The interactions between Clostridium difficile, intestinal microbiota and the host response in hospitalised patients

Lead Research Organisation: London School of Hygiene & Tropical Medicine
Department Name: Infectious and Tropical Diseases

Abstract

Clostridium difficile is a bacterium that causes chronic diarrhoea and sometimes life-threatening disease (referred to as C. difficile infection or CDI) mainly in elderly and hospitalized patients. C. difficile is now the most significant hospital acquired infection with over 34,000 UK cases last year and an estimated cost to be £500 million per annum. The reported incidence of CDI has risen dramatically over the last decade and is related to the emergence of aggressive strains. Given the ability of C. difficile to evolve to be highly virulent coupled with the ageing population and increasing rates of hospitalization, the problem of CDI is likely to continue. It is a current NHS imperative to reduce the burden of CDI.

CDI is unique among infections in that in almost all cases, disease follows the administration of antibiotics that disrupt the "normal" bacteria (called microbiota) present in the gut. It provides C. difficile the opportunity to overgrow, produce toxins and cause disease. It has become apparent that the balance of the microbiota plays a key role in disease. One of the most perplexing questions concerning CDI is the diversity of clinical symptoms. For example, C. difficile colonization can result in a spectrum of clinical outcomes ranging from asymptomatic carriage to death. The relative virulence of C. difficile organism clearly plays a role in determining clinical outcome, but the nature of this role has not been identified. Up to 30% of patients treated successfully for symptomatic CDI succumb to recurrent disease, but it is unclear why only some patients relapse. In addition to the pathogen, the host immune response and/or host microbiota are also likely important determinants of clinical outcome, but remain largely unexplored. Our central hypothesis is that variations in C. difficile genetics, the composition of the resident intestinal microbiota and the host immune response to the bacterium shape the clinical outcome.

We will investigate the three-way interaction between pathogen, host and microbiota by monitoring a unique group of patients with and without CDI. C. difficile serum and faecal samples will be studied in unprecedented detail to provide a platform for follow up studies to understand how C. difficile causes disease. We have established a high quality prospectively collected bioarchive comprising bacterial, blood and serum samples from 300 patients with CDI and full clinical history. These samples are linked to detailed clinical data and a disease severity-scoring index along with 150 control samples from hospitalised patients who have been exposed to antibiotics but did not develop CDI. We will use the existing cohort to validate methodologies and then also recruit another cohort of 150 confirmed CDI cases, 100 diarrhoea controls and 100 healthy volunteers (e.g. patient's spouses) to confirm our findings. This unique resource will be used to monitor the host response (including how the immune system responds to the infection), determine the complete genome sequence of infecting C. difficile and identify the intestinal microbiota by sequencing and culturing. The studies will also allow us to distinguish between re-infection (infection caused by another strain) and relapse (re-infection caused by the same strain).

Robust statistical analysis comparing disease severity, host response, infecting pathogen and the composition of intestinal microbiota will facilitate subsequent studies on C. difficile to determine how and why it causes disease. This will be achieved by selecting C. difficile genes and constructing defined mutants and studying these alongside the parent strain in a range of assays established in the applicants' laboratories.

A comprehensive understanding of C. difficile, the host response and the intestinal microbiota will strengthen our understanding of the microorganism and to develop novel strategies to reduce the burden of CDI.

Technical Summary

Reduction in C. difficile infection (CDI) related morbidity and mortality is a current healthcare imperative. To develop appropriate sustained interventions, a holistic integrated view of the pathogen, the host response and the intestinal microbiota during infection is required. Our central hypothesis is that variation in C. difficile genetics, the composition of the resident intestinal microbiota and the repertoire of host factors, including the humoral immune response, shape the clinical outcome of CDI. To this end we will evaluate in unprecendented detail the pathogen genome sequence, intestinal microbial composition and the host response in a case-control study of CDI hospitalised patients. Rigorous statistical comparisons of data from the organism, intestinal microbiota and host response in relation to a patient disease severity index will enable selected genes/proteins to be chosen for functional analysis. To determine their role, defined/complemented mutants and wild type strains will be compared in several relevant in vivo-relevant assays. Potential biomarkers of disease severity will be assessed based on the combined clinical and molecular profile. Additionally, we will identify key bacterial groups important in re-establishing healthy microbiota during infection. Such analysis will investigate the role of the microbiota in providing colonisation resistance against CDI and will give new information on the bacterial species important in the re-establishment of healthy microbiota after infection, with applications in the rational design of microbial replacement therapy. This integrated clinical case control study will provide for the first time a comprehensive comparison of the pathogen, host response and the role of the intestinal microbiota in CDI that will afford new clues to pathogenesis with practical implications in terms of diagnosis and therapeutic interventions.

