Using genomics to trace Salmonella transmission and antimicrobial resistance (AMR) in the poultry and swine food chains in the Philippines
Lead Research Organisation:
London School of Hygiene & Tropical Medicine
Department Name: Infectious and Tropical Diseases
Abstract
Salmonellosis, caused by Salmonella spp., is among the most commonly reported foodborne diseases globally, and has a high health and economic burden in both animals and humans. Salmonella enterica is a primary cause of cases and outbreaks of diarrhoea worldwide, including in the Philippines. While numerous potential methods of transmission exist, commercial chicken and pig meat have been recognised as crucial food vehicles for S. enterica. The forecasted increase in consumption and utilisation of swine and poultry products in the Philippines in the next 10 years to over 3 million metric tonnes per annum, increases the likelihood for exposure to the bacterium.
Previous studies from our Philippine team have shown that S. enterica is circulating in the chicken and pig food chains in Metropolitan Manila, and is a likely major and increasing cause of food poisoning. Notably, treatment options for salmonellosis are decreasing as the bacteria increase in their resistance to antimicrobial drugs. Due to frequent use of antibiotics, chickens and pigs are now realized as potential risks in disseminating drug-resistant S. enterica, with multi-drug resistant (MDR) strains now reported to be present in the Philippines.
For this study, we propose to compare at the genetic level of past and present samples of S. enterica across live animal and processed meat domains in the chicken and pig food chains in Metropolitan Manilla. We will perform whole genome sequencing (WGS) of historical and prospectively collected S. enterica bacteria isolated from these samples. WGS technology has become a rapid and affordable tool that is revolutionising the fields of genetics, microbiology, and ecology, as well as public health surveillance and response, including animal health. WGS analysis has enabled new and often unpredicted routes to disease by defining resistance genotypes and their historical generation, predicting resistance phenotypes and identifying similar isolate genomes that are part of a transmission chains. The resulting genomic variation will increase our understanding of transmission and drug resistance to permit more effective interventions. These genomic data will be correlated with laboratory determined virulence and drug resistance outcomes and other collected meta data to enable an important contribution in disease control and prevention, particularly in the design of diagnostics and interventions for Salmonellosis across the food domains (e.g. farms, markets).
Previous studies from our Philippine team have shown that S. enterica is circulating in the chicken and pig food chains in Metropolitan Manila, and is a likely major and increasing cause of food poisoning. Notably, treatment options for salmonellosis are decreasing as the bacteria increase in their resistance to antimicrobial drugs. Due to frequent use of antibiotics, chickens and pigs are now realized as potential risks in disseminating drug-resistant S. enterica, with multi-drug resistant (MDR) strains now reported to be present in the Philippines.
For this study, we propose to compare at the genetic level of past and present samples of S. enterica across live animal and processed meat domains in the chicken and pig food chains in Metropolitan Manilla. We will perform whole genome sequencing (WGS) of historical and prospectively collected S. enterica bacteria isolated from these samples. WGS technology has become a rapid and affordable tool that is revolutionising the fields of genetics, microbiology, and ecology, as well as public health surveillance and response, including animal health. WGS analysis has enabled new and often unpredicted routes to disease by defining resistance genotypes and their historical generation, predicting resistance phenotypes and identifying similar isolate genomes that are part of a transmission chains. The resulting genomic variation will increase our understanding of transmission and drug resistance to permit more effective interventions. These genomic data will be correlated with laboratory determined virulence and drug resistance outcomes and other collected meta data to enable an important contribution in disease control and prevention, particularly in the design of diagnostics and interventions for Salmonellosis across the food domains (e.g. farms, markets).
Planned Impact
The economy:
Advances in sequencing technology now allow the genomic characterization of bacteria on an unprecedented scale. These have the potential to greatly accelerate research aimed at understanding the biology of S. enterica and their interaction with animal/human immunity and meat products, the underlying causes of AMR, and the disease transmission and epidemiology. The knowledge generated in this project and its application could ultimately benefit those developing foodborne disease control measures, such as identifying transmission hotspots (e.g. markets) and molecular diagnostic tools for monitoring the development of AMR and presence of virulent strains. Ultimately, the knowledge gained in this study could improve the health & wealth of the Philippines, where >2 million tonnes of pig/chicken meat are consumed per year, but also globally where Salmonellosis is a major public health issue. The methods used in this project could have application beyond bacterial studies, to help more widely in the control & prevention of infectious diseases in humans/animals, with associated economic benefits.
