Draft genome sequences of Listeria monocytogenes and Listeria innocua isolated from frozen corn in Japan

TL;DR

This paper reports draft genome sequences of six Listeria strains isolated from frozen corn in Japan.

Contribution

The novel contribution is the draft genome sequences of Listeria monocytogenes and Listeria innocua strains from frozen corn in Japan.

Findings

Six Listeria strains were isolated from frozen corn in Japan.

Draft genome sequences were generated with coverage ranging from 381× to 564×.

Abstract

Six Listeria spp. strains were isolated from frozen corn in Japan. Here, we report the draft genome sequences of these strains. The genome sizes ranged from 2,853,850 to 3,062,263 bp at 381× to 564× coverage.

Figures

Virulence factors present or absent in the six Listeria spp. strains. Black boxes indicate the presence of the factor, and white boxes indicate its absence.

Tables

TABLE 1. Genome sequences of six Listeria spp. strains

Parameter	Strains
	20V-2-1	20V-2-6	20V-6-1	20V-6-4	20V-6-5	20V-7-1
Genome size (bp)	2,987,150	3,062,263	2,999,782	2,853,850	2,868,389	3,018,180
Coverage depth	437	564	511	381	425	384
No. of Contigs	86	56	89	42	48	43
GC Content (%)	37.3	37.8	37.8	37.9	37.9	37.8
N50	54,984	102,859	61,327	103,635	94,380	131,748
Coding sequences	2,991	3,056	2,983	2,846	2,854	3,004
rRNA	3	2	4	3	3	2
tRNA	53	55	44	55	50	48
CRISPRs	1	0	1	2	2	5
BioSample accession	SAMD00805288	SAMD00805289	SAMD00805290	SAMD00805291	SAMD00805292	SAMD00805293
SRA accession	DRR596087	DRR596088	DRR596089	DRR596090	DRR596091	DRR596092
GenBank accession	BAAFVD010000000	BAAFVE010000000	BAAFVF010000000	BAAFVG010000000	BAAFVH010000000	BAAFVI010000000
Species	L. innocua	L. monocytogenes	L. monocytogenes	L. monocytogenes	L. monocytogenes	L. monocytogenes
Lineagea	−	II	II	II	II	II
MLST	CC1008/ST1008	CC204/ST204	CC8/ST8	CC19/ST398	CC19/ST398	CC121/ST121
Virulence genes	30	90	89	90	90	87

Full text

ANNOUNCEMENT

Listeria is a genus of gram-positive, short rod-shaped bacteria that can grow at refrigerating temperatures and includes 28 species (1). Among these species, Listeria monocytogenes is a foodborne pathogen that causes listeriosis, leading to meningitis and miscarriages, and is isolated from ready-to-eat foods such as natural cheeses, smoked salmon, and raw ham. Conversely, other species, such as Listeria innocua, have been investigated as indicator bacteria for foods in food facilities because they are widely present in natural environments (2). It has been reported that frozen vegetables have the potential to cause listeriosis outbreaks (3, 4); however, the prevalence and genomic information concerning Listeria spp. in frozen produce remain limited. Here, we sequenced Listeria spp. isolates from frozen corn to characterize these genetic traits. The Listeria spp. strains were isolated from retail frozen corn in Japan; briefly, 25 g of each sample was homogenized with 225 mL of demi-Fraser broth (Neogen) and enriched at 37°C for 24 h and performed the assay using the 3M Molecular Detection Assay 2*—Listeria monocytogenes* (Neogen) to identify L. monocytogenes-positive cultures. The positive culture was spread onto CHROMagar Listeria (Chromagar) and incubated at 37°C for 48 h, after which typical colonies were isolated.

Six Listeria spp. isolates (20V-2-1, 20V-2-6, 20V-6-1, 20V-6-4, 20V-6-5, and 20V-7-1), from different corn samples, were incubated on brain heart infusion agar at 37°C for 18 h, after which the genomic DNA of the isolates was extracted from a single colony using a Maxwell RSC blood DNA kit (Promega). The DNA library (approximately 200–300 size) was prepared from 1 µg DNA using the NEBNext Fast DNA Fragmentation and Library Prep set (New England Biolabs) and was analyzed using an Ion Chef/GeneStudio S5 system (Life Technologies). Quality trimming and de novo assembly of the raw reads were performed using CLC Genomics Workbench version 24.0 (Qiagen), and the obtained contigs were annotated using DDBJ Fast Annotation and Submission Tool (DFAST) version 1.6.0 (5). All analyses used default parameters for the software.

The number of raw reads obtained from the six strains ranged from 4,967,663 to 7,658,227 and were assembled into 42–89 contigs with accumulated lengths of 2,853,850–3,062,263 bp at 381× to 564× coverage (Table 1). The sequences included 37.3%–37.9% G + C content and 2,846–3,056 coding sequences. The 20V-2-1 strain was identified as L. innocua belonging to CC1008/ST1008, and the other five strains were L. monocytogenes belonging to the lineage II type and various sequence types using the Institut Pasteur MLST website scheme (6). A total of 30 genes associated with virulence factors were identified in the L. innocua isolate, and 87–90 genes were identified in the L. monocytogenes isolates by in silico analysis using VirulenceFinder 2.0 (7) (Fig. 1). These results provide genome sequence data for L. monocytogenes and L. innocua strains isolated from frozen corn and suggest that these strains may pose potential risks to human health. Furthermore, additional data are needed to understand Listeria spp. in foods.

Virulence factors present or absent in the six Listeria spp. strains. Black boxes indicate the presence of the factor, and white boxes indicate its absence.