Planned Impact

C. difficile is now known to be the most frequent cause of hospital acquired infections in developed countries. Given the continued use of broad-spectrum antibiotics, other drugs and the rising numbers of immuno-compromised and elderly patients, the problems associated with CDI will remain a challenge to healthcare delivery for the foreseeable future. To date, most research on C. difficile has been piecemeal and has not taken into account the role of the microbiota and the host. This study will uniquely follow infection in a cohort of patients and be compared to appropriate controls. This multidisciplinary research programme fits squarely into several priority research areas identified by the MRC, in terms of reducing the burden of hospital acquired infections, health in the ageing population, the application of genomics, to the identification of biomarkers, drug and vaccine candidate and the design of novel treatments.

Given the mortality and morbidity caused by CDI and the enormous cost to the UK economy (estimated to be £500 million per annum), the benefits of improved methods to detect, prevent and understand CDI to health and wealth of society are self-evident. The commercial private sector will potentially benefit from the research in several areas. Specific examples include the investigation of the role of the healthy microbiota in providing colonisation resistance against CDI and will give new information on the bacterial species important in the re-establishment of a healthy microbiota after infection, with applications in the rational design of microbial replacement therapy. The identification of immunodominant antigens from samples of patient serum with the pan-C.difficile protein microarray may identify useful immunodiagnostic markers and provide information on potential vaccine candidates. A deeper understanding of the factors important during relapse may provide clues to novel strategies to curtail the effect of CDI. Given the healthcare issues surrounding hospital-acquired infections and the human microbiota, the project will also engage the public

Additionally, through these studies and our deeper understanding of CDI and recurrent disease, this is likely to influence policy makers and regulators as to the optimum treatment for CDI. C. difficile and CDI are very much in the public and political eye, the co-ordinated program of work described is unique and promises to break new ground in both basic and translational research. The research program should give the UK a significant boost in this important and topical health care issue and will contribute significantly to the UK science base.

Publications

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publication icon
Browne HP (2017) Transmission of the gut microbiota: spreading of health. in Nature reviews. Microbiology

 
Title Additional file 10: Figure S9. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Non-neutral evolution for genes within Clusters of Orthologous Groups (COG*) categories. Boxplots are constructed using (-log10) p-values of non-neutral evolution for each gene. *ppe/Nâ =â pe/ppe genes annotated as COG category N, * COG categories: A RNA processing and modification, B Chromatin Structure and dynamics, C Energy production and conversion, D Cell cycle control and mitosis, E Amino Acid metabolism and transport, F Nucleotide metabolism and transport, G Carbohydrate metabolism and transport, H Coenzyme metabolism, I Lipid metabolism, J Translation, K Transcription, L Replication and repair, M Cell wall/membrane/envelope biogenesis, N Cell motility, O Post-translational modification, protein turnover, chaperone functions, P Inorganic ion transport and metabolism, Q Secondary Structure, T Signal Transduction, U Intracellular trafficking and secretion, Y Nuclear structure, Z Cytoskeleton, R General Functional Prediction only, S Function Unknown. (TIF 127Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_10_Figure_S9_of_Recombination_in...
 
