CatherineWilson511/Circulation-of-Salmonella

Circulation of Salmonella spp. between humans, animals and the environment in animal-owning households in Malawi # Circulation-of-Salmonella Here we deposit the data presented in the upcoming research paper entitled "Circulation of Salmonella spp. between humans, animals and the environment in urban and rural, low-intensity, animal-owning agricultural systems in Malawi". We provide the code for the analysis performed in the associated R code (Salmonella_genome_diversity.R and Salmonella_network.R). metadata_osnp_sharing.csv contains 14 columns containing the overall metadata of the Salmonella isolate from which was part of a ‘sharing pair’. A. HH1 (Lane ID) B. ST_HH1 (Sequence Type) C. Subspecies_HH1 (Salmonella subspecies) D. Serovar_HH1 (Salmonella 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) total_host_hh.csv contains 4 columns containing the overall number of hosts within each household, according to Host category, from which Salmonella was isolated during the study. 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) 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 Salmonella detected within human faecal samples collected from each household. 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 Salmonella detected within environmental samples collected from each …