EXPLOITING GENOMICS TO UNDERSTAND MICROBIAL ADAPTATION AND RESISTANCE TO INDUSTRIAL PRESERVATIVES
Lead Research Organisation:
Cardiff University
Department Name: School of Biosciences
Abstract
Preventing microbial contamination of industrial products and processes is a major area of industrial
biotechnology. Preservatives and detergents are added to products to ensure sterility, stable shelf-life, and reduce potential risk of infection to consumers. The manufacturing industry is one of the largest users of antimicrobial agents, however, with regulatory changes and a global need to reduce environmental impact, the sector is moving towards greener, minimal formulations. Certain bacteria show reduced susceptibility to antimicrobial agents and may also evolve greater resistance upon exposure to preservatives. Bacteria such as Pseudomonas, Burkholderia, Klebsiella, Enterobacter and Acinetobacter bacteria may persist during manufacture of consumer products causing disruptive plant closure or products recalls. Understanding the basis for resistance and anticipating adaptation are important for industry to develop novel product preservation strategies.
This PhD will work with Unilever Research and Development, Port Sunlight, to examine how bacteria adapt to overcome preservative strategies used by industry. State-of-the-art genomic approaches of bacterial whole genome sequencing (WGS) and global gene expression (transcriptomics via RNA-sequencing) will be used to map antimicrobial resistance genes, metabolic pathways and mutations that underpin preservative resistance in bacteria such as Pseudomonas, Burkholderia, Klebsiella, Enterobacter and Acinetobacter. The project will: (i) build custom genomic databases of each bacterial industrial contaminant species to enable their accurate identification and analysis; (ii) systematically map the resistance genes, metabolic pathways, and mutational signatures relevant to preservative resistance in each species; (iii) examine the genetic basis for adaptation to preservative resistance by analysis of bacteria strains which have been exposed to existing or novel preservative formulations. The project will provide an interdisciplinary training in molecular microbiology, industrial microbiology, bioinformatics and statistical analysis of big datasets. Placements with the industrial partner will
facilitate training in the applied aspects of industrial biotechnology, and the business strategies behind the home and personal care industry.
biotechnology. Preservatives and detergents are added to products to ensure sterility, stable shelf-life, and reduce potential risk of infection to consumers. The manufacturing industry is one of the largest users of antimicrobial agents, however, with regulatory changes and a global need to reduce environmental impact, the sector is moving towards greener, minimal formulations. Certain bacteria show reduced susceptibility to antimicrobial agents and may also evolve greater resistance upon exposure to preservatives. Bacteria such as Pseudomonas, Burkholderia, Klebsiella, Enterobacter and Acinetobacter bacteria may persist during manufacture of consumer products causing disruptive plant closure or products recalls. Understanding the basis for resistance and anticipating adaptation are important for industry to develop novel product preservation strategies.
This PhD will work with Unilever Research and Development, Port Sunlight, to examine how bacteria adapt to overcome preservative strategies used by industry. State-of-the-art genomic approaches of bacterial whole genome sequencing (WGS) and global gene expression (transcriptomics via RNA-sequencing) will be used to map antimicrobial resistance genes, metabolic pathways and mutations that underpin preservative resistance in bacteria such as Pseudomonas, Burkholderia, Klebsiella, Enterobacter and Acinetobacter. The project will: (i) build custom genomic databases of each bacterial industrial contaminant species to enable their accurate identification and analysis; (ii) systematically map the resistance genes, metabolic pathways, and mutational signatures relevant to preservative resistance in each species; (iii) examine the genetic basis for adaptation to preservative resistance by analysis of bacteria strains which have been exposed to existing or novel preservative formulations. The project will provide an interdisciplinary training in molecular microbiology, industrial microbiology, bioinformatics and statistical analysis of big datasets. Placements with the industrial partner will
facilitate training in the applied aspects of industrial biotechnology, and the business strategies behind the home and personal care industry.
Publications
Beaton A
(2018)
Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies.
in FEMS microbiology letters
Cunningham-Oakes E
(2019)
Understanding the challenges of non-food industrial product contamination.
in FEMS microbiology letters
Cunningham-Oakes E
(2020)
Genome Sequence of Pluralibacter gergoviae ECO77, a Multireplicon Isolate of Industrial Origin.
in Microbiology resource announcements
Webster G
(2019)
Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, Methanococcoides spp., Isolated from Marine Sediments.
in Microbiology resource announcements
Webster G
(2019)
The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential.
in Microbiology resource announcements
Weiser R
(2019)
Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes.
in Microbial genomics
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M009122/1 | 01/10/2015 | 31/03/2024 | |||
| 1864373 | Studentship | BB/M009122/1 | 01/10/2016 | 18/04/2020 | Edward Cunningham-Oakes |
| Description | Home and personal care product (HPCP) industries use antimicrobial preservatives to prevent bacterial growth. HPCP formulations consist of proteins and varied carbon sources that facilitate the growth of microorganisms, such as intrinsically preservative-tolerant Burkholderia cepacia complex (BCC) bacteria. Until now, the proposed identification of BCC spp. has been via the use of Multi Locus Sequence Typing (MLST), which aims to provide species identification by analyzing seven gene loci. Our studies aimed to characterise the taxonomic diversity of a historical panel of industrial BCC spp., determine appropriate techniques for genomic identification of BCC species, with a focus on B. cenocepacia, BCC Taxon K and B. vietnamiensis as priority industrial contaminants. We also aimed to identify key genomic features in preservative-trained and industrially-derived B. lata isolates. We show that industrial isolates in the panel by MLST were B. lata (n = 13), B. cenocepacia (n = 11), followed other BCC spp. (n = 9). MLST was sufficient for accurate identification of B. cenocepacia, and B. vietnamiensis, but misidentified isolates in Taxon K. We also show that missense mutations can be identified in the regulators of efflux pump operons with a known role in antimicrobial resistance, which display increased expression in preservative-adapted isolates. |
| Exploitation Route | Clear links have been drawn between the identification of unique genetic elements and preservative resistance, many of which have been published upon. This knowledge can be used by manufacturers and policy makers alike to accurate risk assess products for microbial contamination, prevent product recall, and protect consumers. |
| Sectors | Agriculture, Food and Drink,Environment,Manufacturing, including Industrial Biotechology |
| Description | Our characterisation of the bacteria and fungi found routinely in the industrial environment has advised industry as to the relative risk to their product, and how they can work to continue protecting consumers from microbial spoilage. Further work with regards to genomic characterisation and molecular detection of organisms of interest has advised industries as to how they can rapidly detect and characterise potential risk to products, on a rapid basis which is not attainable with current cultivation dependent techniques. |
| First Year Of Impact | 2016 |
| Sector | Agriculture, Food and Drink,Environment,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Economic |