The general public:
Salmonellosis is among the most frequently reported foodborne diseases worldwide, and has a high animal and human health and economic burden. Knowledge generated in the project could lead to better access to safer and more effective disease control measurements (e.g. diagnostics) and improved methods for preventing transmission. Genomics insights into transmission and AMR could lead ultimately to improved control measures adopted globally. The project therefore specifically addresses the BBSRC strategic aim to impact positively on agriculture & food security, and to assist with bringing the health impacts of fundamental research to animals and people more quickly. Similarly, we address the BBSRC aim of driving advances in fundamental bioscience, establishing and using biobanks, and developing and applying new tools in 'omics.
Academic and industrial organisations:
New sequencing technologies have the ability to generate vast amounts of data, but there is a need to translate this information into knowledge useable by other research scientists and industry. Our work will provide tools useful for genomic data analysis, which can be utilized across diseases and in different settings. Scientific developments arising would enhance the commercial private sector for the production of safer food, more effective disease control measures and AMR monitoring across the food chain. We have links with companies (e.g. GSK) and will work through the technology transfer offices to ensure pipelines to translation tool production and exploitation are in place. Developing a basic understanding of the S. enterica genetic diversity across the food domains will be important for understanding the impact of control measurements such as diagnostics and transmission mechanisms, and can have practical applications for other foodborne diseases. Also, any important findings and technology developed may have enormous implications for policy makers. We will work with the Philippines Dept. of Agriculture to improve current diagnostics for routine monitoring.
Training:
The proposal will employ, train and develop scientists in the Philippines and UK with an 'omic mentality that can be applied in academia, the public sector and industry. The multidisciplinary project team will have an important and economically vital research area. The researchers working on the project will develop team working and project management skills, which they can apply in all employment sectors. Importantly, the scope for multidisciplinary interactions in this proposal should not be underestimated. The Philippine-based researchers employed to carry out the planned activities will have unique opportunities for engagement with experts across project in microbiology, biotechnology, veterinary care, genomics and genomic epidemiology, and public health.
Advances in sequencing technology now allow the genomic characterization of bacteria on an unprecedented scale. These have the potential to greatly accelerate research aimed at understanding the biology of S. enterica and their interaction with animal/human immunity and meat products, the underlying causes of AMR, and the disease transmission and epidemiology. The knowledge generated in this project and its application could ultimately benefit those developing foodborne disease control measures, such as identifying transmission hotspots (e.g. markets) and molecular diagnostic tools for monitoring the development of AMR and presence of virulent strains. Ultimately, the knowledge gained in this study could improve the health & wealth of the Philippines, where >2 million tonnes of pig/chicken meat are consumed per year, but also globally where Salmonellosis is a major public health issue. The methods used in this project could have application beyond bacterial studies, to help more widely in the control & prevention of infectious diseases in humans/animals, with associated economic benefits.
The general public:
Salmonellosis is among the most frequently reported foodborne diseases worldwide, and has a high animal and human health and economic burden. Knowledge generated in the project could lead to better access to safer and more effective disease control measurements (e.g. diagnostics) and improved methods for preventing transmission. Genomics insights into transmission and AMR could lead ultimately to improved control measures adopted globally. The project therefore specifically addresses the BBSRC strategic aim to impact positively on agriculture & food security, and to assist with bringing the health impacts of fundamental research to animals and people more quickly. Similarly, we address the BBSRC aim of driving advances in fundamental bioscience, establishing and using biobanks, and developing and applying new tools in 'omics.
Academic and industrial organisations:
New sequencing technologies have the ability to generate vast amounts of data, but there is a need to translate this information into knowledge useable by other research scientists and industry. Our work will provide tools useful for genomic data analysis, which can be utilized across diseases and in different settings. Scientific developments arising would enhance the commercial private sector for the production of safer food, more effective disease control measures and AMR monitoring across the food chain. We have links with companies (e.g. GSK) and will work through the technology transfer offices to ensure pipelines to translation tool production and exploitation are in place. Developing a basic understanding of the S. enterica genetic diversity across the food domains will be important for understanding the impact of control measurements such as diagnostics and transmission mechanisms, and can have practical applications for other foodborne diseases. Also, any important findings and technology developed may have enormous implications for policy makers. We will work with the Philippines Dept. of Agriculture to improve current diagnostics for routine monitoring.
Training:
The proposal will employ, train and develop scientists in the Philippines and UK with an 'omic mentality that can be applied in academia, the public sector and industry. The multidisciplinary project team will have an important and economically vital research area. The researchers working on the project will develop team working and project management skills, which they can apply in all employment sectors. Importantly, the scope for multidisciplinary interactions in this proposal should not be underestimated. The Philippine-based researchers employed to carry out the planned activities will have unique opportunities for engagement with experts across project in microbiology, biotechnology, veterinary care, genomics and genomic epidemiology, and public health.