Title Additional file 10: Figure S9. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Non-neutral evolution for genes within Clusters of Orthologous Groups (COG*) categories. Boxplots are constructed using (-log10) p-values of non-neutral evolution for each gene. *ppe/Nâ =â pe/ppe genes annotated as COG category N, * COG categories: A RNA processing and modification, B Chromatin Structure and dynamics, C Energy production and conversion, D Cell cycle control and mitosis, E Amino Acid metabolism and transport, F Nucleotide metabolism and transport, G Carbohydrate metabolism and transport, H Coenzyme metabolism, I Lipid metabolism, J Translation, K Transcription, L Replication and repair, M Cell wall/membrane/envelope biogenesis, N Cell motility, O Post-translational modification, protein turnover, chaperone functions, P Inorganic ion transport and metabolism, Q Secondary Structure, T Signal Transduction, U Intracellular trafficking and secretion, Y Nuclear structure, Z Cytoskeleton, R General Functional Prediction only, S Function Unknown. (TIF 127Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_10_Figure_S9_of_Recombination_in...
 
Title Additional file 2: Figure S1. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance 
Description The global distribution of geographic origin and lineage of the isolates. Lineages one to four are represented by blue, green, purple, and red, respectively. (PNG 265 kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_2_Figure_S1_of___Mycobacterium_t...
 
Title Additional file 2: Figure S1. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance 
Description The global distribution of geographic origin and lineage of the isolates. Lineages one to four are represented by blue, green, purple, and red, respectively. (PNG 265 kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_2_Figure_S1_of___Mycobacterium_t...
 
Title Additional file 2: Figure S1. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Allele frequency spectra for each lineage by synonymous (blue) and non-synonymous (red) mutations. The peaks at intermediate allele frequencies include sub-lineage defining SNPs (Lineage 1 Indo-Oceanic; Lineage 2 East-Asian (Beijing); Lineage 3 East-African-Indian; Lineage 4 Euro-American). (TIF 207Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_2_Figure_S1_of_Recombination_in_...
 
Title Additional file 2: Figure S1. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Allele frequency spectra for each lineage by synonymous (blue) and non-synonymous (red) mutations. The peaks at intermediate allele frequencies include sub-lineage defining SNPs (Lineage 1 Indo-Oceanic; Lineage 2 East-Asian (Beijing); Lineage 3 East-African-Indian; Lineage 4 Euro-American). (TIF 207Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_2_Figure_S1_of_Recombination_in_...
 
Title Additional file 3: Figure S2. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance 
Description SNP allele frequency spectrum. A large number of rare variants are observed. Peaks with higher allele frequency reflect the presence of lineage and sub-lineage specific SNPs. (PNG 33 kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_3_Figure_S2_of___Mycobacterium_t...
 
Title Additional file 3: Figure S2. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance 
Description SNP allele frequency spectrum. A large number of rare variants are observed. Peaks with higher allele frequency reflect the presence of lineage and sub-lineage specific SNPs. (PNG 33 kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_3_Figure_S2_of___Mycobacterium_t...
 
Title Additional file 3: Figure S2. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Gene-based nucleotide diversity (D ) for the 21 reference genomes. All genes with high nucleotide diversity (D â >â 0.0075) are labelled. (TIF 148Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_3_Figure_S2_of_Recombination_in_...
 
Title Additional file 3: Figure S2. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Gene-based nucleotide diversity (D ) for the 21 reference genomes. All genes with high nucleotide diversity (D â >â 0.0075) are labelled. (TIF 148Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_3_Figure_S2_of_Recombination_in_...
 
Title Additional file 4: Figure S3. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Phylogenetic tree constructed using 50,540 genome-wide SNPs. Clear clustering according to lineage can be seen (Lineage 1 (Indo-Oceanic, green), lineage 2 (East-Asian (Beijing), blue), lineage 3 (East-African-Indian, purple), lineage 4 (Euro-American, red)). Reference genomes are labelled. M. canetti is annotated in cyan. (TIF 69Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_4_Figure_S3_of_Recombination_in_...
 
Title Additional file 4: Figure S3. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Phylogenetic tree constructed using 50,540 genome-wide SNPs. Clear clustering according to lineage can be seen (Lineage 1 (Indo-Oceanic, green), lineage 2 (East-Asian (Beijing), blue), lineage 3 (East-African-Indian, purple), lineage 4 (Euro-American, red)). Reference genomes are labelled. M. canetti is annotated in cyan. (TIF 69Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_4_Figure_S3_of_Recombination_in_...
 
