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2025
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| Online Access: | https://doi.org/10.5281/zenodo.17191987 |
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| _version_ | 1866902266309509120 |
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| author | CatherineWilson511 |
| author_facet | CatherineWilson511 |
| contents | <p>Here we deposit the data and code presented in the upcoming research paper entitled "Circulation of <em>Salmonella</em> spp. between humans, animals and the environment in animal-owning households in Malawi".</p> <p>metadata_osnp_sharing.csv contains 14 columns containing the overall metadata of the <em>Salmonella</em> isolate from which was part of a 'sharing pair'. A. HH1 (Lane ID) B. ST_HH1 (Sequence Type) C. Subspecies_HH1 (<em>Salmonella</em> subspecies) D. Serovar_HH1 (<em>Salmonella</em> serovar) E. HH1_number (Household number) F. study_site_HH1 (Study site) G. Sample.type_HH1 (Sample type) H. Individual.type_HH1 (Individual sample type) I. animal.category_HH1 (Animal category) J. Host_HH1 (Host category) K. AMR_finder_HH1 (Antimicrobial resistance determinant present detected with AMRFinderPlus)) L. abricate_pf_HH1 (Abricate: Plasmid Finder) M. Sample.ID_HH1 (Individual sample number) N. HH1_visit (Household visit number)</p> <p>total_host_hh.csv contains 4 columns containing the overall number of hosts within each household, according to Host category, from which <em>Salmonella</em> was isolated during the study.</p> <p>source_target_p.csv contains 2 columns which contain details of gene IDs. Each row within the dataset therefore contains two genomes which differ by 0 SNPs of the core gene alignment. A. Source (Lane ID of genome 1) B. Target (Lane ID of genome 2)</p> <p>meta_hum_st_wide_wide_extra.csv contains 14 columns. Columns A denotes the household number. The additional 13 columns each denote a different sequence type (ST) of <em>Salmonella</em> detected within human faecal samples collected from each household.</p> <p>meta_env_st_wide_wide_extra.csv contains 16 columns. Columns A denotes the household number. The additional 15 columns denote a different sequence type (ST) of <em>Salmonella</em> detected within environmental samples collected from each household.</p> <p>meta_an_st_wide_wide_extra.csv contains 58 columns. Columns A denotes the household number. The additional 57 columns each denote a different sequence type (ST) of <em>Salmonella</em> detected within animal faeces collected from each household.</p> <p>Source Data- Circulation of <em>Salmonella</em> spp. between humans, animals and the environment in animal-owning households in Malawi. The Source Data file includes five sheets of data. Sheet 1; Metadata and accession numbers includes data used for Figures 1, 2, Table 1 and Supplementary Figures 3, 4 and 5. Sheet 2; Panaroo 227 core gene tree includes the text of the Newick file used to construct the phylogenetic tree in Figure 2. Sheet 3; Core SNP matrix used to construct Table 1 and Supplementary Figure 5. Sheet 4; ST313 metadata used to construct Supplementary Figure 7. Sheet 5; Mapping ST11, used to construct Supplementary Figure 8.</p> <p>We provide the following R code associated with analysis presented in this paper:</p> <p>Salmonella_genome_diversity.R; code used to perform the analysis required to investgate the diversity of the <em>Salmonella</em> spp. within the collection, presented in Figure 1.</p> <p>Salmonella_network.R; code used to construct the network of salmonellae with 0SNP difference of the core gene alignment, presented in Figure 3.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17191987 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | CatherineWilson511/Circulation-of-Salmonella: Circulation of _Salmonella_ spp. between humans, animals and the environment in animal-owning households in Malawi. CatherineWilson511 <p>Here we deposit the data and code presented in the upcoming research paper entitled "Circulation of <em>Salmonella</em> spp. between humans, animals and the environment in animal-owning households in Malawi".</p> <p>metadata_osnp_sharing.csv contains 14 columns containing the overall metadata of the <em>Salmonella</em> isolate from which was part of a 'sharing pair'. A. HH1 (Lane ID) B. ST_HH1 (Sequence Type) C. Subspecies_HH1 (<em>Salmonella</em> subspecies) D. Serovar_HH1 (<em>Salmonella</em> serovar) E. HH1_number (Household number) F. study_site_HH1 (Study site) G. Sample.type_HH1 (Sample type) H. Individual.type_HH1 (Individual sample type) I. animal.category_HH1 (Animal category) J. Host_HH1 (Host category) K. AMR_finder_HH1 (Antimicrobial resistance determinant present detected with AMRFinderPlus)) L. abricate_pf_HH1 (Abricate: Plasmid Finder) M. Sample.ID_HH1 (Individual sample number) N. HH1_visit (Household visit number)</p> <p>total_host_hh.csv contains 4 columns containing the overall number of hosts within each household, according to Host category, from which <em>Salmonella</em> was isolated during the study.</p> <p>source_target_p.csv contains 2 columns which contain details of gene IDs. Each row within the dataset therefore contains two genomes which differ by 0 SNPs of the core gene alignment. A. Source (Lane ID of genome 1) B. Target (Lane ID of genome 2)</p> <p>meta_hum_st_wide_wide_extra.csv contains 14 columns. Columns A denotes the household number. The additional 13 columns each denote a different sequence type (ST) of <em>Salmonella</em> detected within human faecal samples collected from each household.</p> <p>meta_env_st_wide_wide_extra.csv contains 16 columns. Columns A denotes the household number. The additional 15 columns denote a different sequence type (ST) of <em>Salmonella</em> detected within environmental samples collected from each household.</p> <p>meta_an_st_wide_wide_extra.csv contains 58 columns. Columns A denotes the household number. The additional 57 columns each denote a different sequence type (ST) of <em>Salmonella</em> detected within animal faeces collected from each household.</p> <p>Source Data- Circulation of <em>Salmonella</em> spp. between humans, animals and the environment in animal-owning households in Malawi. The Source Data file includes five sheets of data. Sheet 1; Metadata and accession numbers includes data used for Figures 1, 2, Table 1 and Supplementary Figures 3, 4 and 5. Sheet 2; Panaroo 227 core gene tree includes the text of the Newick file used to construct the phylogenetic tree in Figure 2. Sheet 3; Core SNP matrix used to construct Table 1 and Supplementary Figure 5. Sheet 4; ST313 metadata used to construct Supplementary Figure 7. Sheet 5; Mapping ST11, used to construct Supplementary Figure 8.</p> <p>We provide the following R code associated with analysis presented in this paper:</p> <p>Salmonella_genome_diversity.R; code used to perform the analysis required to investgate the diversity of the <em>Salmonella</em> spp. within the collection, presented in Figure 1.</p> <p>Salmonella_network.R; code used to construct the network of salmonellae with 0SNP difference of the core gene alignment, presented in Figure 3.</p> |
| title | CatherineWilson511/Circulation-of-Salmonella: Circulation of _Salmonella_ spp. between humans, animals and the environment in animal-owning households in Malawi. |
| url | https://doi.org/10.5281/zenodo.17191987 |