ANNOUNCEMENT
Listeriosis is a severe foodborne infection. Salmon products contaminated with the bacterium Listeria monocytogenes are one of the major causes of listeriosis in Germany (1), where 24 salmon-associated outbreak clusters have been detected in 2010–2022 based on core genome multi-locus sequence typing (cgMLST) (1–3). Here, we present nine closed genome sequences of representative L. monocytogenes isolates from nine selected salmon-related outbreaks that belong to different sequence types according to multi-locus sequence typing (MLST).
Five of these outbreak clones (Omikron 1, Rho3, Ypsilon6, My2, and Omega5; Table 1) were still causing listeriosis cases in Germany in 2025.
Representative isolates were chosen from the central node of the nine cgMLST outbreak clusters described previously (1) and were thawed from glycerol stocks of the institute’s strain collection. The selected bacterial strains were cultured in 5 mL brain heart infusion broth overnight at 37°C with shaking (250 rpm), and genomic DNA was isolated from 3 mL culture with the GenElute Bacterial Genomic DNA Kit (Sigma-Aldrich) according to the instructions of the manufacturer. DNA quality was analyzed with a NanoDrop spectrophotometer (Thermo Fisher Scientific), and the DNA concentration was determined with a Qubit fluorometer (Thermo Fisher Scientific).
The Rapid barcoding kit (SQK-RBK004) or Native barcoding kit 24 V14 (SQK-NBD114.24, Oxford Nanopore Technologies) was used to prepare the DNA libraries. Libraries were sequenced using FLOMIN 106D or 114 flow cells on a GridION device (Oxford Nanopore Technologies) with ont-guppy-for-gridion base call models in the super-accurate mode, a Q-score threshold of 10, and adapter trimming. The acquired long reads were filtered using Filtlong v0.2.1 (7) with standard settings, and the corresponding Illumina reads, which were taken from previous reports (1, 5), were used as an external reference.
The following modifications were made: the minimal read length was set to 3,000 bp and the target bases to 290,000,000 bp, which equals a 100-fold coverage. A hybrid assembly with Unicycler v0.4.8 (8) was employed to obtain a closed genome sequence from the refined long reads and the Illumina short reads. Annotation was accomplished with the National Center for Biotechnology Information Prokaryotic Genome Annotation Pipeline v6.8 (9).
All genomes were assembled based on a 100-fold sequencing depth and had a GC content of ~38%. Genome sizes ranged from 2,911,786 bp in isolate 19-00348 with one intact prophage according to Phastest (4) to a genome size of 3,068,859 bp with four intact prophages in strain 17-01049 (Table 1). Phastest detected intact prophages in eight out of the nine genomes and indicated the tRNAArg locus (lmot17) as the dominant integration site, since intact prophages in this specific locus were detected in six different outbreak strains.
Intact prophages inserted in this locus shared similarities with phage LP101 (NC_024387) or phage LP_HM00113468 (NC_049900) that were also found to be the most abundant prophages in serovar IIa isolates from Poland (10). Plasmids were not detected.
The genomes provided here may be helpful as reference sequences in genomic analyses, facilitating case finding and the tracing of outbreak clones to their reservoirs.