Title Additional file 5: Figure S4. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Identifying sites leading to differences in tree topologies based on all SNPs (Additional file 4: Figure S3a) and only those from pe/ppe genes (Additional file 4: Figure S3b). The Î Site wise log likelihood score (Î SSLS) is calculated for each SNP in the pe/ppe gene alignments. Negative differences indicate SNP positions favouring the pe/ppe tree. SNPs in pe_pgrs3, ppe57 and ppe60 produce strong phylogenetic signals supporting the pe/ppe tree. (TIF 113Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_5_Figure_S4_of_Recombination_in_...
 
Title Additional file 5: Figure S4. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Identifying sites leading to differences in tree topologies based on all SNPs (Additional file 4: Figure S3a) and only those from pe/ppe genes (Additional file 4: Figure S3b). The Î Site wise log likelihood score (Î SSLS) is calculated for each SNP in the pe/ppe gene alignments. Negative differences indicate SNP positions favouring the pe/ppe tree. SNPs in pe_pgrs3, ppe57 and ppe60 produce strong phylogenetic signals supporting the pe/ppe tree. (TIF 113Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_5_Figure_S4_of_Recombination_in_...
 
Title Additional file 6: Figure S5. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Phylogenetic tree created using only SNPs from pe_pgrs3. No clear clustering by lineage is observed. However there are two major clades, one consistent with H37Rv (bottom-left). (TIF 126Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_6_Figure_S5_of_Recombination_in_...
 
Title Additional file 6: Figure S5. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Phylogenetic tree created using only SNPs from pe_pgrs3. No clear clustering by lineage is observed. However there are two major clades, one consistent with H37Rv (bottom-left). (TIF 126Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_6_Figure_S5_of_Recombination_in_...
 
Title Additional file 7: Figure S6. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance 
Description Molecular interactions established by wild-type residues in katG and rpoB residues. (A) The interactions established by Ser315 in katG. Given the proximity of the residue to the ligands INH and HEM, mutations to Asn and Thr, with slightly larger side chains, would potentially cause steric clashes. (B) The interactions of Asp435 in rpoB. It directly interacts with RMP via polar interactions that would be disrupted by mutations to Val. (C) Thr400 in rpoB is at the end of an alpha helix establishing intra molecular interactions. Giving its distance to RMP, it would be expected that its mutation to Ala would be a lower impact, which would arise from alosteric changes. (D) Ser450 establishes strong intra molecular interactions in the RMP binding site. Mutations to larger residues (Trp and Leu) could disrupt the packing of the region and therefore binding. (E). Ile491 performs hydrophobic interactions with RMP and its neighbouring residues. Mutations to Phe or Val would compromise packing, either inducing steric clashes or compromising packing. (F). His445 performs strong intra molecular interactions, including a donor-pi (blue dashes) and hydrogen bond (red dashes). Mutations to residues Asp, Tyr or Arg would imply in the loss of the pi interaction as well as potential introduction of steric clashes. (PNG 749 kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_7_Figure_S6_of___Mycobacterium_t...
 
Title Additional file 7: Figure S6. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance 
Description Molecular interactions established by wild-type residues in katG and rpoB residues. (A) The interactions established by Ser315 in katG. Given the proximity of the residue to the ligands INH and HEM, mutations to Asn and Thr, with slightly larger side chains, would potentially cause steric clashes. (B) The interactions of Asp435 in rpoB. It directly interacts with RMP via polar interactions that would be disrupted by mutations to Val. (C) Thr400 in rpoB is at the end of an alpha helix establishing intra molecular interactions. Giving its distance to RMP, it would be expected that its mutation to Ala would be a lower impact, which would arise from alosteric changes. (D) Ser450 establishes strong intra molecular interactions in the RMP binding site. Mutations to larger residues (Trp and Leu) could disrupt the packing of the region and therefore binding. (E). Ile491 performs hydrophobic interactions with RMP and its neighbouring residues. Mutations to Phe or Val would compromise packing, either inducing steric clashes or compromising packing. (F). His445 performs strong intra molecular interactions, including a donor-pi (blue dashes) and hydrogen bond (red dashes). Mutations to residues Asp, Tyr or Arg would imply in the loss of the pi interaction as well as potential introduction of steric clashes. (PNG 749 kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_7_Figure_S6_of___Mycobacterium_t...
 