Publications
Ajawatanawong P
(2019)
A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages.
in Scientific reports
Benavente ED
(2018)
Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development.
in Scientific reports
Benavente ED
(2021)
Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa.
in Nature communications
Campos M
(2020)
Surveillance of Aedes aegypti populations in the city of Praia, Cape Verde: Zika virus infection, insecticide resistance and genetic diversity.
in Parasites & vectors
Title | Additional file 10: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Sublineage frequency table, Numbers and percentage by lineage assigned to each sublineage. (PPTX 36 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_10_of_Genome-wide_analysis_of_Mycobacte... |
Title | Additional file 10: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Sublineage frequency table, Numbers and percentage by lineage assigned to each sublineage. (PPTX 36 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_10_of_Genome-wide_analysis_of_Mycobacte... |
Title | Additional file 1: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Variant Summary Tables, Summary tables of variants called in comparison to the H37rv reference, with monomorphic variants removed for each dataset. a Total numbers of variants by lineage; b Number of variants per sample; c Non-reference variant frequency summary; variants called in comparison to the H37rv reference. (PPTX 39 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_1_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 1: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Variant Summary Tables, Summary tables of variants called in comparison to the H37rv reference, with monomorphic variants removed for each dataset. a Total numbers of variants by lineage; b Number of variants per sample; c Non-reference variant frequency summary; variants called in comparison to the H37rv reference. (PPTX 39 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_1_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 2: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Non-reference variant frequency histogram, A histogram showing log10(frequency + 1) of non-reference alleles compared to the H37rv reference for a lineage 2 and b lineage4. (PPTX 69 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_2_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 2: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Non-reference variant frequency histogram, A histogram showing log10(frequency + 1) of non-reference alleles compared to the H37rv reference for a lineage 2 and b lineage4. (PPTX 69 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_2_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 3: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Population diversity within investigated strains, a Principal component 1 (PC1) by principal component 2 (PC2) for lineage 2, The first 10 principal components account for 71.9% of the variation in lineage 2; b Distance plot for lineage 2 showing pairwise number of variant differences between samples; c Principal component 1 (PC1) by principal component 2 (PC2) for lineage 4, the first 10 principal components account for 88.9% of the variation in lineage 4. d Distance plot for lineage 2 showing pairwise number of variant differences between samples. (PPTX 5650 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_3_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 3: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Population diversity within investigated strains, a Principal component 1 (PC1) by principal component 2 (PC2) for lineage 2, The first 10 principal components account for 71.9% of the variation in lineage 2; b Distance plot for lineage 2 showing pairwise number of variant differences between samples; c Principal component 1 (PC1) by principal component 2 (PC2) for lineage 4, the first 10 principal components account for 88.9% of the variation in lineage 4. d Distance plot for lineage 2 showing pairwise number of variant differences between samples. (PPTX 5650 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_3_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 4: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Scree plots for the principal component analyses, Scree plots showing the proportion of variation accounted for by the first ten principal components, calculated for the pairwise distances within a lineage 4 and b lineage 2. (PPTX 142 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_4_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 4: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Scree plots for the principal component analyses, Scree plots showing the proportion of variation accounted for by the first ten principal components, calculated for the pairwise distances within a lineage 4 and b lineage 2. (PPTX 142 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_4_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 5: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Drug-resistance phenotype frequency table, Drug-resistance phenotype frequency table by lineage. 'Totals' shows the number and percentage of each lineage with a known drug-resistance phenotype. (PPTX 45 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_5_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 5: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Drug-resistance phenotype frequency table, Drug-resistance phenotype frequency table by lineage. 