Join our Antimicrobial Research in the
new Lincoln Biodiscovery Lab @JBL
University of Lincoln
Theme 1: Discovering antibiotic resistance in the environment
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Antibiotic resistance of Clostridium perfringens isolates from commercial chicken sources in the
UK
The occurrence and spread of antibiotic-resistant bacteria in heavy metal contaminated
watercourses.
Impact of Extended-spectrum β-lactamase (ESBL) - producing Enterobacteriaceae discharged
from a waste water treatment plant into a pristine river in Lincoln
Emergence of antibiotic resistance in fresh irrigated food
Racehorse manure may harbour diverse new antibiotic resistance genes
Theme 2: Discovery and preclinical evaluation of new antimicrobial agents
and novel applications for existing drugs
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Find drugs for bad bugs (FD4BB) initiative - a crowd sourcing project - antimicrobial peptides
from soils
Further development of an novel infectious model with Galleria mellonella
Developing antibiofilm peptides with endolysin and cyclic peptides against E.coli
Eradicating food related pathogens from biofilms on biomaterials
Theme 3: Discovery of alternatives to antibiotics
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Isolation and characterisation of bacteriophages active against Clostridium perfringens in agriculture
Molecular studies of bacteriophages effective against Propionibacterium acnes
Comparison of biocontrol methods to remove biofilms from fragile cultural heritage materials
Impact of eradicating antibiotic resistant pathogens by coliphage in an artificial 'river' in the
laboratory
identifying bacteriophages to control Vibrio parahaemolyticus in the mussel and oyster industry
We are looking for good (self funded) graduates in the biosciences to join our
research themed groups in the new Lincoln Biodiscovery lab in the JBL
Research themes /projects
Theme 1 Antibiotic resistance in the environment
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Antibiotic resistance of Clostridium perfringens isolates from commercial chicken sources in
the UK
The emergence and dissemination of antibiotic resistance in modern medicine has resulted in
warnings from medical authorities that unless major interventions occur we will revert to the preantibiotic era of the 1930s where few or no effective antmicrobial agents were available. This
inability to cure simple infections will effect modern medical procedures such as transplants, cancer
treatments and we will become vulnerable to simple infections leading to increased mortality. One
intervention taken by the EU has been to change the regulations regarding antibiotic supplements in
animal feed. From 2006 the majority of antibiotics which were used in human medicine have been
banned from animal feed for poultry, cattle and other food animals to prevent transfer of antibiotic
genes to man. Previously, antibiotics given as antimicrobial growth promotors (AGP) were
supplemented to food livestock to increase meat conversion ratios probably by reducing sub-clinical
infections. However removal of AGPs has resulted in emergence of some animal infections which
have been previously suppressed up to now. The emergence of necrotic enteritis in chickens is one
such disease and leads to extensive economic losses. The causative organism is the anaerobe
Clostridium perfringens which occurs very widely in the chicken environment. My research group
has completed a survey of this organism in the commercial producer and has obtained a Knowledge
Transfer Partnership from the TSB (2014-2017) to develop an intervention strategy for the disease.
We have routinely isolated C. perfringens from large and small animal producers as part of the above
study and have acquired a large but uncharacterised collection. Antibiotic resistance in C.
perfringens is relatively unexplored and this UROS project sets out to acquire data in this area. Over
100 C. perfringens strains will be subjected to antimicrobial susceptibility testing against a range of
antibiotics in disk format and unusual pattern reported. We will be paticularly interested if any
antibiotic genes can be identified especially those of major carbapenemase type normally found in
the Enterobacteriaceae. Any Clostridia with antibiotic profiles suggesting that they have acquired a
major carbapenemase gene will screened by PCR, plasmids isolated and analysed by molecular
biological methods. The resistant organisms will be isolated and identified and stored for future
characterisation.
1)Growing anaerobic strains competently
2)Obtaining antibiotic profiles by 2 distinct methods
3) Characterising plasmids containing human-related antibiotic resistance genes
Collaborator Joseph Brown existing RA
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The occurrence and spread of antibiotic-resistant bacteria in heavy metal contaminated
watercourses.
This project aim is to contribute evidence to a working hypothesis that dissemination and spread of
antibiotic-resistance bacteria in the environment may be due to the failure of municipal waste water
treatment plants (WWTP) to eradicate such organisms effectively and enhanced by heavy metal
presence. Effluent from WWTP may be discharged into rivers and could be used to irrigate crops
and provide a potential route for antibiotic-resistant bacteria to enter our food chain. Previous
research has indicated that extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae
are present in significant numbers in the effluent of a Lincoln WWTP which receives hospital,
domestic and agricultural waste. This project aims to investigate whether enhanced resistant
bacteria (ESBLs) occur in a river (Bosseford Beck in Scunthorpe) where increases in heavy metals may
be demonstrated by direct measurement or the isolation of heavy metal resistant bacteria (by AA) .