Title Additional file 7: Figure S6. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Lineage-specific recombination hotspots. Manhattan plots showing genes that are likely to be recombination hotspots in each lineage (Lineage 1 Indo-Oceanic; Lineage 2 East-Asian (Beijing); Lineage 3 East-African-Indian; Lineage 4 Euro-American). The (â log10) p-value for the phi statistic is plotted against genome position. All genes with p-valuesâ 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_7_Figure_S6_of_Recombination_in_...
 
Title Additional file 7: Figure S6. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Lineage-specific recombination hotspots. Manhattan plots showing genes that are likely to be recombination hotspots in each lineage (Lineage 1 Indo-Oceanic; Lineage 2 East-Asian (Beijing); Lineage 3 East-African-Indian; Lineage 4 Euro-American). The (â log10) p-value for the phi statistic is plotted against genome position. All genes with p-valuesâ 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_7_Figure_S6_of_Recombination_in_...
 
Title Additional file 8: Figure S7. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Evidence of recombination at a gene level in the 21 reference genomes. A Manhattan plot showing genes that are likely to be recombination hotspots. The (â log10) p-value for the phi statistic is plotted against genome position. Genes with p-values less than 0.05 are shown. (TIF 120Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_8_Figure_S7_of_Recombination_in_...
 
Title Additional file 8: Figure S7. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Evidence of recombination at a gene level in the 21 reference genomes. A Manhattan plot showing genes that are likely to be recombination hotspots. The (â log10) p-value for the phi statistic is plotted against genome position. Genes with p-values less than 0.05 are shown. (TIF 120Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_8_Figure_S7_of_Recombination_in_...
 
Title Additional file 9: Figure S8. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Selection dN/dS values for each gene within Clusters of Orthologous Groups (COG*) categories. *ppe/Nâ =â pe/ppe genes annotated as COG category N, * COG categories: A RNA processing and modification, B Chromatin Structure and dynamics, C Energy production and conversion, D Cell cycle control and mitosis, E Amino Acid metabolism and transport, F Nucleotide metabolism and transport, G Carbohydrate metabolism and transport, H Coenzyme metabolism, I Lipid metabolism, J Translation, K Transcription, L Replication and repair, M Cell wall/membrane/envelope biogenesis, N Cell motility, O Post-translational modification, protein turnover, chaperone functions, P Inorganic ion transport and metabolism, Q Secondary Structure, T Signal Transduction, U Intracellular trafficking and secretion, Y Nuclear structure, Z Cytoskeleton, R General Functional Prediction only, S Function Unknown. (TIF 124Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_9_Figure_S8_of_Recombination_in_...
 
Title Additional file 9: Figure S8. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages 
Description Selection dN/dS values for each gene within Clusters of Orthologous Groups (COG*) categories. *ppe/Nâ =â pe/ppe genes annotated as COG category N, * COG categories: A RNA processing and modification, B Chromatin Structure and dynamics, C Energy production and conversion, D Cell cycle control and mitosis, E Amino Acid metabolism and transport, F Nucleotide metabolism and transport, G Carbohydrate metabolism and transport, H Coenzyme metabolism, I Lipid metabolism, J Translation, K Transcription, L Replication and repair, M Cell wall/membrane/envelope biogenesis, N Cell motility, O Post-translational modification, protein turnover, chaperone functions, P Inorganic ion transport and metabolism, Q Secondary Structure, T Signal Transduction, U Intracellular trafficking and secretion, Y Nuclear structure, Z Cytoskeleton, R General Functional Prediction only, S Function Unknown. (TIF 124Â kb) 
Type Of Art Film/Video/Animation 
Year Produced 2016 
URL https://springernature.figshare.com/articles/figure/Additional_file_9_Figure_S8_of_Recombination_in_...
 
