Genomic Analysis of Salmonella Enterica

Assembled genomes were imported into Ridom SeqSphere+ software, version 6.0.2 (Jünemann et al., 2013 (link)) and core genome multilocus sequence typing (cgMLST) profiles were assigned using the default Salmonella enterica task template with 3,002 core gene targets created based on EnteroBase S. enterica cgMLST v2 scheme,¹ as previously described (Di Marcantonio et al., 2020 (link)). Default settings were applied for allele calling and cgMLST complex detection [complex cut-off ≤ 7 loci (Dangel et al., 2019 (link))]. Only genomes containing ≥98% good target sequences were used in further in silico analyses. Minimum-spanning tree (MST) was generated by pairwise comparison of cgMLST alleles ignoring missing values. Multilocus sequence typing (MLST) analysis of the set of 103 strains sequenced in this study was performed in Ridom SeqSphere + using the Achtman Salmonella seven locus MLST scheme, available at http://enterobase.warwick.ac.uk/species/index/senterica. A novel MLST profile (ST-8528) was generated for strain 2020-CB-4517-1-2 by submitting the sequencing reads directly to EnteroBase.

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Di Marcantonio L., Romantini R., Marotta F., Chiaverini A., Zilli K., Abass A., Di Giannatale E., Garofolo G, & Janowicz A. (2022). The Current Landscape of Antibiotic Resistance of Salmonella Infantis in Italy: The Expansion of Extended-Spectrum Beta-Lactamase Producers on a Local Scale. Frontiers in Microbiology, 13, 812481.

Publication 2022

SeqSphere+

Alleles Gene template Genome Genome profiles Salmonella Salmonella enterica Strain Tree

Corresponding Organization : Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale

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Variable analysis

independent variables

Assembled genomes were imported into Ridom SeqSphere+ software, version 6.0.2
Core genome multilocus sequence typing (cgMLST) profiles were assigned using the default Salmonella enterica task template with 3,002 core gene targets created based on EnteroBase S. enterica cgMLST v2 scheme

dependent variables

CgMLST allele profiles
Minimum-spanning tree (MST) generated by pairwise comparison of cgMLST alleles
Multilocus sequence typing (MLST) analysis of the set of 103 strains

control variables

Default settings were applied for allele calling and cgMLST complex detection [complex cut-off ≤ 7 loci]
Only genomes containing ≥98% good target sequences were used in further in silico analyses

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