The most well recognised area of heavy metal polluted environment (from the steel works) is in
Scunthorpe and the project will collect relevant samples and process them from there and compare
them to existing data in Lincoln.
Research questions:
Co-resistance in the environment of heavy metal and antibiotic resistance genes
Select areas where historic mining has occurred in the UK and take samples to compare to
unaffected areas focussing on arsenic, cadmium, mercury Is effluent from WWTP in these areas
more likely to be resistant – numbers % of TVC
Collaborator Amy Thompson (existing MSc by research student)
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Impact of Extended-spectrum β-lactamase (ESBL) - producing Enterobacteriaceae discharged
from a waste water treatment plant into a pristine river in Lincoln
a) 150 strains currently isolated from effluent discharge, antibiotic profiles and resistance
status determined. Partially identified to genus level for E.coli.
b) Continue molecular analysis of selected ESBL producing organisms from the preserved
collection - extend analysis to primers targeting sub variants for TEM/CTX/SHV groups.
Compare farm runoff point samples on the river Witham to determine relative contribution to
WWTP.
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Emergence of antibiotic resistance in fresh irrigated food
We have been working for sometime on collecting data of antibiotic resistance in bacteria from
supermarket and farm shop food and found evidence of the presence of potentially harmful ESBL
Enterobacteriaceae. A large proportion of the data collected in this project has been the
assessment of antibiotic resistance or sensitivity of Gram-negative bacteria by antibiotic disc testing.
We want to extend the isolation of bacteria from fish bought at regular supermarkets but sourced
from China and the far east. Recent literature suggests that aquaculture in China has encouraged
the spread of ESBL bacteria in fish and the recent fashion of eating raw imported fish in the UK raises
concerns. Fish samples will be bought (noting country of origin) and prepared by homogenisation in
Ringer’s solution. From this stage, spread plates and streak plates on selective media will be
prepared in order to isolate single colonies after incubation and perform Gram staining. Colonies
will be identified by colonial morphology and antibiotic discs used on spread plates of each different
individual isolate. Resulting zones of clearance were carefully measured to determine antibiotic
sensitivity or resistance to a range of antimicrobials. From this data it will be possible to identify
those species that were ESBL-producing and those that displayed high level of resistance to multiple
antibiotics. The most resistant species will be chosen for molecular analysis to identify those that
were resistant by virtue of possessing CTX-M enzymes (a specific form of ESBL). Plasmid DNA
extraction will be done semi-automatically using a QIAcube, the DNA amplified via PCR and gel
electrophoresis conducted to visualise the bands related to the CTX-M group 1 gene.
Collaborators Daniel and Kieren Brodbridge (technicians)
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Racehorse manure may harbour diverse new antibiotic resistance genes
Manure from racehorses may might contain a surprising number of new antibiotic resistance genes
(ARG) from the horse's gut bacteria. In this case, horse manure may be a potential source of new
types of antibiotic resistance genes that could transfer to indigenous bacteria in soils (where food is
grown) and in the guts of individuals who care for horses. Antibiotic genes have been identified in
many environmental bacteria but the vast majority constitute no hazard. When, however, these
ARG genes appear in pathogenic bacteria that can cause food borne bacteria or hospital infections
they constitute a risk to health and welfare. The first step of this project will be to isolate bacteria
from samples of specific horses
Theme 2 Discovery and evaluation of new antimicrobial agents and
novel applications for existing drugs
2.1) Further development of an infectious model with Galleria mellonella
The establishment of this semi in-vivo model of pathogenesis at Lincoln has been important over the
last two years and allowed us to assess the efficacy of drugs and investigate the relative pathology of
bacterial pathogens. We need to continue to extend the skills to operate this simple model and train
individuals. In addition we would like to investigate response of the model to silver colloids, the
immunohistochemistry of serially cut sections to track infection and the antimicrobial peptide
response of the larvae to it. We have a number of potential naturally occurring Vibrio pathogens
which if lethal in the model could be used to test the eradication of pathogens by vibriophage in
order to cure infection.
Collaborator Alice Gillett (RA RIF funding)
2.2) Biofilms
2.4) Development of endolysin /peptides for new lytic activity in Gram negative bacteria
further details on request
2.5) Further biological characterisation of patented silver nanoparticle solution
further details on request
Theme 3: Discovery of alternatives to antibiotics
3.1 Isolation and characterisation of bacteriophages active against Clostridium perfringens in
agriculture
3.2 Molecular studies of bacteriophages effective against Propionibacterium acnes
3.3 Comparison of biocontrol methods to remove biofilms from fragile cultural heritage materials
3.4 Impact of eradicating antibiotic resistant pathogens by coliphage from an artificial 'river' in the
laboratory
3.5 identifying bacteriophages to control Vibrio parahaemolyticus in the mussel and oyster industry