Description Academic Travel Award
Amount £1,000 (GBP)
Organisation Santander Universities 
Sector Private
Country United Kingdom
Start 02/2016 
End 03/2016
 
Description Full PhD Fellowship
Amount £125,000 (GBP)
Funding ID #200974442 
Organisation Government of Brazil 
Department Science without Borders
Sector Public
Country Brazil
Start 09/2013 
End 03/2017
 
Description LY256: A novel and potent antibiotic for treating Clostridium difficile infection
Amount £1,729,174 (GBP)
Funding ID MR/S019103/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 03/2023
 
Description Wellcome Trust Senior Investigator award
Amount £2,100,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2014 
End 04/2019
 
Title Additional file 1: of Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data 
Description Strain information and full results table for clinically-derived Malawi samples, in silico replicate samples and Portuguese replicate samples. Lineage, total number of SNPs, number of heterozygous sites and the mixture analysis result for both Bayesian clustering and heterozygous sites approaches is included for each sample. (XLSX 162 kb) 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/Additional_file_1_of_Identifying_mixed_Mycobacterium_tu...
 
Title Additional file 1: of Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data 
Description Strain information and full results table for clinically-derived Malawi samples, in silico replicate samples and Portuguese replicate samples. Lineage, total number of SNPs, number of heterozygous sites and the mixture analysis result for both Bayesian clustering and heterozygous sites approaches is included for each sample. (XLSX 162 kb) 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/Additional_file_1_of_Identifying_mixed_Mycobacterium_tu...
 
Title Additional file 3 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus 
Description Additional file 3. All BLASTN hits from AaegL5 assembly. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Flavivirus_integrations_in...
 
Title Additional file 3 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus 
Description Additional file 3. All BLASTN hits from AaegL5 assembly. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Flavivirus_integrations_in...
 
Title Additional file 4 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus 
Description Additional file 4. Accension IDs of all used flavivirus genomes. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_4_of_Flavivirus_integrations_in...
 
Title Additional file 4 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus 
Description Additional file 4. Accension IDs of all used flavivirus genomes. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_4_of_Flavivirus_integrations_in...
 
Title Additional file 4: Figure S3. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance 
Description Population structure analysis of the 144 isolates show clustering by lineage (Lineages one to four are represented by blue, green, purple, and red points, respectively). (a) A phylogenetic tree rooted with M. canetti. (b) First two principal components represent 33Â % and 30.5Â % of the variation explained between isolates, respectively. (ZIP 105 kb) 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_4_Figure_S3_of___Mycobacterium_...
 
Title Additional file 4: Figure S3. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance 
Description Population structure analysis of the 144 isolates show clustering by lineage (Lineages one to four are represented by blue, green, purple, and red points, respectively). (a) A phylogenetic tree rooted with M. canetti. (b) First two principal components represent 33Â % and 30.5Â % of the variation explained between isolates, respectively. (ZIP 105 kb) 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_4_Figure_S3_of___Mycobacterium_...
 
Title Additional file 5 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus 
Description Additional file 5. All BLASTN hits from AaloF2 assembly. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_5_of_Flavivirus_integrations_in...
 
Title Additional file 5 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus 
Description Additional file 5. All BLASTN hits from AaloF2 assembly. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_5_of_Flavivirus_integrations_in...
 
Title Additional file 5: Figure S4. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance 
Description The relationship between the total number of non-synonymous SNPs in candidate loci and the MIC values. The size of the circle represents the number of isolates. a) Ethambutol (embB, embA, embA promoter, embC, embR and ubiA). b) Streptomycin (rpsL, rrs). The size of the circles is proportional to the frequency. The MIC values tend to increase with the number of non-synonymous mutations (ethambutol: rho = 0.24, slope = 0.29, p = 0.003; streptomycin: rho = 0.48, slope = 3.59, p = 1.65 × 10-8). The horizontal blue lines refer to the resistance cut-offs. (ZIP 92 kb) 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_5_Figure_S4_of___Mycobacterium_...
 
