Draft genome of three isolates of Listeria monocytogenes isolated from Stenella coeruleoalba in Italy

ABSTRACT Listeria monocytogenes is the etiological agent of the listeriosis. Here, we described three draft genome sequences of L. monocytogenes isolated in Italy from stranded individuals of the striped dolphin Stenella coeruleoalba. All the genomes have been molecular typed through the multilocus sequence typing to identify the phylogenetic lineage, clonal complex, sublineage, and serogroup.

serious foodborne illness known as listeriosis.Here, we present three draft genome sequences of L. monocytogenes obtained from the central nervous system of three individuals of striped dolphin Stenella coeruleoalba found in Italy (see Table 1 for details).Listeria monocytogenes was detected during routine analysis following the detection protocol for stranded marine mammals (1).Selective cultivation was performed under aerobic conditions by enrichment step in liquid media (1/10 p/v) (FRASER broth, at 30°C for 48 h), followed by subculture on solid media (LSM "Luria-Bertani Solid Medium" and ALOA "Agar Leptospira Medium") at 37°C for 48 h.Confirmation of L. monocytogenes was achieved using the miniaturized biochemical test API Listeria, bioMerieux.The detected strains were subsequently cultured on sheep blood agar (AS) as pure cultures at 37°C for 24-48 h, in preparation for sequencing.Genomic DNA was isolated using Maxwell 16 Cell DNA Purification Kit, according to the manufacturer's instructions (Promega, Madison, WI, USA), as described by Sévellec et al. (2).The genome was sequenced using Whole-Genome Shotgun conducted by the Istituto Zooprofilattico Sperimentale del Piemonte, Liguria, and Valle d'Aosta.DNA processing was performed using the Nextera XT DNA Library Preparation Kit from Illumina, following the manufacturer's instructions.The final library was sequenced on an Illumina MiSeq platform with the MiSeq Reagent Kit v3-600 in a 300-bp paired-end run.The MiSeq runs generated a data output of 11.33 Gbp with 77.48% of bases with Q-score of 30 or higher, and 92.46% of clusters passing filter.The resulting FASTQ files (see Table 1 for technical details) underwent quality assessment using the FastQC tool within the command line package FASTX-Toolkit v0.7 (3).This toolkit was also utilized for the removal of adapter sequences (command line: fastx_clipper -e 0.1 a CTGTCTCTTATA -l 15) and the trimming of sequences that were too short or of low quality (command line: fastq_quality_filter -v -m 30 -Q 33 -q 25 p 50).Following the workflow described in Scarpa et al. (4), a de novo assembly was carried out using SPAdes v3.13.0 (5) with the following command line parameters: spades.py--threads 12 -o .--dataset spades_yaml_file.txt-m 128 --only-assembler.
The estimated coverage for all sequenced genomes was ensured to be greater than or equal to 100×.Details for statistics on genome assembly are listed in Table 1.
The entire draft genomes were annotated using the NCBI Prokaryotic Genome Annotation Pipeline v4.2 (6) with the best-placed reference protein set method and GeneMarkS-2.
The molecular typing was performed through the multilocus sequence typing using BIGSdb-Lm implemented in Listeria monocytogenes web page of the Institute Pasteur (https://bigsdb.pasteur.fr/listeria/)(7) (see Table 1 for results).Default parameters were used for all software unless otherwise specified.a The indicated number of reads represents the amount during the pre-filtering step.

Fabio Scarpa ,
Daria Sanna, and Marco Casu acknowledge the support of NBFC to the University of Sassari, funded by the Italian Ministry of University and Research, PNRR, Missione 4, Componente 2, "Dalla ricerca all'impresa," Investimento 1.4 Project CN00000033.This work was supported by the Italian Ministry of Health.V.M. received funding from the Italian received funding from the Italian Ministry of Health under agreement code IZSPLV 09/18 RC.

TABLE 1
Details on the whole genomes of Listeria monocytogenes and results of MLST typing analyses