'Totals' shows the number and percentage of each lineage with a known drug-resistance phenotype. (PPTX 45 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_5_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 6: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Cross-resistance phenotype table, Cross-Resistance Table upper diagonal shows proportion of samples phenotyped for both vertical and horizontal phenotype, that test positive for vertical phenotype. Diagonal shows number of samples with each phenotype. Lower diagonal shows number of samples with phenotype for both horizontal and vertical phenotype. (PPTX 45 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_6_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 6: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Cross-resistance phenotype table, Cross-Resistance Table upper diagonal shows proportion of samples phenotyped for both vertical and horizontal phenotype, that test positive for vertical phenotype. Diagonal shows number of samples with each phenotype. Lower diagonal shows number of samples with phenotype for both horizontal and vertical phenotype. (PPTX 45 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_6_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 7: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Variant Position Table, Table detailing variants at all positions with at least one non-synonymous variant found to be significantly associated with a phenotype in any of the variant-based analyses. (PPTX 52 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_7_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 7: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Variant Position Table, Table detailing variants at all positions with at least one non-synonymous variant found to be significantly associated with a phenotype in any of the variant-based analyses. (PPTX 52 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_7_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 8: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Locus Comparison Table, Locus comparison table showing which analyses and in which lineage each loci was identified. An 'x' indicates a locus which was not identified by the method of analysis in question. Loci without a known association with the phenotype are highlighted in bold. (PPTX 44 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_8_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 8: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Locus Comparison Table, Locus comparison table showing which analyses and in which lineage each loci was identified. An 'x' indicates a locus which was not identified by the method of analysis in question. Loci without a known association with the phenotype are highlighted in bold. (PPTX 44 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_8_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 9: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Study frequency table, Study frequency table, showing numbers and percentage of strains from each study by lineage. (PPTX 40 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_9_of_Genome-wide_analysis_of_Mycobacter... |
Title | Additional file 9: of Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance |
Description | Study frequency table, Study frequency table, showing numbers and percentage of strains from each study by lineage. (PPTX 40 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_9_of_Genome-wide_analysis_of_Mycobacter... |
Description | We now understand the AMR profiles and phylogenetic relationship of Salmonella sourced from poultry and swine samples in Manilla meat markets. In particular, more than half the samples were resistant to at least one antibiotic, and there is evidence of strains in transmission chains. We also reviewed the hygiene practices with the wet markets and abattoirs through staff surveys, and the anonymised results forwarded to national meat inspection service. By tracing the source of meat back to farms, it will assist with understanding antibiotic usage. By looking at clinical cases involving Salmonella infections, it will be possible to look at the transmission from farm to fork. |
Exploitation Route | The sequencing of Salmonella isolates from other regions and sources (e.g. environmental). The development of rapid diagnostics for a farm or market setting. We are now working with vets in Pampanga state on related work, and will seek funding for these projects. |
Sectors | Environment Healthcare Government Democracy and Justice |
Description | The National Meat Inspection Service is developing policies for detection of AMR pathogens in the food chain and antibiotic usage in agricultural settings, and is coordinating activities with the Department of Health for an integrated public health response. A database of AMR mutations is being used to develop new diagnostic tools for environmental and clinical settings. Further, a snapshot of current wet market hygiene practice will assist the public health authorities with reducing any transmission of AMR pathogens through the processing of meat. |
Sector | Agriculture, Food and Drink,Environment,Healthcare,Government, Democracy and Justice |
Impact Types | Cultural Societal Economic Policy & public services |
Description | Use of genomics to assist AMR characterisation in the food chain |
Geographic Reach | Asia |
Policy Influence Type | Influenced training of practitioners or researchers |
Description | One Health for One Environment: an A-Z Approach for Tackling Zoonoses |
Amount | £1,738,736 (GBP) |
Funding ID | NE/X016714/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 09/2023 |
End | 09/2029 |
Title | Bioinformatic analysis pipelines |
Description | This pipeline takes as input all the raw sequence data, performs genomic variation calling and transmission analysis using a phylogenetic tree approach. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2019 |
Provided To Others? | No |
Impact | It will lead to the characterisation of transmission chains, which will assist control programs. |
Title | Bioinformatics pipeline |
Description | A bioinformatics pipeline has been established to process the >1000 salmonella isolates sequenced by LSHTM. This has been transferred to UPD, leading to an analysis resulting in a MSc dissertation and publication. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | This pipeline will strengthen the UPD for the analysis of sequence data. |
Title | Additional file 1: of Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs |
Description | Data S1. Mutations in the library (CSV 51 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_1_of_Integrating_informatics_tools_and_... |
Title | Additional file 1: of Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs |
Description | Data S1. Mutations in the library (CSV 51 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_1_of_Integrating_informatics_tools_and_... |