Title Additional file 5: Figure S4. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance 
Description The relationship between the total number of non-synonymous SNPs in candidate loci and the MIC values. The size of the circle represents the number of isolates. a) Ethambutol (embB, embA, embA promoter, embC, embR and ubiA). b) Streptomycin (rpsL, rrs). The size of the circles is proportional to the frequency. The MIC values tend to increase with the number of non-synonymous mutations (ethambutol: rho = 0.24, slope = 0.29, p = 0.003; streptomycin: rho = 0.48, slope = 3.59, p = 1.65 × 10-8). The horizontal blue lines refer to the resistance cut-offs. (ZIP 92 kb) 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_5_Figure_S4_of___Mycobacterium_...
 
Title Additional file 6 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus 
Description Additional file 6. EVE coordinates and sequences identified in AaloF2. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_6_of_Flavivirus_integrations_in...
 
Title Additional file 6 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus 
Description Additional file 6. EVE coordinates and sequences identified in AaloF2. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_6_of_Flavivirus_integrations_in...
 
Title Additional file 6: Figure S5. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance 
Description Percentage of the variation in MIC values explained by each mutated codon in candidate genes. Bars in red represent significant independent associations with increased MIC (pâ 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_6_Figure_S5_of___Mycobacterium_...
 
Title Additional file 6: Figure S5. of Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance 
Description Percentage of the variation in MIC values explained by each mutated codon in candidate genes. Bars in red represent significant independent associations with increased MIC (pâ 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_6_Figure_S5_of___Mycobacterium_...
 
Title Additional file 7 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus 
Description Additional file 7. EVE bedfiles for AaegL5 and AaloF2 assemblies; phylogenetic trees and corresponding metadata for Ae. aegypti EVEs and cox1 gene. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_7_of_Flavivirus_integrations_in...
 
Title Additional file 7 of Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus 
Description Additional file 7. EVE bedfiles for AaegL5 and AaloF2 assemblies; phylogenetic trees and corresponding metadata for Ae. aegypti EVEs and cox1 gene. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_7_of_Flavivirus_integrations_in...
 
Title MOESM1 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines 
Description Additional file 1: Table S1. SNPs identified in the three lines 3D7A, A4 and F12. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/MOESM1_of_Genomic_variation_in_two_gametocyte_n...
 
Title MOESM1 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines 
Description Additional file 1: Table S1. SNPs identified in the three lines 3D7A, A4 and F12. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/MOESM1_of_Genomic_variation_in_two_gametocyte_n...
 
Title MOESM2 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines 
Description Additional file 2: Table S2. Insertions (INS) and deletions (DEL) identified in the three lines 3D7A, A4 and F12. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/MOESM2_of_Genomic_variation_in_two_gametocyte_n...
 
Title MOESM2 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines 
Description Additional file 2: Table S2. Insertions (INS) and deletions (DEL) identified in the three lines 3D7A, A4 and F12. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/MOESM2_of_Genomic_variation_in_two_gametocyte_n...
 
Title MOESM3 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines 
Description Additional file 3: Table S3. SNPs and Indels identified in the PF3D7_1222600 gene among P. falciparum field isolates from Africa and Asia. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/MOESM3_of_Genomic_variation_in_two_gametocyte_n...
 
Title MOESM3 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines 
Description Additional file 3: Table S3. SNPs and Indels identified in the PF3D7_1222600 gene among P. falciparum field isolates from Africa and Asia. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/MOESM3_of_Genomic_variation_in_two_gametocyte_n...
 
Title MOESM4 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines 
Description Additional file 4: Table S4. Structural variants identified in the three lines 3D7A, A4 and F12. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/MOESM4_of_Genomic_variation_in_two_gametocyte_n...
 
Title MOESM4 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines 
Description Additional file 4: Table S4. Structural variants identified in the three lines 3D7A, A4 and F12. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/MOESM4_of_Genomic_variation_in_two_gametocyte_n...
 
