of shotgun metagenomic
libraries from phage fraction.
Functional genomics to identify novel AMRs
in phage fraction
Confirmation of novel AMRs
Characterisation of novel AMR mechanism(s)
Metagenomics of viral fraction from seawater.
Bioinformatic analysis of viral metagenomes
Further reading:
1. Hatosy SM, Martiny AC. 2015. The ocean as a
global reservoir of antibiotic resistance genes.
Appl Environ Microbiol AEM.00736–15.
2. Parsley LC, Consuegra EJ, Kakirde KS, Land AM,
Harper WF, Liles MR. 2010. Identification of
diverse antimicrobial resistance determinants
carried on bacterial, plasmid, or viral
metagenomes from an activated sludge
microbial assemblage. Appl Environ Microbiol
76:3753–3757.
3. Modi SR, Lee HH, Spina CS, Collins JJ. 2013.
Antibiotic treatment expands the resistance
reservoir and ecological network of the phage
metagenome. Nature 499:219–22.
4. Malki K, Kula A, Bruder K, Sible E, Hatzopoulos T,
Steidel S, Watkins SC, Putonti C. 2015.
Bacteriophages isolated from Lake Michigan
demonstrate broad host-range across several
bacterial phyla. Virol J 12:164.
Further details:
Potential applicants are encouraged to contact:
Andrew Millard (a.d.millard@warwick.ac.uk)