Computational protocol: Draft Genome Sequences of 23 Salmonella enterica Strains Isolated from Cattle in Ibadan, Nigeria, Representing 21 Salmonella Serovars

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Protocol publication

[…] The taxonomic classification of Salmonella enterica includes more than 2,600 serovars, which subsequently can be divided into typhoidal and nontyphoidal Salmonella (NTS) serovars (). Typhoidal serovars (S. enterica subsp. enterica serovars Typhi, Sendai, Paratyphi A, Paratyphi B, and Paratyphi C) primarily infect humans, while NTS serovars have a broad spectrum of hosts, such as mammals (including humans), birds, and reptiles (). Globalization has increased the availability of diverse strains of S. enterica across the world. Consequently, different serovars have crossed borders and emerging antimicrobial resistance (AMR) phenotypes have been described (), thus presenting the need to study the genotypic diversity of S. enterica serovars. We announce here 23 draft genomes from S. enterica strains isolated from fecal samples of cattle in Nigeria, including genomes from serovars that are not currently available at GenBank, e.g., S. enterica subsp. enterica serovars Agoueve, Marseille, Sundsvall, Takoradi, Ekotedo, Tees, Plymouth, Hato, 47:z4,z23:-, Altendorf, Essen, and Glostrup.Bacterial DNA was extracted from overnight cultures by using the DNeasy blood and tissue kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. Sequencing libraries were constructed with 0.2 ng/μl of prepared DNA using the Nextera XT DNA library prep kit (Illumina, San Diego, CA, USA).Sequencing was performed on the MiSeq Illumina instrument with the 500-cycle MiSeq reagent V2 kit (2 × 250 bp) following the manufacturer’s guidelines. Raw data were subjected to genome assembly using SPAdes version 3.8 (), and genome annotation was performed with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (). Salmonella serotyping by whole-genome sequencing was predicted with the SeqSero version 1.0 software tool (). The NCBI pathogen detection website (https://www.ncbi.nlm.nih.gov/pathogens) and annotation pipeline () were queried to extract information regarding AMR genes present in these genomes. In silico multilocus sequence typing (MLST) data were extracted from the Enterobase online tool (http://enterobase.warwick.ac.uk). Salmonella pathogenicity islands (SPIs) were identified using the SPIFinder version 1.0 online tool (https://cge.cbs.dtu.dk/services/SPIFinder). The total lengths of these genomes range from 4.6 to 5.2 Mb, with an average GC content of 52%, and the numbers of contigs range from 25 to 102. The numbers of predicted genes, noncoding RNAs (ncRNAs), tRNAs, and clustered regularly interspaced short palindromic repeat (CRISPR) arrays range from 4,353 to 5,075, 10 to 18, 71 to 82, and 1 to 4, respectively, as previously described for Salmonella genomes (). In silico MLST analysis shows that each genome belongs to different sequencing types (STs), and 12 of them have not been previously reported. AMR genes were predicted in 6 out of 23 strains, including those encoding chloramphenicol, quinolone, tetracycline, and fosfomycin resistance. Up to seven SPIs were detected in these genomes, including SPI-1, SPI-2, and SPI-4, which encode a predicted type III and type I secretion system.Analysis of these genomes will offer a better understanding of the genomic events responsible for AMR, disease transmission, and pathogenicity of Salmonella enterica. […]

Pipeline specifications

Software tools SPAdes, PGAP, SeqSero, SPIFinder
Applications Genome annotation, WGS analysis
Organisms Salmonella enterica, Bos taurus