Title MOESM7 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines 
Description Additional file 7: Table S5. A scan for motifs in gene sequences (coding and UTR regions). 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/MOESM7_of_Genomic_variation_in_two_gametocyte_n...
 
Title MOESM7 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines 
Description Additional file 7: Table S5. A scan for motifs in gene sequences (coding and UTR regions). 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/MOESM7_of_Genomic_variation_in_two_gametocyte_n...
 
Title Oligosaccharyltransferase Polypeptide 
Description New enzyme to improve glycoengineering in E. coli 
IP Reference GB1704103.9 
Protection Patent application published
Year Protection Granted 2018
Licensed Commercial In Confidence
Impact Improve glycoengineering in the E. coli cell
 
Title THERAPEUTIC FOR TREATING CLOSTRIDIUM DIFFICILE INFECTION 
Description The invention relates to deoxyribonuclease for use in the treatment of a suspected or existing C. difficile infection; a pharmaceutical or veterinary composition or formulation comprising at least deoxyribonucleasefor use in the treatment of a suspected or existing C. difficile infection; a combination therapeutic comprising at least deoxyribonucleasefor use in the treatment of a suspected or existing C. difficile infection; a method of treating a mammal suspected of being infected with, or infected with, C. difficile comprising the use of at least deoxyribonuclease; a method of cleaning or sterilising a material or product comprising the use of at least deoxyribonuclease; and a cleaning or sterilising product impregnated with or containing at least deoxyribonuclease. 
IP Reference WO2013175172 
Protection Patent application published
Year Protection Granted 2013
Licensed No
Impact Simple treatment to reduce C. difficile disease
 
Description 8th International Conference on the Molecular Biology and Pathogenesis of the Clostridia, 22-26th October 2013 (Andrew Swale and Fabio Miyajima) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Presentation of 2 posters which attracted significant attention from the audience.

Interactions with several leading research groups represented in the field, access to most current expertise and trends in the field. Set up of strategic collaborations and access to new methodologies and materials, such as protein epitopes and immunogenic.
Year(s) Of Engagement Activity 2013
URL http://www.clostridia.net/ClostPath.htm
 
Description 8th International Conference on the Molecular Biology and Pathogenesis of the Clostridia, 22-26th October 2013 -conference cast (Andrew Swale) 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Conference Cast made by Scitable (Nature education group) in which one of the members of the team (Andrew Swale: PhD Student) shared his experience related to his research and attendance at the 8th International Conference on the Molecular Biology and Pathogenesis of the Clostridia, 22-26th October 2013 in Australia.

Provided further insights for postgraduate students about the conference experience for a junior researcher. Requests for further contributions have been made.
Year(s) Of Engagement Activity 2013
URL http://www.nature.com/scitable/blog/conferencecast/molecular_biology_pathogenesis_of_the
 
Description BBC Breakfast 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Interview on Antibiotic resistance, Vaccine development and Government plans
Year(s) Of Engagement Activity 2019
 
Description BBC News 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Interview on Antibiotic resistance, Vaccine development and Government plans
Year(s) Of Engagement Activity 2019
 
Description Steering Committee Meeting on Clostridium difficile infection (Royal Liverpool and Broadgreen Hospitals - NHS Trust) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Our team is frequently invited to take part of the meetings and provide regular updates of our research findings to the committee.
This interaction with NHS is highly beneficial for both parts and has assisted the Hospitals to shape their guidelines and keep CDI and other nosocomial infections under control.
Year(s) Of Engagement Activity 2012,2013,2014,2015
 
Description TV Broadcasts 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact BBC Breakfast TV interview on vaccine design and antimicrobial resistance
BBC one interview on Campylobacter in Food chain
One Show BBC on antimicrobial resistance
Year(s) Of Engagement Activity 2015
 
Description University Open Day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact 50-60 prospective undergraduate students attended the University open day with their parents, relatives and friends, and paid a visit to our research facilities. This was an important initiative to attract future talents for the courses offered in the area of biomedical sciences and medicine and the event as a whole has certainly sparked further interest from the audience as courses have been well sought after.
Year(s) Of Engagement Activity 2014,2015