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 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 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 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 | Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto-Beijing genotype |
Description | Tuberculosis disease (TB), caused by Mycobacterium tuberculosis, is a major public health issue in Thailand. The high prevalence of modern Beijing (Lineage 2.2.1) strains has been associated with multi- and extensively drug-resistant infections (MDR-, XDR-TB), complicating disease control. The impact of rarer proto-Beijing (L2.1) strains is less clear. In our study of thirty-seven L2.1 clinical isolates spanning thirteen years, we found a high prevalence of XDR-TB cases (32.4%). With = 12 pairwise SNP distances, 43.2% of L2.1 patients belong to MDR-TB or XDR-TB transmission clusters suggesting a high level of clonal expansion across four Thai provinces. All XDR-TB (100%) were likely due to transmission rather than inadequate treatment. We found a 47 mutation signature and a partial deletion of the fadD14 gene in the circulating XDR-TB cluster, which can be used for surveillance of this rare and resilient M. tuberculosis strain-type that is causing increasing health burden. We also detected three novel deletion positions, a deletion of 1285 bp within desA3 (Rv3230c), large deletions in the plcB, plcA, and ppe38 gene which may play a role in the virulence, pathogenesis or evolution of the L2.1 strain-type. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | https://tandf.figshare.com/articles/dataset/Genomic_evidence_supporting_the_clonal_expansion_of_exte... |
Title | Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto-Beijing genotype |
Description | Tuberculosis disease (TB), caused by Mycobacterium tuberculosis, is a major public health issue in Thailand. The high prevalence of modern Beijing (Lineage 2.2.1) strains has been associated with multi- and extensively drug-resistant infections (MDR-, XDR-TB), complicating disease control. The impact of rarer proto-Beijing (L2.1) strains is less clear. In our study of thirty-seven L2.1 clinical isolates spanning thirteen years, we found a high prevalence of XDR-TB cases (32.4%). With = 12 pairwise SNP distances, 43.2% of L2.1 patients belong to MDR-TB or XDR-TB transmission clusters suggesting a high level of clonal expansion across four Thai provinces. All XDR-TB (100%) were likely due to transmission rather than inadequate treatment. We found a 47 mutation signature and a partial deletion of the fadD14 gene in the circulating XDR-TB cluster, which can be used for surveillance of this rare and resilient M. tuberculosis strain-type that is causing increasing health burden. We also detected three novel deletion positions, a deletion of 1285 bp within desA3 (Rv3230c), large deletions in the plcB, plcA, and ppe38 gene which may play a role in the virulence, pathogenesis or evolution of the L2.1 strain-type. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | https://tandf.figshare.com/articles/dataset/Genomic_evidence_supporting_the_clonal_expansion_of_exte... |
Title | S.enterica sequence data |
Description | Whole genome sequence data for S. enterica sourced from meat samples in wet markets (n=1500). Phenotypic AMR data are available. |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | No |
Impact | It has led to a library of circulating AMR genes/plasmids, which will be useful for the design of diagnostics. |
Title | Whole genome sequencing and an AMR database |
Description | Whole genome sequencing data for Salmonella pathogens and uploading their genomic variants (including AMR related ones) into a database for the research and stakeholder community. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | This database can be mined to develop new diagnostics, and launch functional studies to provide insights into new control tools. |
Description | National Meat Inspection Service |
Organisation | Department of Agriculture and Natural Resources |
Country | Philippines |
Sector | Public |
PI Contribution | Sequencing of Salmonella enterica sourced from meat samples. Bioinformatic pipelines for analysis. |
Collaborator Contribution | Advising on the collection of meat samples. |
Impact | Protocols for: the collection of meat samples, the culturing of the bacteria, the characterisation of AMR profiles and genomic sequencing of the pathogen DNA. |
Start Year | 2018 |
Description | University of Philippines |
Organisation | University of the Philippines |
Country | Philippines |
Sector | Academic/University |
PI Contribution | We are sequencing Salmonella samples, analysing the resulting genomic data. We are building capacity for genomic investigations in the Philippines. |
Collaborator Contribution | They are selecting markets to collect samples and meta data from, and then processing those samples and data. |
Impact | To date, |
Start Year | 2018 |
Description | BBSRC organised meeting in Bracknell 2020 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Study participants or study members |
Results and Impact | This was a BBSRC funded meeting in Bracknell, where all projects funded under the call gave study updates. |
Year(s) Of Engagement Activity | 2020 |
Description | Project meeting in the Philippines |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Study participants or study members |
Results and Impact | This was a project meeting in Manilla in February 2020. |
Year(s) Of Engagement Activity | 2020 |
Description | Visit to Philippines for capacity strengthening |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | A symposium, data analysis workshop and study meetings in UP Diliman and Pampanga State Agricultural University (June 2022). |
Year(s) Of Engagement Activity | 2022 |
Description | Workshop on genomic data analysis |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Study participants or study members |
Results and Impact | A hands-on workshop to train researchers (including project partners) in genomic data analysis. Fifty researchers participated, and received a USB with all software, data and other materials, which can be used on their other projects. |
Year(s) Of Engagement Activity | 2018 |