Enhancing genomics-based outbreak detection of endemic <i>Salmonella enterica</i> serovar Typhimurium using dynamic thresholds.

"pmc pmc8627665 pmc8627665 8627665 31682222 31682222 000310 10 1099/mgen 0 000310 research articles pathogens and epidemiology enhancing genomics-based outbreak detection of endemic salmonella enterica serovar typhimurium using dynamic thresholds http://mgen microbiologyresearch org + these authors contributed equally to this work *correspondence: ruiting lan r lan@unsw edu au raw sequence data are available from the ncbi under bioproject number prjna555108 2021 4 11 2019 4 11 2019 [ comment ] 7 6 000310 22 7 2019 09 10 2019 (c) 2019 the authors2019 https://creativecommons org/licenses/by/4 0/ this is an open-access article distributed under the terms of the creative commons attribution license salmonella enterica serovar typhimurium is the leading cause of salmonellosis in australia and the ability to identify outbreaks and their sources is vital to public health.; these findings have general applicability to outbreak detection of bacterial pathogens genomic epidemiology outbreak detection salmonella typhimurium bacterial population genomics genetic clustering openaccessembargo 0 sequencing data have been deposited at the national center for biotechnology information under bioproject number prjna555108.; the genome sequencing data (illumina and oxford nanopore) are available from the national center for biotechnology information (ncbi) under bioproject number prjna555108."

"nucleotides for each position where a snp was called were extracted for each strain using a custom python script to generate an alignment (supplementary_data_snp_align_gen py)."

"Conflicts of interest The authors declare that there are no conflicts of interest."

"Funding information This work was supported by a National Health and Medical Research Council project grant (grant number 1129713)."